From dobrien@osrhe.edu Wed May 1 13:52:58 2002 Received: from tabloid.onenet.net (tabloid.onenet.net [156.110.12.2]) by lists.onenet.net (8.10.2+Sun/8.10.2) with ESMTP id g41IqwT01892 for ; Wed, 1 May 2002 13:52:58 -0500 (CDT) Received: from conversion-daemon by tabloid.onenet.net (Sun Internet Mail Server sims.4.0.2001.07.26.11.50.p9) id <0GVG00J0136TIZ@tabloid.onenet.net> for okmicroarray@lists.onenet.net; Wed, 1 May 2002 13:25:54 -0500 (CDT) Received: from ms.osrhe.edu (ms.osrhe.edu [164.58.253.145]) by tabloid.onenet.net (Sun Internet Mail Server sims.4.0.2001.07.26.11.50.p9) with ESMTP id <0GVG007S036NKU@tabloid.onenet.net> for okmicroarray@lists.onenet.net; Wed, 01 May 2002 13:25:35 -0500 (CDT) Date: Wed, 01 May 2002 13:25:17 -0500 From: "O'Brien, Dawn" To: okmicroarray@lists.onenet.net Message-id: <4499418E013CC64FB4B56892982850040287CD@ms.osrhe.edu> MIME-version: 1.0 X-MIMEOLE: Produced By Microsoft Exchange V6.0.5762.3 Content-type: text/plain Content-transfer-encoding: 7BIT Thread-Topic: test Thread-Index: AcHxPYtB4u8CLudbQSqfAn6VJzBscg== X-MS-Has-Attach: X-MS-TNEF-Correlator: Subject: [Okmicroarray] test Sender: okmicroarray-admin@lists.onenet.net Errors-To: okmicroarray-admin@lists.onenet.net X-BeenThere: okmicroarray@lists.onenet.net X-Mailman-Version: 2.0.5 Precedence: bulk List-Help: List-Post: List-Subscribe: , List-Id: Oklahoma Microarray Facility List-Unsubscribe: , List-Archive: This is a test. Dawn O'Brien From dobrien@osrhe.edu Wed May 1 14:08:31 2002 Received: from tabloid.onenet.net (tabloid.onenet.net [156.110.12.2]) by lists.onenet.net (8.10.2+Sun/8.10.2) with ESMTP id g41J8VT02033 for ; Wed, 1 May 2002 14:08:31 -0500 (CDT) Received: from conversion-daemon by tabloid.onenet.net (Sun Internet Mail Server sims.4.0.2001.07.26.11.50.p9) id <0GVG007013WRR3@tabloid.onenet.net> for okmicroarray@lists.onenet.net; Wed, 1 May 2002 13:41:27 -0500 (CDT) Received: from ms.osrhe.edu (ms.osrhe.edu [164.58.253.145]) by tabloid.onenet.net (Sun Internet Mail Server sims.4.0.2001.07.26.11.50.p9) with ESMTP id <0GVG007SM3WB35@tabloid.onenet.net> for okmicroarray@lists.onenet.net; Wed, 01 May 2002 13:40:59 -0500 (CDT) Date: Wed, 01 May 2002 13:40:41 -0500 From: "O'Brien, Dawn" To: okmicroarray@lists.onenet.net Message-id: <4499418E013CC64FB4B56892982850040287CF@ms.osrhe.edu> MIME-version: 1.0 X-MIMEOLE: Produced By Microsoft Exchange V6.0.5762.3 Content-type: text/plain Content-transfer-encoding: 7BIT Thread-Topic: test Thread-Index: AcHxP7Iy8W9GFsaHQZ+OhmRqkFIKZw== X-MS-Has-Attach: X-MS-TNEF-Correlator: Subject: [Okmicroarray] test Sender: okmicroarray-admin@lists.onenet.net Errors-To: okmicroarray-admin@lists.onenet.net X-BeenThere: okmicroarray@lists.onenet.net X-Mailman-Version: 2.0.5 Precedence: bulk List-Help: List-Post: List-Subscribe: , List-Id: Oklahoma Microarray Facility List-Unsubscribe: , List-Archive: This is another test. Dawn O'Brien From dobrien@osrhe.edu Wed May 1 14:17:23 2002 Received: from tabloid.onenet.net (tabloid.onenet.net [156.110.12.2]) by lists.onenet.net (8.10.2+Sun/8.10.2) with ESMTP id g41JHNT02127 for ; Wed, 1 May 2002 14:17:23 -0500 (CDT) Received: from conversion-daemon by tabloid.onenet.net (Sun Internet Mail Server sims.4.0.2001.07.26.11.50.p9) id <0GVG00E014BCCE@tabloid.onenet.net> for okmicroarray@lists.onenet.net; Wed, 1 May 2002 13:50:19 -0500 (CDT) Received: from ms.osrhe.edu (ms.osrhe.edu [164.58.253.145]) by tabloid.onenet.net (Sun Internet Mail Server sims.4.0.2001.07.26.11.50.p9) with ESMTP id <0GVG00D394BB0W@tabloid.onenet.net> for okmicroarray@lists.onenet.net; Wed, 01 May 2002 13:49:59 -0500 (CDT) Date: Wed, 01 May 2002 13:49:41 -0500 From: "O'Brien, Dawn" To: okmicroarray@lists.onenet.net Message-id: <4499418E013CC64FB4B56892982850040287D1@ms.osrhe.edu> MIME-version: 1.0 X-MIMEOLE: Produced By Microsoft Exchange V6.0.5762.3 Content-type: text/plain Content-transfer-encoding: 7BIT Thread-Topic: test Thread-Index: AcHxQPOalvoISz1NSIK/CnnmmgtwAg== X-MS-Has-Attach: X-MS-TNEF-Correlator: Subject: [Okmicroarray] test Sender: okmicroarray-admin@lists.onenet.net Errors-To: okmicroarray-admin@lists.onenet.net X-BeenThere: okmicroarray@lists.onenet.net X-Mailman-Version: 2.0.5 Precedence: bulk List-Help: List-Post: List-Subscribe: , List-Id: Oklahoma Microarray Facility List-Unsubscribe: , List-Archive: yet another test. Dawn O'Brien From lborin@osrhe.edu Wed May 1 14:23:46 2002 Received: from tabloid.onenet.net (tabloid.onenet.net [156.110.12.2]) by lists.onenet.net (8.10.2+Sun/8.10.2) with ESMTP id g41JNkT02160 for ; Wed, 1 May 2002 14:23:46 -0500 (CDT) Received: from conversion-daemon by tabloid.onenet.net (Sun Internet Mail Server sims.4.0.2001.07.26.11.50.p9) id <0GVG00J014M65S@tabloid.onenet.net> for okmicroarray@lists.onenet.net; Wed, 1 May 2002 13:56:41 -0500 (CDT) Received: from ms.osrhe.edu (ms.osrhe.edu [164.58.253.145]) by tabloid.onenet.net (Sun Internet Mail Server sims.4.0.2001.07.26.11.50.p9) with ESMTP id <0GVG003NQ4LX2D@tabloid.onenet.net> for okmicroarray@lists.onenet.net; Wed, 01 May 2002 13:56:21 -0500 (CDT) Date: Wed, 01 May 2002 13:56:03 -0500 From: "Borin, Lesa" To: okmicroarray@lists.onenet.net Message-id: <4499418E013CC64FB4B5689298285004033206@ms.osrhe.edu> MIME-version: 1.0 X-MIMEOLE: Produced By Microsoft Exchange V6.0.5762.3 Content-type: MULTIPART/ALTERNATIVE; BOUNDARY="Boundary_(ID_DXvTdWuZh1HBhTipHBX0vA)" Thread-Topic: test Thread-Index: AcHxQddQLfq40LZDRi2a2es/dmRyPA== content-class: urn:content-classes:message X-MS-Has-Attach: X-MS-TNEF-Correlator: Subject: [Okmicroarray] test Sender: okmicroarray-admin@lists.onenet.net Errors-To: okmicroarray-admin@lists.onenet.net X-BeenThere: okmicroarray@lists.onenet.net X-Mailman-Version: 2.0.5 Precedence: bulk List-Help: List-Post: List-Subscribe: , List-Id: Oklahoma Microarray Facility List-Unsubscribe: , List-Archive: This is a multi-part message in MIME format. --Boundary_(ID_DXvTdWuZh1HBhTipHBX0vA) Content-type: text/plain Content-transfer-encoding: 7BIT This is a test. Lesa K. Jolly-Borin Fiscal Policy Analyst Oklahoma State Regents for Higher Education 655 Research Parkway, Suite 200 Oklahoma City, OK 73101 405.225.9134 - FAX 405.225.9230 lborin@osrhe.edu --Boundary_(ID_DXvTdWuZh1HBhTipHBX0vA) Content-type: text/html; charset=iso-8859-1 Content-transfer-encoding: 7BIT
This is a test.
Lesa K. Jolly-Borin
Fiscal Policy Analyst
Oklahoma State Regents for Higher Education
655 Research Parkway, Suite 200
Oklahoma City, OK 73101
405.225.9134 - FAX 405.225.9230
 
 
--Boundary_(ID_DXvTdWuZh1HBhTipHBX0vA)-- From centolam@omrf.ouhsc.edu Fri May 10 14:17:24 2002 Received: from omrfnt2.omrf.ouhsc.edu ([157.142.201.251]) by lists.onenet.net (8.10.2+Sun/8.10.2) with ESMTP id g4AJHOT00438 for ; Fri, 10 May 2002 14:17:24 -0500 (CDT) Received: from omrf.ouhsc.edu (157.142.200.28 [157.142.200.28]) by omrfnt2.omrf.ouhsc.edu with SMTP (Microsoft Exchange Internet Mail Service Version 5.5.2653.13) id KNG9QLH0; Fri, 10 May 2002 13:49:24 -0500 Message-ID: <3CDC1651.1B5E5F@omrf.ouhsc.edu> Date: Fri, 10 May 2002 13:49:53 -0500 From: Michael Centola Reply-To: centolam@omrf.ouhsc.edu Organization: Oklahoma Medical Research Foundation X-Mailer: Mozilla 4.76 (Macintosh; U; PPC) X-Accept-Language: en MIME-Version: 1.0 To: okmicroarray@lists.onenet.net Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Transfer-Encoding: 7bit Subject: [Okmicroarray] Help for microarray talk Sender: okmicroarray-admin@lists.onenet.net Errors-To: okmicroarray-admin@lists.onenet.net X-BeenThere: okmicroarray@lists.onenet.net X-Mailman-Version: 2.0.5 Precedence: bulk List-Help: List-Post: List-Subscribe: , List-Id: Oklahoma Microarray Facility List-Unsubscribe: , List-Archive: Welcome okmicroarray listserve members I need your help, I am giving a talk on Tuesday to an NIH grant oversight committee on the state of microarrays in the state. Can you send me lists of pending and active grants, papers, and corporate contracts from your lab that involve microarrays. I'm just going to show gross numbers on the amounts and number of grants and if there are only a few papers I may list them by name. I'm putting the slides together this weekend and I apologize for this late appeal for assistance. Thanks, Mike Centola Director OMRF Microarray core facility From chris-aston@omrf.ouhsc.edu Mon May 20 15:16:24 2002 Received: from omrfnt2.omrf.ouhsc.edu ([157.142.201.251]) by lists.onenet.net (8.10.2+Sun/8.10.2) with ESMTP id g4KKGNT27368 for ; Mon, 20 May 2002 15:16:23 -0500 (CDT) Received: from omrf.ouhsc.edu (BUNYIP2 [157.142.201.230]) by omrfnt2.omrf.ouhsc.edu with SMTP (Microsoft Exchange Internet Mail Service Version 5.5.2653.13) id LD69H7WH; Mon, 20 May 2002 14:47:48 -0500 Message-ID: <3CE95292.8040808@omrf.ouhsc.edu> Date: Mon, 20 May 2002 14:46:26 -0500 From: Chris Aston User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.0; en-US; rv:0.9.4) Gecko/20011128 Netscape6/6.2.1 X-Accept-Language: en-us MIME-Version: 1.0 To: okmicroarray@lists.onenet.net Content-Type: multipart/alternative; boundary="------------040907080006050005040308" Subject: [Okmicroarray] [Fwd: Monday PM News Headlines from GenomeWeb.com] Sender: okmicroarray-admin@lists.onenet.net Errors-To: okmicroarray-admin@lists.onenet.net X-BeenThere: okmicroarray@lists.onenet.net X-Mailman-Version: 2.0.5 Precedence: bulk List-Help: List-Post: List-Subscribe: , List-Id: Oklahoma Microarray Facility List-Unsubscribe: , List-Archive: --------------040907080006050005040308 Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit -------- Original Message -------- Subject: Monday PM News Headlines from GenomeWeb.com Date: Mon, 20 May 2002 14:42:28 -0500 From: emailNews@genomeweb.com To: chris-aston@omrf.ouhsc.edu IBM launches a new on-demand Life Sciences Web Lecture Series for scientists and R&D IT professionals. The convergence of IT and the life sciences is a fast moving field. Review the latest information from IBM on topics that bridge these two technology areas right from your desktop. "Gene Expression Pattern Discovery in Gene Expression Microarrays" is one lecture presented by IBM Research. IBM's Functional Genomics Group evaluates methods to better define the functional relationship between genes. One problem is to identify "patterns" of gene expression that maximally differentiate between cells characterized by a specific phenotype, and control cells. This lecture presents a method for discovering such patterns. Other on-demand lectures in the series examine the critical need for data integration and the creation of a flexible R&D IT infrastructure to help accelerate drug discovery and development. Register for the full web lecture series at http://www.ibm.com/solutions/lifesciences/datae14 ====================================================================== 05/20/2002 Hybridon Granted Patent on Circular Oligonucleotides For Antisense http://www.genomeweb.com/articles/view.asp?Article=2002520124350 05/20/2002 Boston University, Beyond Genomics Form Research Alliance http://www.genomeweb.com/articles/view.asp?Article=2002520121528 05/20/2002 Collins: NHGRI's Future Will Take Shape Next Fall http://www.genomeweb.com/articles/view.asp?Article=200252012107 05/20/2002 Agilent Licenses Callida Genomics' DNA Chip Patents http://www.genomeweb.com/articles/view.asp?Article=2002520105025 05/20/2002 MediGene Licenses Gene Regulation System From Valentis http://www.genomeweb.com/articles/view.asp?Article=2002520105520 05/20/2002 Matritech, Bruker Daltonics To Develop Mass Spec For Cancer Diagnostics http://www.genomeweb.com/articles/view.asp?Article=200252011059 05/20/2002 PROTEOMONITOR SUBSCRIBERS: Analysis of Protein-Protein Interactions in Nature Highlights Biases of Methodologies http://www.genomeweb.com/articles/view.asp?Article=2002520104845 ====================================================================== Give your colleagues the benefit of free email reports from GenomeWeb News. Forward this message right now and have them click on http://www.genomeweb.com/subscribersignup.htm To unsubscribe, click on http://www.genomeweb.com/subscriberupdate.htm. --------------040907080006050005040308 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit

-------- Original Message --------
Subject: Monday PM News Headlines from GenomeWeb.com
Date: Mon, 20 May 2002 14:42:28 -0500
From: emailNews@genomeweb.com
To: chris-aston@omrf.ouhsc.edu 


IBM launches a new on-demand Life Sciences Web Lecture Series for
scientists and R&D IT professionals. The convergence of IT and the life
sciences is a fast moving field. Review the latest information from IBM
on topics that bridge these two technology areas right from your
desktop. "Gene Expression Pattern Discovery in Gene Expression
Microarrays" is one lecture presented by IBM Research. IBM's Functional
Genomics Group evaluates methods to better define the functional
relationship between genes. One problem is to identify "patterns" of
gene expression that maximally differentiate between cells characterized
by a specific phenotype, and control cells. This lecture presents a
method for discovering such patterns. Other on-demand lectures in the
series examine the critical need for data integration and the creation
of a flexible R&D IT infrastructure to help accelerate drug discovery
and development.

Register for the full web lecture series at
http://www.ibm.com/solutions/lifesciences/datae14
======================================================================

      05/20/2002 Hybridon Granted Patent on Circular Oligonucleotides
For Antisense  
 
http://www.genomeweb.com/articles/view.asp?Article=2002520124350

      05/20/2002 Boston University, Beyond Genomics Form Research
Alliance  
 
http://www.genomeweb.com/articles/view.asp?Article=2002520121528

      05/20/2002 Collins: NHGRI's Future Will Take Shape Next Fall  
 
http://www.genomeweb.com/articles/view.asp?Article=200252012107

      05/20/2002 Agilent Licens
es Callida Genomics' DNA Chip Patents  
 
http://www.genomeweb.com/articles/view.asp?Article=2002520105025

      05/20/2002 MediGene Licenses Gene Regulation System From Valentis
  
 
http://www.genomeweb.com/articles/view.asp?Article=2002520105520

      05/20/2002 Matritech, Bruker Daltonics To Develop Mass Spec For
Cancer Diagnostics  
 
http://www.genomeweb.com/articles/view.asp?Article=200252011059

      05/20/2002 PROTEOMONITOR SUBSCRIBERS: Analysis of Protein-Protein
Interactions in Nature Highlights Biases of Methodologies  
 
http://www.genom
eweb.com/articles/view.asp?Article=2002520104845


======================================================================

Give your colleagues the benefit of free email reports from GenomeWeb
News. Forward this message right now and have them click on
http://www.genomeweb.com/subscribersignup.htm

To unsubscribe, click on http://www.genomeweb.com/subscriberupdate.htm.
--------------040907080006050005040308-- From centolam@omrf.ouhsc.edu Tue May 21 00:26:01 2002 Received: from lakemtao08.cox.net (lakemtao08.cox.net [68.1.17.113]) by lists.onenet.net (8.10.2+Sun/8.10.2) with ESMTP id g4L5Q1T28958 for ; Tue, 21 May 2002 00:26:01 -0500 (CDT) Received: from omrf.ouhsc.edu ([68.12.66.85]) by lakemtao08.cox.net (InterMail vM.5.01.04.05 201-253-122-122-105-20011231) with ESMTP id <20020521045825.SNHZ4796.lakemtao08.cox.net@omrf.ouhsc.edu>; Mon, 20 May 2002 23:58:25 -0500 Message-ID: <3CE9D3F2.9060109@omrf.ouhsc.edu> Date: Mon, 20 May 2002 23:58:26 -0500 From: Michael Centola User-Agent: Mozilla/5.0 (Macintosh; U; PPC; en-US; rv:0.9.4.1) Gecko/20020318 Netscape6/6.2.2 X-Accept-Language: en-us MIME-Version: 1.0 To: okmicroarray@lists.onenet.net, MourningBlade@bigfoot.com Content-Type: multipart/alternative; boundary="------------000301040209040707090903" Subject: [Okmicroarray] [Fwd: BASE v1.0 is available now] Sender: okmicroarray-admin@lists.onenet.net Errors-To: okmicroarray-admin@lists.onenet.net X-BeenThere: okmicroarray@lists.onenet.net X-Mailman-Version: 2.0.5 Precedence: bulk List-Help: List-Post: List-Subscribe: , List-Id: Oklahoma Microarray Facility List-Unsubscribe: , List-Archive: --------------000301040209040707090903 Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit This message was sent out over the UCSF microarray listserve on a free microarray database that can run on a linux platform (see below). Alan Shields (the database manager) at the OMRF microarray facility has recently come to the lab to set up our database system and he begun evaluating the BASE database last week. We are hoping that it could provide a free platform that will allow us to get the expression data on a sever so that it can be accessed by facility users involved in the projects from remote locations. Please contact Alan (MourningBlade@bigfoot.com) if you have any comments on this database of suggestions on database setup, we are just getting started. Mike Centola -------- Original Message -------- Subject: BASE v1.0 is available now Date: Mon, 20 May 2002 17:18:46 +0200 From: Lao Saal Reply-To: "To share info regarding GeneChips tech. and Microarrays in general" To: GENE-ARRAYS@ITSSRV1.UCSF.EDU Hello list, If anyone is interested, we've publicly released our microarray database and analysis platform called BioArray Software Environment (BASE). It's a server solution that runs under Linux, where users can login from any web browser to load in data and perform analyses. BASE v1.0 is publicly available for free and open source to all academic and commercial entities under the GNU General Public License. To read up more about BASE, and to download it, visit the website http://base.thep.lu.se. Regards, Lao Saal --------------000301040209040707090903 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit This message was sent out over the UCSF microarray listserve on a free microarray database that can run on a linux platform (see below).

Alan Shields (the database manager) at the OMRF microarray facility has recently come to the lab to set up our database system and he begun evaluating the BASE database last week.  We are hoping that it could provide a free platform that will allow us to get the expression data on a sever so that it can be accessed by facility users involved in the projects from remote locations.  Please contact Alan (MourningBlade@bigfoot.com) if you have any comments on this database of suggestions on database setup, we are just getting started.

Mike Centola

-------- Original Message --------
Subject: BASE v1.0 is available now
Date: Mon, 20 May 2002 17:18:46 +0200
From: Lao Saal <lao.saal@ONK.LU.SE>
Reply-To: "To share info regarding GeneChips tech. and Microarrays in general" <GENE-ARRAYS@ITSSRV1.UCSF.EDU>
To: GENE-ARRAYS@ITSSRV1.UCSF.EDU 


Hello list,

If anyone is interested, we've publicly released our microarray database
and analysis platform called BioArray Software Environment (BASE).  It's a
server solution that runs under Linux, where users can login from any web
browser to load in data and perform analyses.  BASE v1.0 is publicly
available for free and open source to all academic and commercial entities
under the GNU General Public License.

To read up more about BASE, and to download it, visit the website
http://base.thep.lu.se.

Regards,

Lao Saal
--------------000301040209040707090903-- From dobrien@osrhe.edu Tue May 21 16:00:27 2002 Received: from tabloid.onenet.net (tabloid.onenet.net [156.110.12.2]) by lists.onenet.net (8.10.2+Sun/8.10.2) with ESMTP id g4LL0RT03003 for ; Tue, 21 May 2002 16:00:27 -0500 (CDT) Received: from conversion-daemon by tabloid.onenet.net (Sun Internet Mail Server sims.4.0.2001.07.26.11.50.p9) id <0GWH00M01AEI2Q@tabloid.onenet.net> for okmicroarray@lists.onenet.net; Tue, 21 May 2002 15:33:09 -0500 (CDT) Received: from ms.osrhe.edu (ms.osrhe.edu [164.58.253.145]) by tabloid.onenet.net (Sun Internet Mail Server sims.4.0.2001.07.26.11.50.p9) with ESMTP id <0GWH003JMAE7CD@tabloid.onenet.net> for okmicroarray@lists.onenet.net; Tue, 21 May 2002 15:32:31 -0500 (CDT) Date: Tue, 21 May 2002 15:32:07 -0500 From: "O'Brien, Dawn" To: okmicroarray@lists.onenet.net Message-id: <4499418E013CC64FB4B568929828500402887E@ms.osrhe.edu> MIME-version: 1.0 X-MIMEOLE: Produced By Microsoft Exchange V6.0.5762.3 Content-type: text/plain Content-transfer-encoding: 7BIT Thread-Topic: TEST Thread-Index: AcIBBpOja6BehN7oSRmyx+zjqJ7g6g== X-MS-Has-Attach: X-MS-TNEF-Correlator: Subject: [Okmicroarray] TEST Sender: okmicroarray-admin@lists.onenet.net Errors-To: okmicroarray-admin@lists.onenet.net X-BeenThere: okmicroarray@lists.onenet.net X-Mailman-Version: 2.0.5 Precedence: bulk List-Help: List-Post: List-Subscribe: , List-Id: Oklahoma Microarray Facility List-Unsubscribe: , List-Archive: THIS IS A TEST. PLEASE DO NOT RESPOND. From centolam@omrf.ouhsc.edu Mon May 27 00:15:27 2002 Received: from lakemtao06.cox.net (lakemtao06.cox.net [68.1.17.115]) by lists.onenet.net (8.10.2+Sun/8.10.2) with ESMTP id g4R5FQT00036 for ; Mon, 27 May 2002 00:15:27 -0500 (CDT) Received: from omrf.ouhsc.edu ([68.12.66.85]) by lakemtao06.cox.net (InterMail vM.5.01.04.05 201-253-122-122-105-20011231) with ESMTP id <20020527044744.RJLU8234.lakemtao06.cox.net@omrf.ouhsc.edu> for ; Mon, 27 May 2002 00:47:44 -0400 Message-ID: <3CF1BA70.6010302@omrf.ouhsc.edu> Date: Sun, 26 May 2002 23:47:44 -0500 From: Michael Centola User-Agent: Mozilla/5.0 (Macintosh; U; PPC; en-US; rv:0.9.4.1) Gecko/20020318 Netscape6/6.2.2 X-Accept-Language: en-us MIME-Version: 1.0 To: okmicroarray@lists.onenet.net Content-Type: multipart/alternative; boundary="------------070108050606060507050100" Subject: [Okmicroarray] [Fwd: RE: [Fwd: FW: GENOMICS / PROTEOMICS / BIOINFORMATICS DISCUSSION GROUP]] Sender: okmicroarray-admin@lists.onenet.net Errors-To: okmicroarray-admin@lists.onenet.net X-BeenThere: okmicroarray@lists.onenet.net X-Mailman-Version: 2.0.5 Precedence: bulk List-Help: List-Post: List-Subscribe: , List-Id: Oklahoma Microarray Facility List-Unsubscribe: , List-Archive: --------------070108050606060507050100 Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit > -----Original Message----- > From: Brackett, Daniel J. > Sent: Friday, May 24, 2002 11:03 AM > To: Distribution List Moderator - HSC Faculty; Distribution List Moderator - HSC Staff; Distribution List Moderator - HSC Student; Angela Dorman; BRUCE ROE; Doris Kupfer; Henry Neeman; Jim White; JIMMY BALLARD; O Rear, Edgar A, III; Thomas Ray; TYRRELL CONWAY; YUHONG TANG; BRENDA SMITH; OSU BRIN GROUP; GLEN COLLIER > Subject: GENOMICS / PROTEOMICS / BIOINFORMATICS DISCUSSION GROUP > > > > Dear Colleagues > > The Genomics / Proteomics / Bioinformatics discussion group series sponsored by the Department of Microbiology & Immunology and the Department of Surgery and serving as a forum for BRIN participants will be held on Wednesday, May 29 at 2:00 pm. The meeting will in the auditorium of the Biomedical Research Center. . > > The topic for discussion this month presented by Dr. Darren Smalley will be "Temporal Regulation of the Hydrogen Peroxide Stress Response in Escherichia coli". This session will be moderated by Dr. Darrin Akins. > > For further information call Darrin Akins at 46640 or me at 2108. > > Looking forward to seeing you there. > > > Daniel J. Brackett Darrin Akins > Professor & Director of Research Assistant Professor > Department of Surgery Department of Microbiology & Immunology > > > > > --------------070108050606060507050100 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit 
 >  -----Original Message-----
> From: 	Brackett, Daniel J.  
> Sent:	Friday, May 24, 2002 11:03 AM
> To:	Distribution List Moderator - HSC Faculty; Distribution List
Moderator - HSC Staff; Distribution List Moderator - HSC Student; Angela
Dorman; BRUCE ROE; Doris Kupfer; Henry Neeman; Jim White; JIMMY BALLARD;
O Rear, Edgar A, III; Thomas Ray; TYRRELL CONWAY; YUHONG TANG; BRENDA
SMITH; OSU BRIN GROUP; GLEN COLLIER
> Subject:	GENOMICS / PROTEOMICS / BIOINFORMATICS DISCUSSION GROUP
> 
> 
> 
> 	Dear Colleagues
> 
>         	The Genomics / Proteomics / Bioinformatics discussion
group series sponsored by the Department of 	Microbiology &
Immunology and the Department of Surgery and serving as a forum for BRIN
participants 	will be held on Wednesday, May 29 at 2:00 pm.  The
meeting will in the auditorium of the Biomedical 	Research Center.
.
> 	
> 	The topic for discussion this month presented by Dr. Darren
Smalley will be "Temporal Regulation of the 	Hydrogen Peroxide Stress
Response in Escherichia coli".  This session will be moderated by Dr.
Darrin 	Akins.
> 	 
> 	For further information call Darrin Akins at 46640 or me at
2108.               	
> 
> 	Looking forward to seeing you there.   
> 
> 
> 	Daniel J. Brackett
Darrin Akins
> 	Professor & Director of Research
Assistant Professor
> 	Department of Surgery
Department of Microbiology & Immunology
> 
> 
> 
> 
>
--------------070108050606060507050100-- From centolam@omrf.ouhsc.edu Wed May 29 00:17:10 2002 Received: from lakemtao08.cox.net (lakemtao08.cox.net [68.1.17.113]) by lists.onenet.net (8.10.2+Sun/8.10.2) with ESMTP id g4T5H9T09068 for ; Wed, 29 May 2002 00:17:09 -0500 (CDT) Received: from omrf.ouhsc.edu ([68.12.66.85]) by lakemtao08.cox.net (InterMail vM.5.01.04.05 201-253-122-122-105-20011231) with ESMTP id <20020529044926.BOCM4796.lakemtao08.cox.net@omrf.ouhsc.edu>; Tue, 28 May 2002 23:49:26 -0500 Message-ID: <3CF46BE8.5040101@omrf.ouhsc.edu> Date: Tue, 28 May 2002 23:49:28 -0600 From: Michael Centola User-Agent: Mozilla/5.0 (Macintosh; U; PPC; en-US; rv:0.9.4.1) Gecko/20020318 Netscape6/6.2.2 X-Accept-Language: en-us MIME-Version: 1.0 To: "To share info regarding GeneChips tech. and Microarrays in general" , okmicroarray@lists.onenet.net References: <3D043DFF@webmail.mcgill.ca> Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Subject: [Okmicroarray] Will the new genisphere 50 kit work with oligo slides? Sender: okmicroarray-admin@lists.onenet.net Errors-To: okmicroarray-admin@lists.onenet.net X-BeenThere: okmicroarray@lists.onenet.net X-Mailman-Version: 2.0.5 Precedence: bulk List-Help: List-Post: List-Subscribe: , List-Id: Oklahoma Microarray Facility List-Unsubscribe: , List-Archive: If anyone has tried using the new Genisphere Array 50 labeling kit on home made long oligo slides can you share your experiences with me. We are printing Operon Human and Mouse ver 2 libraries onto Corning GAP2 slides and are considering taking a chance and trying Genisphere out for a second time. We had tried out a microkit nearly 8 months ago and it didn't go well. I've heard they've improved the system since that time, but I've not heard if the improved systems works with oligos? Mike Centola From liulin@cvm.okstate.edu Wed May 29 12:43:25 2002 Received: from cvm-d.cvm.okstate.edu (cvm-d.cvm.okstate.edu [139.78.19.89]) by lists.onenet.net (8.10.2+Sun/8.10.2) with SMTP id g4THhPT11428; Wed, 29 May 2002 12:43:25 -0500 (CDT) Received: from cvm-g.cvm.okstate.edu ([139.78.19.178]) by cvm-d.cvm.okstate.edu (NAVIEG 2.1 bld 63) with SMTP id M2002052912154202203 ; Wed, 29 May 2002 12:15:42 -0500 Received: from cvm-ns01.cvm.okstate.edu ([139.78.19.87]) by cvm-g.cvm.okstate.edu with Microsoft SMTPSVC(5.0.2195.4905); Wed, 29 May 2002 12:15:42 -0500 To: okmicroarray@lists.onenet.net Cc: okmicroarray@lists.onenet.net, okmicroarray-admin@lists.onenet.net X-Mailer: Lotus Notes Release 5.0.8 June 18, 2001 Message-ID: From: "Lin Liu/phsi/Cvm" Date: Wed, 29 May 2002 12:15:41 -0500 X-MIMETrack: Serialize by Router on cvm-ns01/Cvm(Release 5.0.9 |November 16, 2001) at 05/29/2002 12:15:43 PM MIME-Version: 1.0 Content-type: text/plain; charset=us-ascii X-OriginalArrivalTime: 29 May 2002 17:15:43.0177 (UTC) FILETIME=[76BFCB90:01C20734] Subject: [Okmicroarray] Re: Okmicroarray digest, Vol 1 #6 - 1 msg Sender: okmicroarray-admin@lists.onenet.net Errors-To: okmicroarray-admin@lists.onenet.net X-BeenThere: okmicroarray@lists.onenet.net X-Mailman-Version: 2.0.5 Precedence: bulk List-Help: List-Post: List-Subscribe: , List-Id: Oklahoma Microarray Facility List-Unsubscribe: , List-Archive: We have tried FluoSpheres fluorescent microspheres (Molecular Probes) on our home-made rat oligo slides. It did not go well. I assume that this is similar to genisphere (although I am not sure about it). Lin Liu okmicroarray-request@lists .onenet.net To: okmicroarray@lists.onenet.net Sent by: cc: (bcc: Lin Liu/phsi/Cvm) okmicroarray-admin@lists.o Subject: Okmicroarray digest, Vol 1 #6 - 1 msg nenet.net 05/29/02 12:01 PM Please respond to okmicroarray Send Okmicroarray mailing list submissions to okmicroarray@lists.onenet.net To subscribe or unsubscribe via the World Wide Web, visit http://lists.onenet.net/mailman/listinfo/okmicroarray or, via email, send a message with subject or body 'help' to okmicroarray-request@lists.onenet.net You can reach the person managing the list at okmicroarray-admin@lists.onenet.net When replying, please edit your Subject line so it is more specific than "Re: Contents of Okmicroarray digest..." The Oklahoma Microarray Question and Answer Forum Today's Topics: 1. Will the new genisphere 50 kit work with oligo slides? (Michael Centola) --__--__-- Message: 1 Date: Tue, 28 May 2002 23:49:28 -0600 From: Michael Centola To: "To share info regarding GeneChips tech. and Microarrays in general" , okmicroarray@lists.onenet.net Subject: [Okmicroarray] Will the new genisphere 50 kit work with oligo slides? If anyone has tried using the new Genisphere Array 50 labeling kit on home made long oligo slides can you share your experiences with me. We are printing Operon Human and Mouse ver 2 libraries onto Corning GAP2 slides and are considering taking a chance and trying Genisphere out for a second time. We had tried out a microkit nearly 8 months ago and it didn't go well. I've heard they've improved the system since that time, but I've not heard if the improved systems works with oligos? Mike Centola --__--__-- _______________________________________________ Okmicroarray mailing list Okmicroarray@lists.onenet.net http://lists.onenet.net/mailman/listinfo/okmicroarray End of Okmicroarray Digest From kjc8@duke.edu Thu May 30 12:17:25 2002 Received: from simak.acpub.duke.edu (simak.acpub.duke.edu [152.3.232.12]) by lists.onenet.net (8.10.2+Sun/8.10.2) with ESMTP id g4UHHOT16296 for ; Thu, 30 May 2002 12:17:24 -0500 (CDT) Received: from PCAL04 ([152.3.184.136]) by simak.acpub.duke.edu (8.11.5/8.11.3/Duke-5.0.0) with ESMTP id g4UGncN09608; Thu, 30 May 2002 12:49:39 -0400 (EDT) Date: Thu, 30 May 2002 12:51:36 -0600 From: kjc8@duke.edu To: okmicroarray@lists.onenet.net Message-ID: <560880292.1022763096@PCAL04> X-Mailer: Mulberry/2.0.0 (Win32) MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Content-Disposition: inline Subject: [Okmicroarray] Formamide? Sender: okmicroarray-admin@lists.onenet.net Errors-To: okmicroarray-admin@lists.onenet.net X-BeenThere: okmicroarray@lists.onenet.net X-Mailman-Version: 2.0.5 Precedence: bulk List-Help: List-Post: List-Subscribe: , List-Id: Oklahoma Microarray Facility List-Unsubscribe: , List-Archive: Has anyone ever used Formamide to lower the Tm of RNA/ssDNA strands? I am thinking about trying it, but I dont know if it is successful or not. No use in wasting money... even if it isn't my money! Later, Centola's Prodigy From willy.valdivia@ndsu.nodak.edu Thu May 30 15:18:30 2002 Received: from smtp1.ndsu.nodak.edu (smtp1.ndsu.NoDak.edu [134.129.111.146]) by lists.onenet.net (8.10.2+Sun/8.10.2) with ESMTP id g4UKIUT17233 for ; Thu, 30 May 2002 15:18:30 -0500 (CDT) Received: from datasurg14 (dyn110.lofts-117.ndsu.NoDak.edu [134.129.117.110]) by smtp1.ndsu.nodak.edu (8.12.1/8.12.1) with SMTP id g4UJokHZ029635 for ; Thu, 30 May 2002 14:50:46 -0500 From: "Willy Valdivia Granda" To: Date: Thu, 30 May 2002 14:50:40 -0500 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2910.0) Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 Subject: [Okmicroarray] second virtual conference Sender: okmicroarray-admin@lists.onenet.net Errors-To: okmicroarray-admin@lists.onenet.net X-BeenThere: okmicroarray@lists.onenet.net X-Mailman-Version: 2.0.5 Precedence: bulk List-Help: List-Post: List-Subscribe: , List-Id: Oklahoma Microarray Facility List-Unsubscribe: , List-Archive: ***Second Virtual Conference on Genomics and Bioinformatics*** Sharing Knowledge with the World September 24-26, 2002 The "Virtual Conference on Genomics and Bioinformatics" is an advanced environment for the exchange and discussion of information related to innovations of the post-genomic era. Since genomic research has led to an explosive rate of data accumulation and to a shift in the way biological research is conducted, the conference features high profile researchers and educators working actively in the development of new applications in the areas of genomics and bioinformatics. While genomic technologies offer an enormous scientific potential to understand genome functions, structure and interaction, the increasing amount of data generated present new challenges for biologists, sociologists, mathematicians, computer scientists and biological modelers. Therefore the main goals of the Virtual Conference in Genomics and Bioinformatics are: 1) Transcend geographical and economical barriers to the exchange of ideas that facilitates the interaction and collaboration among scientists and educators around the world. 2) Address the benefits and limitations of the newest developments in post-genomic technologies. 3) Explore the social and ethical implications of genomic and bioinformatic research 4) Establish new ways to introduce high school community about today's multidisciplinary science. . Topics of the Virtual Conference includes but not limited to: · Structural and Functional Genomics · Post-Genomic Data Standardization, Management, and Integration · Statistical and Computational Approaches for Gene Expression Analysis · Sequence Anotation · Metabolic Profiling and Simulation of Cellular Processes · Social and Ethical Implications of Genomic Research · High Throughput Computing and Distributed Memory Infrastructures Ways to Participate: 1) Fargo Acess Grid Location. 2) Other Acess Grid Locations around the world (to be determined soon). 3) Real Player Live Streaming at selected locations around the world (to be determined soon). The Access Grid creates an environment that allows participants to feel as if they are engaged personally rather than in the stiff structured environment of a typical videoconference. The Access Grid nodes are typically housed in small rooms; however the Fargo Access Grid will seat about 300 people. Most of the other nodes will remain in the smaller rooms. About 20 Access Grid nodes (world-wide) will participate in this second conference. Participants at all Acess Grid Locations can ask questions directly to the speakers. About ten of the speakers will present from the Fargo Access Grid location and the remaining from other Access Grid Locations. Tutorials including: strategies for microarray data analysis, micorarray normalization techniques and use of different slide surfaces for printing microarrays are also planned at the Fargo Access Grid Location. The Real Player Live version will be hosted in locations where an Access Grid is not available. This is a real time communication medium that connects participants in multiple physical locations, utilizing both their visual image and audio. Participants at all Real Player Locations can ask questions to the speaker via a "chat session" and the question or comment will be read to the speaker from the Fargo Acess Grid Location. We invite you to organize small to medium size groups to participate in the conference together via this media. If you are interested in hosting such a group please contact us The URL will be provided to the organiser of these groups prior to the conference. Registration and Fees: Although registration is required, there are no required registration fees to participate in the conference. To attend at the Fargo Access Grid Location please register using this form Registration procedures for the other Access Grid Locations and Real Player Locations will be available soon. To recieve further information on these registration procedures please susbscribe to our mailing list Abstract and Papers: In addition to the invited presentations, we invite you to consider additional participation by sumitting your research advances. Abstracts and papers should describe unpublished research that is not under review. Abstracts describing novel applications and theoretical contributions are also requested. This is a fully refereed meeting and each submitted abstract will be peer-reviewed. Selected abstracts will be invited for full paper review. Please submit your abstract of no more than 250 words by June 30, 2002 through our web page Electronic Paper Session: Accepted papers will be published in the "Proceedings of the Virtual Conferences on Genomics and Bioinformatics". To allow the maximum participation between the attendees and the authors, accepted papers, as well as documents submitted by invited speakers, will be available in an electronic forum discussion format. Deadline: June 30, 2002 for abstracts Deadline: August 15, 2002 for complete documents Speakers List http://www.ndsu.nodak.edu/virtual-genomics/program.htm Review Committee List http://www.ndsu.nodak.edu/virtual-genomics/reviewpanel.htm Willy Valdivia Granda Plant Stress Genomics and Bioinformatics Group North Dakota State University PO BOX 5130 Fargo, USA 701 231-8440 (Lab) 701 231 8255 (Fax) www.ndsu.edu/virtual-genomics From centolam@omrf.ouhsc.edu Thu Jul 4 18:33:56 2002 Received: from lakemtao07.cox.net (lakemtao07.cox.net [68.1.17.114]) by lists.onenet.net (8.10.2+Sun/8.10.2) with ESMTP id g64NXtT05587 for ; Thu, 4 Jul 2002 18:33:55 -0500 (CDT) Received: from omrf.ouhsc.edu ([68.12.66.85]) by lakemtao07.cox.net (InterMail vM.5.01.04.05 201-253-122-122-105-20011231) with ESMTP id <20020704230541.NOBS1131.lakemtao07.cox.net@omrf.ouhsc.edu> for ; Thu, 4 Jul 2002 19:05:41 -0400 Message-ID: <3D24D4C5.5050605@omrf.ouhsc.edu> Date: Thu, 04 Jul 2002 18:05:41 -0500 From: Michael Centola User-Agent: Mozilla/5.0 (Macintosh; U; PPC; en-US; rv:0.9.4.1) Gecko/20020318 Netscape6/6.2.2 X-Accept-Language: en-us MIME-Version: 1.0 To: okmicroarray@lists.onenet.net Content-Type: multipart/alternative; boundary="------------080408070501020602040301" Subject: [Okmicroarray] Chips are available Sender: okmicroarray-admin@lists.onenet.net Errors-To: okmicroarray-admin@lists.onenet.net X-BeenThere: okmicroarray@lists.onenet.net X-Mailman-Version: 2.0.5 Precedence: bulk List-Help: List-Post: List-Subscribe: , List-Id: Oklahoma Microarray Facility List-Unsubscribe: , List-Archive: --------------080408070501020602040301 Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Hi All, The OMRF microarray facility has mouse and human microarrays available and custom biostatistical techniques for analysis. We are producing about 100 chips every 2-3 weeks and we are looking for collaborators. If you have a mouse or human microarray project in mind please contact us at: Centolam@omrf.ouhsc.edu Here's a description of the human chips that I just put into a grant: Our facility has developed next-generation genome-scale oligo-based microarray production and hybridization technology. These arrays are produced using a commercially available library of 70 base pair long DNA oligos (70-mers, Qiagen/Operon Technologies). The oligos were derived from the functionally defined genes present in the UniGene and RefSeq databases (http://www.ncbi.nlm.nih.gov). Each oligo corresponds to a unique region within or proximal to the 3'end of a given gene. Length and sequence specificity have therefore been optimized, reducing or eliminating the cross-hybridization problems encountered with cDNA-based arrays. Our human arrays have 21,329 human genes represented. The library utilized for array production is therefore among the most comprehensive commercially available set of array-ready functionally defined human genes with all known human genes described prior to Dec. 2001 and over 10,000 undefined human cDNAs represented. These chips allow us to comprehensively identify key differences in experimental and control samples. A complete listing of the genes can be seen at the following web address:http://www.operon.com/arrays/humangenome.prn. Our two research and development scientists have been collaborating with Qiagen/Operon to enhance the dynamic range and signal-to-noise ratios of these oligo-based arrays. Our oligo microarray production and processing method is now distributed by Qiagen/Operon to microarray labs setting up to use oligo array technology. In addition, we are preparing a manuscript describing the development of our production and processing methods. The mouse chips are similarly comprehensive. They have 16,463 gene represented as 70mer oligo probes. A list of genes can be found at: http://www.operon.com/arrays/mouse_V2_384.prn The oligos are designed from the UniGene Database Build Mm 102 (February 2002) and the Mouse Reference Sequence (RefSeq) Database, both developed and maintained at the National Center of Biotechnology Information (NCBI) www.ncbi.nlm.nih.gov . We also have a team of bioinformatics scientists that can analyze the data from microarray experiments. Analysis is based on the research of Dr. Igor Dozmorov and includes differential gene expression and molecular pathway identification. Also in the group are Nicholas Knowlton, Parima Pathipvanich, and Alan Shields. These scientists incorporate our analytical methods into user-friendly software and are developing an integrated database system for datamining among clinical, genetic, and gene expression data sets. Mike Centola OMRF microarray facility director centolam@omrf.ouhsc.edu --------------080408070501020602040301 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Hi All,

The OMRF microarray facility has mouse and human microarrays available and custom biostatistical techniques for analysis.

We are producing about 100 chips every 2-3 weeks and we are looking for collaborators.  If you have a mouse or human microarray project in mind please contact us at:

Centolam@omrf.ouhsc.edu

Here's a description of the human chips that I just put into a grant:

Our facility has developed next-generation genome-scale oligo-based microarray production and hybridization technology.  These arrays are produced using a commercially available library of 70 base pair long DNA oligos (70-mers, Qiagen/Operon Technologies).  The oligos were derived from the functionally defined genes present in the UniGene and RefSeq databases (http://www.ncbi.nlm.nih.gov). Each oligo corresponds to a unique region within or proximal to the 3’end of a given gene.  Length and sequence specificity have therefore been optimized, reducing or eliminating the cross-hybridization problems encountered with cDNA-based arrays.

Our human arrays have 21,329 human genes represented. The library utilized for array production is therefore among the most comprehensive commercially available set of array-ready functionally defined human genes with all known human genes described prior to Dec. 2001 and over 10,000 undefined human cDNAs represented. These chips allow us to comprehensively identify key differences in experimental and control samples. A complete listing of the genes can be seen at the following web address:http://www.operon.com/arrays/humangenome.prn.

Our two research and development scientists have been collaborating with Qiagen/Operon to enhance the dynamic range and signal-to-noise ratios of these oligo-based arrays.  Our oligo microarray production and processing method is now distributed by Qiagen/Operon to microarray labs setting up to use oligo array technology.  In addition, we are preparing a manuscript describing the development of our production and processing methods.


The mouse chips are similarly comprehensive.

They have 16,463 gene represented as 70mer oligo probes.  A list of genes can be found at:
http://www.operon.com/arrays/mouse_V2_384.prn
The oligos are designed from the UniGene Database Build Mm 102 (February 2002) and the Mouse Reference Sequence (RefSeq) Database, both developed and maintained at the National Center of Biotechnology Information (NCBI) www.ncbi.nlm.nih.gov .


We also have a team of bioinformatics scientists that can analyze the data from microarray experiments.  Analysis is based on the research of Dr. Igor Dozmorov and includes differential gene expression and molecular pathway identification.  Also in the group are Nicholas Knowlton, Parima Pathipvanich, and Alan Shields.  These scientists incorporate our analytical methods into user-friendly software and are developing an integrated database system for datamining among clinical, genetic, and gene expression data sets.

Mike Centola
OMRF microarray facility director
centolam@omrf.ouhsc.edu




--------------080408070501020602040301-- From targetemailextractor@btamail.net.cn Sat Jul 20 01:16:49 2002 Received: from localhost.com ([61.174.203.44]) by lists.onenet.net (8.10.2+Sun/8.10.2) with SMTP id g6K6GhT14855 for ; Sat, 20 Jul 2002 01:16:48 -0500 (CDT) Message-Id: <200207200616.g6K6GhT14855@lists.onenet.net> From: targetemailextractor@btamail.net.cn Reply-To: targetemailextractor@btamail.net.cn To: okmicroarray@lists.onenet.net Date: Sat, 20 Jul 2002 13:48:22 +0800 X-Mailer: QuickSender 1.05 MIME-Version: 1.0 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Subject: [Okmicroarray] ADV: Direct email blaster, email addresses extractor, maillist verify, maillist manager........... Sender: okmicroarray-admin@lists.onenet.net Errors-To: okmicroarray-admin@lists.onenet.net X-BeenThere: okmicroarray@lists.onenet.net X-Mailman-Version: 2.0.5 Precedence: bulk List-Help: List-Post: List-Subscribe: , List-Id: Oklahoma Microarray Facility List-Unsubscribe: , List-Archive: =3CBODY bgColor=3D#ffffff=3E =3CDIV=3E=3CFONT size=3D2=3E =3CDIV=3E=3CFONT face=3DArial=3E =3B=3C=2FFONT=3E =3C=2FDIV=3E =3CDIV=3E =3B=3C=2FDIV=3E =3CDIV=3E=3CSTRONG=3E=3CFONT color=3D#ff0080 face=3DArial size=3D4=3EDirect Email Blaster=3C=2FFONT=3E=3C=2FSTRONG=3E =3C=2FDIV=3E=3CFONT size=3D2=3E =3CP=3E=3CFONT face=3DArial=3E=3CB=3E=3CFONT color=3D#006600=3E=3CI=3EThe program will send mail at the rate of over 1=2C 000 e-mails per minute=2E =3B=3C=2FI=3E=3C=2FFONT=3E=3CBR=3ELegal and Fast sending bulk emails =3B=3CBR=3E=3CFONT color=3D#006600=3E=3CI=3EBuilt in SMTP server =3B=3C=2FI=3E=3C=2FFONT=3E=3CBR=3EHave Return Path =3B=3CBR=3ECan Check Mail Address =3B=3CBR=3E=3CFONT color=3D#006600=3E=3CI=3EMake Error Send Address List=28 Remove or Send Again=29 =3B=3C=2FI=3E=3C=2FFONT=3E=3CBR=3ESupport multi-threads=2E =3B=3CBR=3ESupport multi-smtp servers=2E =3B=3CBR=3EManages your opt-in E-Mail Lists =3B=3CBR=3EOffers an easy-to-use interface! =3B=3CBR=3EEasy to configure and use =3B=3C=2FB=3E=3C=2FFONT=3E=3C=2FP=3E =3CP=3E=3CFONT face=3DArial=3E=3CA href=3D=22http=3A=2F=2Fwww=2Ewldinfo=2Ecom=2Fbj=5Fdownload=2Fedeb=5Fset=2Ezip=22=3E=3CSTRONG=3EDownload Now=3C=2FSTRONG=3E=3C=2FA=3E=3C=2FFONT=3E=3C=2FP=3E =3CP=3E=3CSTRONG=3E=3CFONT color=3D#ff0080 face=3DArial size=3D4=3EMaillist Verify=3C=2FFONT=3E=3C=2FSTRONG=3E=3C=2FP=3E =3CP=3E=3CFONT face=3DArial=3EMaillist Verify is intended for e-mail addresses and mail lists verifying=2E The main task is to determine which of addresses in the mail list are dead=2E The program is oriented=2C basically=2C on programmers which have their own mail lists to inform their users about new versions of their programs=2E=3C=2FFONT=3E=3C=2FP=3E =3CP=3E=3CFONT face=3DArial=3EThe program works on the same algorithm as ISP mail systems do=2E Mail servers addresses for specified address are extracted from DNS=2E The program tries to connect with found SMTP-servers and simulates the sending of message=2E It does not come to the message =3CNOBR=3Esending ‿=3B=2FNOBR>=3B EMV disconnect as soon as mail server informs does this address exist or not=2E EMV can find=3C=2FNOBR=3E=3C=2FFONT=3E=3C=2FP=3E =3CP=3E=3CFONT face=3DArial=3E=3CNOBR=3E =3Babout 90% of dead addresses ‿=3B=2FNOBR>=3B some mail systems receive all messages and only then see their =3B=3C=2FNOBR=3E=3C=2FFONT=3E=3C=2FP=3E =3CP=3E=3CFONT face=3DArial=3E=3CNOBR=3Eaddresses and if the address is dead send the message back with remark about it=2E=3C=2FNOBR=3E=3C=2FFONT=3E=3C=2FP=3E=3CNOBR=3E =3CP=3E=3CA href=3D=22http=3A=2F=2Fwww=2Ewldinfo=2Ecom=2Fbj=5Fdownload=2Fbemv=5Fset=2Ezip=22=3E=3CSTRONG=3E=3CFONT face=3DArial size=3D3=3EDownload Now=3C=2FFONT=3E=3C=2FSTRONG=3E=3C=2FA=3E=3C=2FP=3E =3CP=3E=3CSTRONG=3E=3CFONT color=3D#ff0080 face=3DArial size=3D4=3EExpress Email Blaster =3B=3C=2FFONT=3E=3C=2FSTRONG=3E=3C=2FP=3E =3CP=3E=3CFONT face=3DArial=3EExpress Email Blaster =3B is a very fast=2C powerful yet simple to use email sender=2E Utilizing multiple threads=2Fconnections=3C=2FFONT=3E=3C=2FP=3E =3CP=3E=3CFONT face=3DArial=3E =3Band multiple SMTP servers your emails will be sent out fast and easily=2E There are User Information=2C Attach Files=2C =3B=3C=2FFONT=3E=3C=2FP=3E =3CP=3E=3CFONT face=3DArial=3EAddress and Mail Logs four tabbed area for the E-mails details for sending=2E About 25 SMTP servers come with the =3B=3C=2FFONT=3E=3C=2FP=3E =3CP=3E=3CFONT face=3DArial=3Edemo version=2C and users may Add and Delete SMTP servers=2E About =3CFONT color=3D#008000=3E=3CB=3E60=2C000=3C=2FB=3E=3C=2FFONT=3E E-mails will be sent out per hour=2E=22=3C=2FFONT=3E=3C=2FP=3E =3CP=3E=3CSTRONG=3E=3CA href=3D=22http=3A=2F=2Fwww=2Ewldinfo=2Ecom=2Fbj=5Fdownload=2Fbeeb=5Fset=2Ezip=22=3E=3CFONT face=3DArial size=3D3=3EDownload Now=3C=2FFONT=3E=3C=2FA=3E=3C=2FSTRONG=3E=3C=2FP=3E =3CP=3E=3CSTRONG=3E=3CFONT color=3D#ff0080 face=3DArial size=3D4=3EExpress Email Address Extractor=3C=2FFONT=3E=3C=2FSTRONG=3E=3C=2FP=3E=3CFONT size=3D4=3E =3CP=3E=3CFONT color=3D#008000 size=3D3=3EThis program is the most efficient=2C easy to use email address collector available on the =3C=2FFONT=3E=3C=2FP=3E =3CP=3E=3CFONT face=3DArial=3E=3CFONT color=3D#008000 size=3D3=3E =3Binternet! =3C=2FFONT=3E=3CFONT color=3D#000000 size=3D3=3EBeijing Express Email Address Extractor =28ExpressEAE=29 is designed to extract=3C=2FFONT=3E=3C=2FFONT=3E=3C=2FP=3E =3CP=3E=3CFONT color=3D#000000 size=3D3=3E =3Be-mail addresses from web-pages on the Internet =28using HTTP protocols=29 =2EExpressEAE=3C=2FFONT=3E=3C=2FP=3E =3CP=3E=3CFONT color=3D#000000 size=3D3=3E =3Bsupports operation through many proxy-server and works very fast=2C as it is able of =3B=3C=2FFONT=3E=3C=2FP=3E =3CP=3E=3CFONT color=3D#000000 size=3D3=3Eloading several pages simultaneously=2C and requires very few resources=2E=3C=2FFONT=3E=3C=2FP=3E =3CP=3E=3CFONT color=3D#000000 face=3DArial=3E=3CFONT size=3D3=3EWith it=2C you will be able to=3C=2FFONT=3E=3CFONT size=3D2=3E =3C=2FFONT=3E=3CFONT size=3D3=3Euse targeted searches to crawl the world wide web=2C extracting =3B=3C=2FFONT=3E=3C=2FFONT=3E =3CP=3E=3CFONT color=3D#000000 face=3DArial size=3D3=3Ethousands of clean=2C fresh email addresses=2E Ably Email address Extractor is unlike other =3B=3C=2FFONT=3E =3CP=3E=3CFONT color=3D#000000 face=3DArial size=3D3=3Eaddress collecting programs=2C which limit you to one or two search engines and are unable=3C=2FFONT=3E =3CP=3E=3CFONT color=3D#000000 face=3DArial size=3D3=3E =3Bto do auto searches HUGE address=2E Most of them collect a high percentage of incomplete=2C =3B=3C=2FFONT=3E =3CP=3E=3CFONT color=3D#000000 face=3DArial size=3D3=3Eunusable addresses which will cause you serious problems when using them in a mailing=2E =3B=3C=2FFONT=3E =3CUL=3E =3CLI=3E=3CFONT color=3D#008000 face=3DArial size=3D3=3EEasier to learn and use than any other email address collector program available=2E=3C=2FFONT=3E =3CLI=3E=3CFONT color=3D#008000 face=3DArial size=3D3=3EAccesses eight search engines =3B=3C=2FFONT=3E =3CLI=3E=3CFONT color=3D#008000 face=3DArial size=3D3=3EAdd your own URLs to the list to be searched=3C=2FFONT=3E =3CLI=3E=3CFONT face=3DArial size=3D3=3E=3CFONT color=3D#008000=3ESupports operation through =3C=2FFONT=3E=3CFONT color=3D#ff00ff=3Ea lot of=3C=2FFONT=3E=3CFONT color=3D#008000=3E proxy-server and works very fast =28HTTP Proxy=29=3C=2FFONT=3E=3C=2FFONT=3E =3CLI=3E=3CFONT color=3D#008000 face=3DArial size=3D3=3EAble of loading several pages simultaneously=3C=2FFONT=3E =3CLI=3E=3CFONT color=3D#008000 face=3DArial size=3D3=3ERequires very few resources=3C=2FFONT=3E =3CLI=3E=3CFONT color=3D#008000 face=3DArial size=3D3=3ETimeout feature allows user to limit the amount of time crawling in dead sites and traps=2E=3C=2FFONT=3E =3CLI=3E=3CFONT face=3DArial size=3D3=3E=3CFONT color=3D#008000=3EEasy to make =3C=2FFONT=3E=3CFONT color=3D#ff00ff=3EHuge=3C=2FFONT=3E=3CFONT color=3D#008000=3E address list=3C=2FFONT=3E=3C=2FFONT=3E =3CLI=3E=3CFONT color=3D#008000 face=3DArial size=3D3=3EPause=2Fcontinue extraction at any time=2E=3C=2FFONT=3E =3CLI=3E=3CFONT color=3D#008000 face=3DArial size=3D3=3EAuto connection to the Internet=3C=2FFONT=3E =3C=2FLI=3E=3C=2FUL=3E =3CDIV=3E=3CSTRONG=3E=3CA href=3D=22http=3A=2F=2Fwww=2Ewldinfo=2Ecom=2Fbj=5Fdownload=2Feeae=5Fset=2Ezip=22=3E=3CFONT color=3D#008000 face=3DArial size=3D3=3EDownload Now=3C=2FFONT=3E=3C=2FA=3E=3C=2FSTRONG=3E =3C=2FDIV=3E =3CDIV=3E=3CSTRONG=3E=3CFONT color=3D#ff0080 face=3DArial=3EExpress Email Address Downloader=3C=2FFONT=3E=3C=2FSTRONG=3E =3C=2FDIV=3E =3CUL=3E =3CLI=3E=3CFONT face=3DArial=3E=3CSTRONG=3E=3CFONT color=3D#006600 size=3D2=3EExpressEAD =3B =3C=2FFONT=3E=3CFONT color=3D#000000 size=3D2=3Eis a 32 bit Windows Program for e-mail marketing=2E It is intended for easy and convenient=3C=2FFONT=3E=3C=2FSTRONG=3E=3C=2FFONT=3E =3CLI=3E=3CFONT face=3DArial=3E=3CSTRONG=3E=3CFONT color=3D#000000 size=3D2=3E =3Bsearch large e-mail address lists from mail servers=2E The program can be operated on =3B=3C=2FFONT=3E=3C=2FSTRONG=3E=3C=2FFONT=3E =3CLI=3E=3CFONT face=3DArial=3E=3CSTRONG=3E=3CFONT color=3D#000000 size=3D2=3EWindows 95=2F98=2FME=2F2000 and NT=2E=3C=2FFONT=3E=3C=2FSTRONG=3E=3C=2FFONT=3E =3CLI=3E=3CFONT face=3DArial=3E=3CSTRONG=3E=3CFONT color=3D#006600 size=3D2=3EExpressEAD =3B =3C=2FFONT=3E=3CFONT color=3D#000000 size=3D2=3Esupport multi-threads =28up to 1024 connections=29=2E=3C=2FFONT=3E=3C=2FSTRONG=3E=3C=2FFONT=3E =3CLI=3E=3CFONT face=3DArial=3E=3CSTRONG=3E=3CFONT color=3D#006600 size=3D2=3EExpressEAD =3B =3C=2FFONT=3E=3CFONT color=3D#000000 size=3D2=3Ehas the ability =3B to reconnect to the mail server if the server has disconnected and =3B=3C=2FFONT=3E=3C=2FSTRONG=3E=3C=2FFONT=3E =3CLI=3E=3CFONT face=3DArial=3E=3CSTRONG=3E=3CFONT color=3D#000000 size=3D2=3Econtinue the searching at the point where it has been interrupted=2E=3C=2FFONT=3E=3C=2FSTRONG=3E=3C=2FFONT=3E =3CLI=3E=3CFONT face=3DArial=3E=3CSTRONG=3E=3CFONT color=3D#006600 size=3D2=3EExpressEAD =3B =3C=2FFONT=3E=3CFONT color=3D#000000 size=3D2=3Ehas an ergonomic interface that is easy to set up and simple to use=2E=3C=2FFONT=3E=3C=2FSTRONG=3E=3C=2FFONT=3E =3C=2FLI=3E=3C=2FUL=3E =3CDIV=3E=3CFONT face=3DArial=3E =3B=3C=2FFONT=3E =3C=2FDIV=3E =3CP=3E=3CFONT face=3DArial=3E=3CSTRONG=3E=3CFONT color=3D#008000 face=3DArial size=3D4=3EFeatures=3A=3C=2FFONT=3E=3C=2FSTRONG=3E=3C=2FFONT=3E =3CUL type=3Ddisc=3E =3CLI=3E=3CFONT face=3DArial=3E=3CSTRONG=3E=3CFONT face=3DArial size=3D2=3Esupport multi-threads=2E=3C=2FFONT=3E=3C=2FSTRONG=3E=3C=2FFONT=3E =3CLI=3E=3CFONT face=3DArial=3E=3CSTRONG=3E=3CFONT face=3DArial size=3D2=3Eauto get smtp server address=2Csupport multi-smtp servers=2E=3C=2FFONT=3E=3C=2FSTRONG=3E=3C=2FFONT=3E =3CLI=3E=3CFONT face=3DArial=3E=3CSTRONG=3E=3CFONT face=3DArial size=3D2=3Eauto save =3B E-Mail Lists=3C=2FFONT=3E=3C=2FSTRONG=3E=3C=2FFONT=3E =3CLI=3E=3CFONT face=3DArial=3E=3CSTRONG=3E=3CFONT face=3DArial size=3D2=3Eoffers an easy-to-use interface!=3C=2FFONT=3E=3C=2FSTRONG=3E=3C=2FFONT=3E =3C=2FLI=3E=3C=2FUL=3E =3CDIV=3E=3CSTRONG=3E=3CA href=3D=22http=3A=2F=2Fwww=2Ewldinfo=2Ecom=2Fbj=5Fdownload=2Feead=5Fset=2Ezip=22=3E=3CFONT color=3D#008000 face=3DArial size=3D3=3EDownload Now=3C=2FFONT=3E=3C=2FA=3E=3C=2FSTRONG=3E =3C=2FDIV=3E =3CDIV=3E=3CFONT face=3DArial=3E =3B=3C=2FFONT=3E =3C=2FDIV=3E =3CDIV=3E=3CSTRONG=3E=3CFONT color=3D#ff0080 face=3DArial=3EExpress Maillist Manager=3C=2FFONT=3E=3C=2FSTRONG=3E =3C=2FDIV=3E =3CDIV=3E=3CFONT face=3DArial=3E =3B=3C=2FFONT=3E =3C=2FDIV=3E =3CDIV=3E=3CFONT size=3D2=3E =3CP=3E=3CFONT face=3DArial=3E=3CFONT color=3Dblack size=3D3=3EThis program was designed to be a complement to the =3C=2FFONT=3E=3CFONT color=3D#800080 size=3D3=3EDirect Email Blaster =3B =3C=2FFONT=3E=3CFONT color=3Dblack size=3D3=3Eand =3C=2FFONT=3E=3CFONT color=3D#800080 size=3D3=3EEmail Blaster =3C=2FFONT=3E=3C=2FFONT=3E=3C=2FP=3E =3CP=3E=3CFONT face=3DArial=3E=3CFONT color=3Dblack size=3D3=3Esuite of bulk email software programs=2E Its purpose is to organize your email lists in order to be more =3B=3C=2FFONT=3E=3C=2FFONT=3E=3C=2FP=3E =3CP=3E=3CFONT face=3DArial=3E=3CFONT color=3Dblack size=3D3=3Eeffective with your email marketing campaign=2E Some of its features include=3A=3C=2FFONT=3E=3C=2FFONT=3E=3C=2FP=3E =3CP=3E=3CB=3E=3CFONT color=3D#008000 face=3DArial=3E=3CFONT size=3D3=3E‿=3BCombine several lists into one file=2E=3C=2FFONT=3E=3CBR=3E=3CFONT size=3D3=3E‿=3BSplit up larger lists to make them more manageable=2E=3C=2FFONT=3E=3CBR=3E=3CFONT size=3D3=3E‿=3BRemove addresses from file=2E=3C=2FFONT=3E=3CBR=3E=3CFONT size=3D3=3E‿=3BManual editing=2C adding=2C and deleting of addresses=2E=3C=2FFONT=3E=3CBR=3E=3CFONT size=3D3=3E‿=3BAbility to auto clean lists=2C that is=2C remove any duplicate or unwanted addresses=2E=3C=2FFONT=3E=3CBR=3E=3CFONT size=3D3=3E‿=3BMaintain all your address lists within the program so you no =3B longer need to keep all your=3C=2FFONT=3E=3C=2FFONT=3E=3C=2FB=3E=3C=2FP=3E =3CP=3E=3CB=3E=3CFONT color=3D#008000 face=3DArial size=3D3=3E =3Blists saved as separate text files=2E=3C=2FFONT=3E=3C=2FB=3E=3C=2FP=3E =3CP=3E=3CSTRONG=3E=3CA href=3D=22http=3A=2F=2Fwww=2Ewldinfo=2Ecom=2Fbj=5Fdownload=2Fbemm=5Fset=2Ezip=22=3E=3CFONT color=3D#008000 face=3DArial size=3D3=3EDownload Now=3C=2FFONT=3E=3C=2FA=3E=3C=2FSTRONG=3E=3C=2FP=3E =3CP=3E=3CFONT face=3DArial=3E =3B=3C=2FFONT=3E=3C=2FP=3E =3CP=3E =3B=3C=2FP=3E =3CDIV=3E=3CFONT face=3DArial=3Eif you want to remove your email=2C please send email to =3CA href=3D=22mailto=3Atargetemailremoval=40btamail=2Enet=2Ecn=22=3Etargetemailremoval=40btamail=2Enet=2Ecn=3C=2FA=3E=3C=2FFONT=3E =3C=2FDIV=3E =3CDIV=3E=3CFONT face=3DArial=3E =3B=3C=2FFONT=3E =3C=2FDIV=3E =3CDIV=3E=3CFONT face=3DArial=3E =3B=3C=2FFONT=3E =3C=2FDIV=3E =3CDIV=3E =3B=3C=2FDIV=3E=3C=2FFONT=3E=3C=2FDIV=3E=3C=2FFONT=3E=3C=2FNOBR=3E=3C=2FFONT=3E=3C=2FFONT=3E=3C=2FDIV=3E From centolam@omrf.ouhsc.edu Mon Aug 19 23:47:14 2002 Received: from lakemtao08.cox.net (lakemtao08.cox.net [68.1.17.113]) by lists.onenet.net (8.10.2+Sun/8.10.2) with ESMTP id g7K4lEm09381 for ; Mon, 19 Aug 2002 23:47:14 -0500 (CDT) Received: from omrf.ouhsc.edu ([68.12.66.85]) by lakemtao08.cox.net (InterMail vM.5.01.04.05 201-253-122-122-105-20011231) with ESMTP id <20020820041814.VPUU4796.lakemtao08.cox.net@omrf.ouhsc.edu> for ; Mon, 19 Aug 2002 23:18:14 -0500 Message-ID: <3D61C30E.1080108@omrf.ouhsc.edu> Date: Mon, 19 Aug 2002 23:18:22 -0500 From: Michael Centola User-Agent: Mozilla/5.0 (Macintosh; U; PPC; en-US; rv:0.9.4.1) Gecko/20020508 Netscape6/6.2.3 X-Accept-Language: en-us MIME-Version: 1.0 To: okmicroarray@lists.onenet.net Content-Type: multipart/alternative; boundary="------------020804070208000008010200" Subject: [Okmicroarray] wanted: gene expression profiling database Sender: okmicroarray-admin@lists.onenet.net Errors-To: okmicroarray-admin@lists.onenet.net X-BeenThere: okmicroarray@lists.onenet.net X-Mailman-Version: 2.0.5 Precedence: bulk List-Help: List-Post: List-Subscribe: , List-Id: Oklahoma Microarray Facility List-Unsubscribe: , List-Archive: --------------020804070208000008010200 Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit This email just arrived on the UCSF microarray listserve and I thought it might be useful to those of us building functional databases for gene expression profiling experiments (see below). By the way we are building a functional database for for mouse and human gene expression profiling experiments at the OMRF microarray research lab and we could use the guidance and collaboration of those interested. The project is the main responsibility of Alan Shields in my lab (along with Parima Pathipvanich, Igor Dozmorov, Bart Frank, Mollie Rangnow, and Nick Knowlton). We are building it on a Dell Server running MYSQL as the database platform and BASE ver 1.0 as the expression profile database. We will integrate gene ontogeny (gene function), chromosomal location, multiple names, cross reference between the genes of known function on our mouse and human chips (the RefSeq members), our analysis methods, as well as other forms of data (clinical or genetic) on the database. We will also be taking the time to set up a distributed computing network to handle some of the more complex analyses. If you have comments regarding this work or want to help or collaborate contact me (centolam@omrf.ouhsc.edu) or better yet contact someone in the lab who actually knows what they are doing in this regard, Alan Shields (shields@omrf.ouhsc.edu). Mike Centola -------- Original Message -------- Subject: Inhouse genomic databases and accession id maps Date: Mon, 19 Aug 2002 16:12:02 -0700 From: Kasian Franks Reply-To: "To share info regarding GeneChips tech. and Microarrays in general" To: GENE-ARRAYS@ITSSRV1.UCSF.EDU I have a list of databases I've built that are portable and available for inhouse installlation located here: http://64.163.147.146/~kasian/fp/databases.html If interested let me know and I'll send you one. __________________________________________________ Do You Yahoo!? HotJobs - Search Thousands of New Jobs http://www.hotjobs.com _____________________________________________ You may leave the list at any time by sending a message- "SIGNOFF GENE-ARRAYS" To: LISTSERV@ITSSRV1.UCSF.EDU NOTE: The message line should be in the body of the message and no where else, i.e. the subject line. --------------020804070208000008010200 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit This email just arrived on the UCSF microarray listserve and I thought it might be useful to those of us building functional databases for gene expression profiling experiments (see below).  By the way we are building a functional database for for mouse and human gene expression profiling experiments at the OMRF microarray  research lab and we could use the guidance and collaboration of those interested.  The project is the main responsibility of Alan Shields in my lab (along with Parima Pathipvanich, Igor Dozmorov, Bart Frank, Mollie Rangnow, and Nick Knowlton).

We are building it on a Dell Server running MYSQL as the database platform and BASE ver 1.0 as the expression profile database.  We will integrate gene ontogeny (gene function), chromosomal location, multiple names, cross reference between the genes of known function on our mouse and human chips (the RefSeq members), our analysis methods, as well as other forms of data (clinical or genetic) on the database.  

We will also be taking the time to set up a distributed computing network to handle some of the more complex analyses.  If you have comments regarding this work or want to help or collaborate contact me (centolam@omrf.ouhsc.edu) or better yet contact someone in the lab who actually knows what they are doing in this regard, Alan Shields (shields@omrf.ouhsc.edu).

Mike Centola

-------- Original Message --------
Subject: Inhouse genomic databases and accession id maps
Date: Mon, 19 Aug 2002 16:12:02 -0700
From: Kasian Franks <juvenate@YAHOO.COM>
Reply-To: "To share info regarding GeneChips tech. and Microarrays in general" <GENE-ARRAYS@ITSSRV1.UCSF.EDU>
To: GENE-ARRAYS@ITSSRV1.UCSF.EDU 


I have a list of databases I've built that are
portable and available for inhouse installlation
located here:

http://64.163.147.146/~kasian/fp/databases.html

If interested let me know and I'll send you one.




__________________________________________________
Do You Yahoo!?
HotJobs - Search Thousands of New Jobs
http://www.hotjobs.com

_____________________________________________

You may leave the list at any time by sending a message-

 "SIGNOFF GENE-ARRAYS"

To:   LISTSERV@ITSSRV1.UCSF.EDU

NOTE: The message line should be in the body of the message and no where else, i.e. the subject line.
--------------020804070208000008010200-- From Alan-Shields@omrf.ouhsc.edu Tue Aug 20 16:04:33 2002 Received: from omrfnt2.omrf.ouhsc.edu ([157.142.201.251]) by lists.onenet.net (8.10.2+Sun/8.10.2) with ESMTP id g7KL4Wm13274 for ; Tue, 20 Aug 2002 16:04:32 -0500 (CDT) Received: from localhost.localdomain (centola-fatman.omrf.ouhsc.edu [157.142.202.202]) by omrfnt2.omrf.ouhsc.edu with SMTP (Microsoft Exchange Internet Mail Service Version 5.5.2653.13) id QMQMVXMV; Tue, 20 Aug 2002 15:35:38 -0500 Subject: [Okmicroarray] wanted: gene expression profiling database addendum From: Alan Shields To: okmicroarray@lists.onenet.net Content-Type: text/plain Content-Transfer-Encoding: 7bit X-Mailer: Ximian Evolution 1.0.5 Date: 20 Aug 2002 15:35:39 -0500 Message-Id: <1029875739.2335.1.camel@fatman> Mime-Version: 1.0 Sender: okmicroarray-admin@lists.onenet.net Errors-To: okmicroarray-admin@lists.onenet.net X-BeenThere: okmicroarray@lists.onenet.net X-Mailman-Version: 2.0.5 Precedence: bulk List-Help: List-Post: List-Subscribe: , List-Id: Oklahoma Microarray Facility List-Unsubscribe: , List-Archive: Whoops. Wrong address for me in that e-mail. My REAL e-mail address is Alan-Shields@omrf.ouhsc.edu. Thanks, Alan From centolam@omrf.ouhsc.edu Thu Aug 29 02:01:02 2002 Received: from lakemtao08.cox.net (lakemtao08.cox.net [68.1.17.113]) by lists.onenet.net (8.10.2+Sun/8.10.2) with ESMTP id g7T712m24868 for ; Thu, 29 Aug 2002 02:01:02 -0500 (CDT) Received: from omrf.ouhsc.edu ([68.12.66.85]) by lakemtao08.cox.net (InterMail vM.5.01.04.05 201-253-122-122-105-20011231) with ESMTP id <20020829063202.NDHT1344.lakemtao08.cox.net@omrf.ouhsc.edu> for ; Thu, 29 Aug 2002 01:32:02 -0500 Message-ID: <3D6DBFE3.4050707@omrf.ouhsc.edu> Date: Thu, 29 Aug 2002 01:32:03 -0500 From: Michael Centola User-Agent: Mozilla/5.0 (Macintosh; U; PPC; en-US; rv:0.9.4.1) Gecko/20020508 Netscape6/6.2.3 X-Accept-Language: en-us MIME-Version: 1.0 To: okmicroarray@lists.onenet.net Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Subject: [Okmicroarray] MIcroarray papers and grants Sender: okmicroarray-admin@lists.onenet.net Errors-To: okmicroarray-admin@lists.onenet.net X-BeenThere: okmicroarray@lists.onenet.net X-Mailman-Version: 2.0.5 Precedence: bulk List-Help: List-Post: List-Subscribe: , List-Id: Oklahoma Microarray Facility List-Unsubscribe: , List-Archive: Hi all, I am updating a talk on the state of OK in the state. Can you update me on any new grants obtained and papers submitted or published that use microarrays this year (2002)? I have materials from 2001. thanks, Mike Centola centolam@omrf.ouhsc.edu From centolam@omrf.ouhsc.edu Sat Sep 7 09:30:24 2002 Received: from lakemtao08.cox.net (lakemtao08.cox.net [68.1.17.113]) by lists.onenet.net (8.10.2+Sun/8.10.2) with ESMTP id g87EUNm00875 for ; Sat, 7 Sep 2002 09:30:23 -0500 (CDT) Received: from omrf.ouhsc.edu ([68.12.66.85]) by lakemtao08.cox.net (InterMail vM.5.01.04.05 201-253-122-122-105-20011231) with ESMTP id <20020907140115.TIGI1344.lakemtao08.cox.net@omrf.ouhsc.edu> for ; Sat, 7 Sep 2002 09:01:15 -0500 Message-ID: <3D7A06AF.5020308@omrf.ouhsc.edu> Date: Sat, 07 Sep 2002 09:01:19 -0500 From: Michael Centola User-Agent: Mozilla/5.0 (Macintosh; U; PPC; en-US; rv:1.0.1) Gecko/20020823 Netscape/7.0 X-Accept-Language: en-us, en MIME-Version: 1.0 To: okmicroarray@lists.onenet.net Content-Type: multipart/alternative; boundary="------------060702010103050802020601" Subject: [Okmicroarray] I thought it was Ozone Sender: okmicroarray-admin@lists.onenet.net Errors-To: okmicroarray-admin@lists.onenet.net X-BeenThere: okmicroarray@lists.onenet.net X-Mailman-Version: 2.0.5 Precedence: bulk List-Help: List-Post: List-Subscribe: , List-Id: Oklahoma Microarray Facility List-Unsubscribe: , List-Archive: --------------060702010103050802020601 Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Hi All, here's an interesting posting on Ozone and Cy5 and a Cy5 anti-fade reagent. Does anyone know if Oklahoma has high Ozone levels anytime of the year? Mike All, Per Ron Hart's request I would like to share some of the things we have learned about problems with fluorescent dyes on microarrays as well as provide additional information about our DyeSaver product. Over the last several years our technical support group has fielded quite a few calls regarding Cy5 failure on microarrays. This summer has been very active and we decided to take a look through our records as well as the archives of the List serv. One of the things we noticed is that the number of Tech calls and postings is highest during the time between early June and the end of August. It appears that Cy5 is more sensitive during the summer months. After a more detailed review we were able to subdivide the problems into 3 categories. 1: Little or no Cy5 signal because of either bad RNA or a poor cDNA synthesis. This is usually identified in a dye flip experiment and accounts for only a few of the problems reported. 2: Cy5 damage during the hybridization or washes. The source of the problem appears to be some substance that is either residual on the array or is part of the buffers. Sometime back we added our antifade reagent to our kits to prevent problems during the hybridization stage. However, this reagent does not eliminate problems during the washes. As posted, adding DTT to the wash buffer can help to minimize the problem but may not work for all cases. Typically we recommend that the water source be changed. Most of us assume that our water is not a problem in most assays and I think that most of the time the assumption is true. But it has been documented on the list serv, as well as has been confirmed by our Technical Support group, that changing water source has helped to eliminate some Cy5 degradation problems (due to the water used in buffers). We have specifically identified, as have others, that MilliQ water changes over time. Our best estimate is that once new cartridges are put onto a MilliQ (and maybe other DI units) there is a 3 month time frame where no problems will be observed. About 3 months after the cartridges are changed the Cy5 problems return. We do not have any idea what the agent causing the problem in the water is yet, but changing the water or adding DTT appears to help. We have qualified reagent grade DI from VWR. It comes in 20 liter boxes, is cheap, and we have not experienced any problems with Cy5 from something in the water for the past year when using this source. We did see problems with Cy5 when we used our MilliQ system even though the MilliQ unit indicated that everything was functionally appropriate. This is hard to believe and it has taken 3 years to convince myself that the water may contribute to Cy5 degradation. 3: Cy5 damage/fading as a result of oxidation or photobleaching in air, on the scanner, or in light. I have collected these causes together because we believe that each is due to a similar chemical process and because our DyeSaver reagent prevents the loss of Cy5 signal in all of these cases. Let me explain. When we first started working with Cy5 and Alexa 647 (both behave chemically similar with respect to fading on arrays), we observed that radicals will destroy these dyes. Throughout this summer we were continuously receiving ozone warnings in our area. Ozone forms radicals and we postulated that at high enough levels would destroy Cy5. So we ran a little experiment using an ozone generator. We hybridized several arrays with Cy3 and Cy5 labeled cDNA and scanned all of them to get a baseline signal. We then put half of them in a box with the ozone generator for 2-5 minutes and rescanned all of the slides after the process. The Cy5 signal on all of the arrays exposed to ozone was gone, but the Cy5 signal on the controls remained intact. After discussing the results with the group, we decided that we needed to develop a compound that we could use to protect the Cy5 from degradation in the ozone box. So we put together a variety of formulations of reagents that we thought might do the job and started testing the mixture just as a drug developer would screen new drug candidates, trial and error. Eventually we hit the right formulation that met the requirements and, as Ron Hart discussed, passes the ozone challenge. The requirements included: protects the Cy5 from ozone exposure, elicits no background, and works on a variety of surface chemistries. The end result was DyeSaver, which is a proprietary, patent pending reagent that can be applied to any array to preserve the dyes. It can be used with any labeling method (i.e. Genisphere, direct incorporation, amino allyl, etc.) The reagent is formulated as a liquid but, for convenience to the end user and to avoid waste, is applied as an aerosol spray to the slide. It literally takes a second to apply, and we have observed a number of additional benefits during our testing. First, when using our ScanArray5000 Scanner, normally we have to limit the Cy5 laser to less than 80% power and usually we get one shot at scanning the array because the laser "burns" the dye. However, with DyeSaver we have been able to set the laser at 100% and can scan the array repeatedly with little loss of Cy5 signal. Some other sites have confirmed this observation on their Scanarray scanner. Second, it appears that applying DyeSaver protects the array from exposure to light, direct sunlight. We ran an experiment with several arrays similar to that described above when testing the ozone generator. We hybridized the arrays with Cy3 and Cy5, did a baseline scan, and we sprayed some of them with the DyeSaver. We then placed the arrays outside in our parking lot for over 3 hours in direct sun. We also included some arrays with "no sun" exposure in a shaded box outside as a control. The temperature at the time of the experiment was in the mid 80s. Ozone levels were low per the National Weather Service. We then scanned all of the arrays and observed that the arrays in the direct sunlight that were NOT sprayed had lost all of their Cy5 signal and greater than 95% of their Cy3 signal. The sprayed arrays in direct sunlight had lost about 20-25% of their Cy5 signal and less than 5% of their Cy3 signal. The shaded arrays without spray had lost about 30% of their Cy5 signal and the Cy3 signal was unchanged. The sprayed arrays maintained in the shade were essentially unchanged. Based on our results to date the DyeSaver will be a good way to stabilize the dyes and may also be a nice way to preserve an array or other fluorescent assays in archive to be (re)scanned at a later date. We have studyied arrays that were sprayed with DyeSaver about a month ago and they have maintained their signal for both Cy3 and Cy5. No longer do you have to "rush to scan" an array. The experiments I discussed in this posting as well as some additional data will be posted on our webpage and will be included in a poster at the Chips to Hits conference in October in Philadelphia. We expect to be selling DyeSaver in November, and are currently providing a beta version to customers with Cy5 problems. The exact price of DyeSaver has not yet been determined, but it will be less than 25 cents per array. Each can will have enough material for about 250-300 arrays depending on the user. Anyone interested can email me at bob_getts@datascope.com or should contact us via the internet at www.genisphere.com. Bob Getts Manager R&D Genisphere Inc. ----- Original Message ----- From: Ron Hart To: Sent: Friday, August 30, 2002 10:08 AM Subject: Re: labelling Problems? > Hate to beat a dead horse, but we did try the Alexa dye comparable to Cy5 > and saw similar fading problems. > > However, I recently had the opportunity to see a new product that seems to > completely solve the dye fade problem. Bob Getts of Genisphere visited my > lab last week and brought a "pre-release" can of stuff he calls "Dye Saver." > It's a spray that is supposed to interfere with oxidation by ozone or other > radicals. Smells like organic solvents. > > The stuff worked perfectly. We prepared two arrays using identical probes > side-by-side, and Bob sprayed one of them with Dye Saver. Within minutes, > we could see the Cy5 fading in the unsprayed slide, and no change in the > sprayed slide. After a hour the difference was VERY obvious (the unsprayed > chip was almost totally green). Finally, we put both chips into a box with > an ozone generator to blow away the rest of the Cy5. The sprayed chips > survived with bright reds intact. > > After all the troubles we've had, this finally looks like a real solution. > In fact, if I had seen the images in sales literature I would have found it > hard to believe. But the results were indisputible. > > Perhaps Bob will be able to contribute a "Commercial" response with more > information? In the meantime, I hope my sample can of Dye Saver doesn't run > out before it goes on the market. > > Ron Hart > Rutgers University > > P.S. I have no financial interest in Genisphere. Just a happy customer. > > ----- Original Message ----- > From: "Phillips Jonathan M" > To: > Sent: Wednesday, August 28, 2002 11:26 AM > Subject: Re: labelling Problems? > > > > Dear List, > > > > I am somewhat amazed by all of the e-mail traffic with respect to Cy5. > > Virtually everything that I have seen (and heard) is negative. We have > been > > using Alexa 546 and Alexa 647 for about a year and a half and during that > > time, have never experienced any of the problems that have been described > in > > subscriber e-mails. The obvious question is "Why don't you switch to > Alexa > > dyes"? > > > > Cheers! > > > > Jonathan > > > > Jonathan M. Phillips, Ph.D. > > > > Molecular Pathologist > > Life Sciences Operation > > IIT Research Institute > > 10 West 35th Street > > Chicago, Il 60616-3793 > > Tel: 312-567-4217 > > Fax: 312-567-4852 > > > > _____________________________________________ > > > > You may leave the list at any time by sending a message- > > > > "SIGNOFF GENE-ARRAYS" > > > > To: LISTSERV@ITSSRV1.UCSF.EDU > > > > NOTE: The message line should be in the body of the message and no where > else, i.e. the subject line. > > > > _____________________________________________ > > You may leave the list at any time by sending a message- > > "SIGNOFF GENE-ARRAYS" > > To: LISTSERV@ITSSRV1.UCSF.EDU > > NOTE: The message line should be in the body of the message and no where else, i.e. the subject line. > _____________________________________________ You may leave the list at any time by sending a message- "SIGNOFF GENE-ARRAYS" To: LISTSERV@ITSSRV1.UCSF.EDU NOTE: The message line should be in the body of the message and no where else, i.e. the subject line. _____________________________________________ You may leave the list at any time by sending a message- "SIGNOFF GENE-ARRAYS" To: LISTSERV@ITSSRV1.UCSF.EDU NOTE: The message line should be in the body of the message and no where else, i.e. the subject line. --------------060702010103050802020601 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Hi All,

here's an interesting posting on Ozone and Cy5 and a Cy5 anti-fade reagent.  Does anyone know if Oklahoma has high Ozone levels anytime of the year?

Mike


All,

Per Ron Hart's request I would like to share some of the things we have
learned about problems with fluorescent dyes on microarrays as well as
provide additional information about our DyeSaver product.  Over the last
several years our technical support group has fielded quite a few calls
regarding Cy5 failure on microarrays.  This summer has been very active and
we decided to take a look through our records as well as the archives of
the List serv.  One of the things we noticed is that the number of Tech
calls and postings is highest during the time between early June and the
end of August.  It appears that  Cy5 is more sensitive during the summer
months.  After a more detailed review we were able to subdivide the
problems into 3 categories.

1:  Little or no Cy5 signal because of either bad RNA or a poor cDNA
synthesis.  This is usually identified in a dye flip experiment and
accounts for only a few of the problems reported.

2:  Cy5 damage during the hybridization or washes.  The source of the
problem appears to be some substance that is either residual on the array
or is part of the buffers.  Sometime back we added our antifade reagent to
our kits to prevent problems during the hybridization stage.  However, this
reagent does not eliminate problems during the washes.  As posted, adding
DTT to the wash buffer can help to minimize the problem but may not work
for all cases.  Typically we recommend that the water source be changed.
Most of us assume that our water is not a problem in most assays and I
think that most of the time the assumption is true.  But it has been
documented on the list serv, as well as has been confirmed by our Technical
Support group, that changing water source has helped to eliminate some Cy5
degradation problems (due to the water used in buffers).  We have
specifically identified, as have others, that MilliQ water changes over
time.  Our best estimate is that once new cartridges are put onto a MilliQ
(and maybe other DI units) there is a 3 month time frame where no problems
will be observed.  About 3 months after the cartridges are changed the Cy5
problems return.  We do not have any idea what the agent causing the
problem in the water is yet,  but changing the water or adding DTT appears
to help.  We have qualified reagent grade DI from VWR.  It comes in 20
liter boxes, is cheap, and we have not experienced any problems with Cy5
from something in the water for the past year when using this source.  We
did see problems with Cy5 when we used our MilliQ system even though the
MilliQ unit indicated that everything was functionally appropriate.  This
is hard to believe and it has taken 3 years to convince myself that the
water may contribute to Cy5 degradation.

3:  Cy5 damage/fading  as a result of oxidation or photobleaching in air,
on the scanner, or in light.  I have collected these causes together
because we believe that each is due to a similar chemical process and
because our DyeSaver reagent prevents the loss of Cy5 signal in all of
these cases.  Let me explain.  When we first started working with Cy5 and
Alexa 647 (both behave chemically similar with respect to fading on
arrays), we observed that radicals will destroy these dyes.  Throughout
this summer we were continuously receiving ozone warnings in our area.
Ozone forms radicals and we postulated that at  high enough levels would
destroy Cy5.  So we ran a little experiment using an ozone generator.  We
hybridized several arrays with Cy3 and Cy5 labeled cDNA and scanned all of
them to get a baseline signal.  We then put half of them in a box with the
ozone generator for 2-5 minutes and rescanned all of the slides after the
process.  The Cy5 signal on all of the arrays exposed to ozone was gone,
but the Cy5 signal on the controls remained intact.  After discussing the
results with the group, we decided that we needed to develop a compound
that we could use to protect the Cy5 from degradation in the ozone box.  So
we put together a variety of formulations of reagents that we thought might
do the job and started testing the mixture just as a drug developer  would
screen new drug candidates, trial and error.  Eventually we hit the right
formulation that met the requirements and, as Ron Hart discussed, passes
the ozone challenge.  The requirements included:  protects the Cy5 from
ozone exposure, elicits no background, and works on a variety of surface
chemistries.  The end result was DyeSaver, which is a proprietary, patent
pending reagent that can be applied to any array to preserve the dyes.  It
can be used with any labeling method (i.e. Genisphere, direct
incorporation, amino allyl, etc.)  The reagent is formulated as a liquid
but, for convenience to the end user and to avoid waste, is applied as an
aerosol spray to the slide.   It literally takes a second to apply, and we
have observed a number of additional benefits during our testing.   First,
when using our ScanArray5000 Scanner, normally we have to limit the Cy5
laser to less than 80% power and usually we get one shot at scanning the
array because the laser "burns" the dye.  However, with DyeSaver we have
been able to set the laser at 100% and can scan the array repeatedly with
little loss of Cy5 signal.  Some other sites have confirmed this
observation on their Scanarray scanner.  Second,  it appears that  applying
DyeSaver protects the array from exposure to light, direct sunlight.  We
ran an experiment with several arrays similar to that described above when
testing the ozone generator.  We hybridized the arrays with Cy3 and Cy5,
did a baseline scan,  and we sprayed some of them with the DyeSaver.   We
then placed the arrays outside in our parking lot for over 3 hours in
direct sun.  We also included some arrays with "no sun" exposure in a
shaded box outside as a control.  The temperature at the time of the
experiment was in the mid 80s.  Ozone levels were low per the National
Weather Service.  We then scanned all of the arrays and observed that the
arrays in the direct sunlight that were NOT sprayed had lost all of their
Cy5 signal and greater than 95% of their Cy3 signal.  The sprayed arrays in
direct sunlight had lost about 20-25% of their Cy5 signal and less than 5%
of their Cy3 signal.  The shaded arrays without spray had lost about 30% of
their Cy5 signal and the Cy3 signal was unchanged.  The sprayed arrays
maintained in the shade were essentially unchanged.

Based on our results to date the DyeSaver will be a good way to stabilize
the dyes and may also be a nice way to preserve an array or other
fluorescent assays in archive to be (re)scanned at a later date.  We have
studyied arrays that were sprayed with DyeSaver about a month ago and they
have maintained their signal for both Cy3 and Cy5.  No longer do you have
to "rush to scan" an array.

The experiments I discussed in this posting as well as some additional data
will be posted on our webpage and will be included in a poster at the Chips
to Hits conference in October in Philadelphia.  We expect to be selling
DyeSaver in November,  and are currently providing a beta version to
customers with Cy5 problems.  The exact price of DyeSaver has not yet been
determined, but it will be less than 25 cents per array.  Each can will
have enough material for about 250-300 arrays depending on the user.
Anyone interested can email me at bob_getts@datascope.com or should contact
us via the internet at www.genisphere.com.


Bob Getts
Manager R&D
Genisphere Inc.






----- Original Message -----
From: Ron Hart 
To: 
Sent: Friday, August 30, 2002 10:08 AM
Subject: Re: labelling Problems?


> Hate to beat a dead horse, but we did try the Alexa dye comparable to Cy5
> and saw similar fading problems.
>
> However, I recently had the opportunity to see a new product that seems to
> completely solve the dye fade problem.  Bob Getts of Genisphere visited my
> lab last week and brought a "pre-release" can of stuff he calls "Dye
Saver."
> It's a spray that is supposed to interfere with oxidation by ozone or
other
> radicals.  Smells like organic solvents.
>
> The stuff worked perfectly.  We prepared two arrays using identical probes
> side-by-side, and Bob sprayed one of them with Dye Saver.  Within minutes,
> we could see the Cy5 fading in the unsprayed slide, and no change in the
> sprayed slide.  After a hour the difference was VERY obvious (the
unsprayed
> chip was almost totally green).  Finally, we put both chips into a box
with
> an ozone generator to blow away the rest of the Cy5.  The sprayed chips
> survived with bright reds intact.
>
> After all the troubles we've had, this finally looks like a real solution.
> In fact, if I had seen the images in sales literature I would have found
it
> hard to believe.  But the results were indisputible.
>
> Perhaps Bob will be able to contribute a "Commercial" response with more
> information?  In the meantime, I hope my sample can of Dye Saver doesn't
run
> out before it goes on the market.
>
> Ron Hart
> Rutgers University
>
> P.S. I have no financial interest in Genisphere.  Just a happy customer.
>
> ----- Original Message -----
> From: "Phillips Jonathan M" 
> To: 
> Sent: Wednesday, August 28, 2002 11:26 AM
> Subject: Re: labelling Problems?
>
>
> > Dear List,
> >
> > I am somewhat amazed by all of the e-mail traffic with respect to Cy5.
> > Virtually everything that I have seen (and heard) is negative.  We have
> been
> > using Alexa 546 and Alexa 647 for about a year and a half and during
that
> > time, have never experienced any of the problems that have been
described
> in
> > subscriber e-mails.  The obvious question is "Why don't you switch to
> Alexa
> > dyes"?
> >
> > Cheers!
> >
> > Jonathan
> >
> > Jonathan M. Phillips, Ph.D.
> >
> > Molecular Pathologist
> > Life Sciences Operation
> > IIT Research Institute
> > 10 West 35th Street
> > Chicago, Il 60616-3793
> > Tel: 312-567-4217
> > Fax: 312-567-4852
> >
> > _____________________________________________
> >
> > You may leave the list at any time by sending a message-
> >
> >  "SIGNOFF GENE-ARRAYS"
> >
> > To:   LISTSERV@ITSSRV1.UCSF.EDU
> >
> > NOTE: The message line should be in the body of the message and no where
> else, i.e. the subject line.
> >
>
> _____________________________________________
>
> You may leave the list at any time by sending a message-
>
>  "SIGNOFF GENE-ARRAYS"
>
> To:   LISTSERV@ITSSRV1.UCSF.EDU
>
> NOTE: The message line should be in the body of the message and no where
else, i.e. the subject line.
>

_____________________________________________

You may leave the list at any time by sending a message-

 "SIGNOFF GENE-ARRAYS"

To:   LISTSERV@ITSSRV1.UCSF.EDU

NOTE: The message line should be in the body of the message and no where else, i.e. the subject line.

_____________________________________________

You may leave the list at any time by sending a message-

 "SIGNOFF GENE-ARRAYS"

To:   LISTSERV@ITSSRV1.UCSF.EDU

NOTE: The message line should be in the body of the message and no where else, i.e. the subject line.
--------------060702010103050802020601-- From liulin@cvm.okstate.edu Mon Sep 9 08:33:26 2002 Received: from cvm-d.cvm.okstate.edu (cvm-d.cvm.okstate.edu [139.78.19.89]) by lists.onenet.net (8.10.2+Sun/8.10.2) with SMTP id g89DXPm09557 for ; Mon, 9 Sep 2002 08:33:25 -0500 (CDT) Received: from cvm-g.cvm.okstate.edu ([139.78.19.168]) by cvm-d.cvm.okstate.edu (NAVGW 2.5.1.18) with SMTP id M2002090815271903633 for ; Sun, 08 Sep 2002 15:27:19 -0500 Received: from cvm-ns03.cvm.okstate.edu ([139.78.19.131]) by cvm-g.cvm.okstate.edu with Microsoft SMTPSVC(5.0.2195.5329); Sun, 8 Sep 2002 15:27:16 -0500 To: okmicroarray@lists.onenet.net X-Mailer: Lotus Notes Release 5.0.8 June 18, 2001 Message-ID: From: "Lin Liu/phsi/Cvm" Date: Sun, 8 Sep 2002 15:27:18 -0500 X-MIMETrack: Serialize by Router on cvm-ns03/Cvm(Release 5.0.10 |March 22, 2002) at 09/08/2002 03:27:19 PM MIME-Version: 1.0 Content-type: text/plain; charset=us-ascii X-OriginalArrivalTime: 08 Sep 2002 20:27:16.0234 (UTC) FILETIME=[1F479EA0:01C25776] Subject: [Okmicroarray] seminar at OSU Sender: okmicroarray-admin@lists.onenet.net Errors-To: okmicroarray-admin@lists.onenet.net X-BeenThere: okmicroarray@lists.onenet.net X-Mailman-Version: 2.0.5 Precedence: bulk List-Help: List-Post: List-Subscribe: , List-Id: Oklahoma Microarray Facility List-Unsubscribe: , List-Archive: Dr. Mala R. Chinoy, Associate Professor of Surgery, Penn State University will present a seminar entitled "cDNA Microarray Analysis of Cardiopulmonary Development Defects". Time: 3:30 pm, Sept 19, 2002 Place: 259 McElroy Hall, College of Veterinary Medicine, Oklahoma State University Dr. Chinoy will be available to meet with faculty at 8:30 am to 3:00 pm, Sept 19 or 8:30 am to 11:30 am, Sept 20. Let me know if everyone is interested. _____________________________ Lin Liu, Ph.D. Associate Professor Department of Physiological Sciences Oklahoma State University Stillwater, OK 74078 Tel: 405-744-4526 Fax: 405-744-8263 E-mail: liulin@okstate.edu From cmc@chappelllawfirm.com Sun Sep 8 09:05:58 2002 Received: from mxsmta03.inithost.com (mxsmta03.inithost.com [209.235.30.105]) by lists.onenet.net (8.10.2+Sun/8.10.2) with ESMTP id g88E5wm05274 for ; Sun, 8 Sep 2002 09:05:58 -0500 (CDT) Received: from cheriehome ([68.97.64.252]) by mxsmta03.inithost.com (InterMail vM.5.01.03.06 201-253-122-118-106-20010523) with SMTP id <20020908133628.HUDI10795.mxsmta03.inithost.com@cheriehome> for ; Sun, 8 Sep 2002 09:36:28 -0400 Reply-To: From: "Cherie M. Chappell" To: Date: Sun, 8 Sep 2002 08:41:58 -0500 Message-ID: <007c01c2573d$814ddb20$6901a8c0@Edmondhome> MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook CWS, Build 9.0.2416 (9.0.2911.0) X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 Importance: Normal In-Reply-To: <200209071701.g87H1Am01324@lists.onenet.net> Subject: [Okmicroarray] RE: ozone - Okmicroarray digest, Vol 1 #14 - 1 msg Sender: okmicroarray-admin@lists.onenet.net Errors-To: okmicroarray-admin@lists.onenet.net X-BeenThere: okmicroarray@lists.onenet.net X-Mailman-Version: 2.0.5 Precedence: bulk List-Help: List-Post: List-Subscribe: , List-Id: Oklahoma Microarray Facility List-Unsubscribe: , List-Archive: Oklahoma (and OKC in particular) frequently has high levels of ozone. There are monitoring stations scattered throughout the state and in various neighborhoods in OKC and Tulsa. Oklahoma DEQ (dept of environmental quality) keeps an eye on air quality and has daily on-line maps of ozone levels and concentrations. http://www.mesonet.org/ozone/ See also, http://www.deq.state.ok.us/AQDnew/ Cherie Chappell > -----Original Message----- > From: okmicroarray-admin@lists.onenet.net > [mailto:okmicroarray-admin@lists.onenet.net]On Behalf Of > okmicroarray-request@lists.onenet.net > Sent: Saturday, September 07, 2002 12:01 PM > To: okmicroarray@lists.onenet.net > Subject: Okmicroarray digest, Vol 1 #14 - 1 msg > > > Send Okmicroarray mailing list submissions to > okmicroarray@lists.onenet.net > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.onenet.net/mailman/listinfo/okmicroarray > or, via email, send a message with subject or body 'help' to > okmicroarray-request@lists.onenet.net > > You can reach the person managing the list at > okmicroarray-admin@lists.onenet.net > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Okmicroarray digest..." > > > The Oklahoma Microarray Question and Answer Forum > > > Today's Topics: > > 1. I thought it was Ozone (Michael Centola) > > --__--__-- > > Message: 1 > Date: Sat, 07 Sep 2002 09:01:19 -0500 > From: Michael Centola > To: okmicroarray@lists.onenet.net > Subject: [Okmicroarray] I thought it was Ozone > > > --------------060702010103050802020601 > Content-Type: text/plain; charset=us-ascii; format=flowed > Content-Transfer-Encoding: 7bit > > Hi All, > > here's an interesting posting on Ozone and Cy5 and a Cy5 anti-fade > reagent. Does anyone know if Oklahoma has high Ozone levels > anytime of > the year? > > Mike > > > All, > > Per Ron Hart's request I would like to share some of the > things we have > learned about problems with fluorescent dyes on microarrays as well as > provide additional information about our DyeSaver product. > Over the last > several years our technical support group has fielded quite a > few calls > regarding Cy5 failure on microarrays. This summer has been > very active and > we decided to take a look through our records as well as the > archives of > the List serv. One of the things we noticed is that the > number of Tech > calls and postings is highest during the time between early > June and the > end of August. It appears that Cy5 is more sensitive during > the summer > months. After a more detailed review we were able to subdivide the > problems into 3 categories. > > 1: Little or no Cy5 signal because of either bad RNA or a poor cDNA > synthesis. This is usually identified in a dye flip experiment and > accounts for only a few of the problems reported. > > 2: Cy5 damage during the hybridization or washes. The source of the > problem appears to be some substance that is either residual > on the array > or is part of the buffers. Sometime back we added our > antifade reagent to > our kits to prevent problems during the hybridization stage. > However, this > reagent does not eliminate problems during the washes. As > posted, adding > DTT to the wash buffer can help to minimize the problem but > may not work > for all cases. Typically we recommend that the water source > be changed. > Most of us assume that our water is not a problem in most assays and I > think that most of the time the assumption is true. But it has been > documented on the list serv, as well as has been confirmed by > our Technical > Support group, that changing water source has helped to > eliminate some Cy5 > degradation problems (due to the water used in buffers). We have > specifically identified, as have others, that MilliQ water > changes over > time. Our best estimate is that once new cartridges are put > onto a MilliQ > (and maybe other DI units) there is a 3 month time frame > where no problems > will be observed. About 3 months after the cartridges are > changed the Cy5 > problems return. We do not have any idea what the agent causing the > problem in the water is yet, but changing the water or > adding DTT appears > to help. We have qualified reagent grade DI from VWR. It comes in 20 > liter boxes, is cheap, and we have not experienced any > problems with Cy5 > from something in the water for the past year when using this > source. We > did see problems with Cy5 when we used our MilliQ system even > though the > MilliQ unit indicated that everything was functionally > appropriate. This > is hard to believe and it has taken 3 years to convince > myself that the > water may contribute to Cy5 degradation. > > 3: Cy5 damage/fading as a result of oxidation or > photobleaching in air, > on the scanner, or in light. I have collected these causes together > because we believe that each is due to a similar chemical process and > because our DyeSaver reagent prevents the loss of Cy5 signal in all of > these cases. Let me explain. When we first started working > with Cy5 and > Alexa 647 (both behave chemically similar with respect to fading on > arrays), we observed that radicals will destroy these dyes. > Throughout > this summer we were continuously receiving ozone warnings in our area. > Ozone forms radicals and we postulated that at high enough > levels would > destroy Cy5. So we ran a little experiment using an ozone > generator. We > hybridized several arrays with Cy3 and Cy5 labeled cDNA and > scanned all of > them to get a baseline signal. We then put half of them in a > box with the > ozone generator for 2-5 minutes and rescanned all of the > slides after the > process. The Cy5 signal on all of the arrays exposed to > ozone was gone, > but the Cy5 signal on the controls remained intact. After > discussing the > results with the group, we decided that we needed to develop > a compound > that we could use to protect the Cy5 from degradation in the > ozone box. So > we put together a variety of formulations of reagents that we > thought might > do the job and started testing the mixture just as a drug > developer would > screen new drug candidates, trial and error. Eventually we > hit the right > formulation that met the requirements and, as Ron Hart > discussed, passes > the ozone challenge. The requirements included: protects > the Cy5 from > ozone exposure, elicits no background, and works on a variety > of surface > chemistries. The end result was DyeSaver, which is a > proprietary, patent > pending reagent that can be applied to any array to preserve > the dyes. It > can be used with any labeling method (i.e. Genisphere, direct > incorporation, amino allyl, etc.) The reagent is formulated > as a liquid > but, for convenience to the end user and to avoid waste, is > applied as an > aerosol spray to the slide. It literally takes a second to > apply, and we > have observed a number of additional benefits during our > testing. First, > when using our ScanArray5000 Scanner, normally we have to > limit the Cy5 > laser to less than 80% power and usually we get one shot at > scanning the > array because the laser "burns" the dye. However, with > DyeSaver we have > been able to set the laser at 100% and can scan the array > repeatedly with > little loss of Cy5 signal. Some other sites have confirmed this > observation on their Scanarray scanner. Second, it appears > that applying > DyeSaver protects the array from exposure to light, direct > sunlight. We > ran an experiment with several arrays similar to that > described above when > testing the ozone generator. We hybridized the arrays with > Cy3 and Cy5, > did a baseline scan, and we sprayed some of them with the > DyeSaver. We > then placed the arrays outside in our parking lot for over 3 hours in > direct sun. We also included some arrays with "no sun" exposure in a > shaded box outside as a control. The temperature at the time of the > experiment was in the mid 80s. Ozone levels were low per the National > Weather Service. We then scanned all of the arrays and > observed that the > arrays in the direct sunlight that were NOT sprayed had lost > all of their > Cy5 signal and greater than 95% of their Cy3 signal. The > sprayed arrays in > direct sunlight had lost about 20-25% of their Cy5 signal and > less than 5% > of their Cy3 signal. The shaded arrays without spray had > lost about 30% of > their Cy5 signal and the Cy3 signal was unchanged. The sprayed arrays > maintained in the shade were essentially unchanged. > > Based on our results to date the DyeSaver will be a good way > to stabilize > the dyes and may also be a nice way to preserve an array or other > fluorescent assays in archive to be (re)scanned at a later > date. We have > studyied arrays that were sprayed with DyeSaver about a month > ago and they > have maintained their signal for both Cy3 and Cy5. No longer > do you have > to "rush to scan" an array. > > The experiments I discussed in this posting as well as some > additional data > will be posted on our webpage and will be included in a > poster at the Chips > to Hits conference in October in Philadelphia. We expect to > be selling > DyeSaver in November, and are currently providing a beta version to > customers with Cy5 problems. The exact price of DyeSaver has > not yet been > determined, but it will be less than 25 cents per array. > Each can will > have enough material for about 250-300 arrays depending on the user. > Anyone interested can email me at bob_getts@datascope.com or > should contact > us via the internet at www.genisphere.com. > > > Bob Getts > Manager R&D > Genisphere Inc. > > > > > > > ----- Original Message ----- > From: Ron Hart > To: > Sent: Friday, August 30, 2002 10:08 AM > Subject: Re: labelling Problems? > > > > Hate to beat a dead horse, but we did try the Alexa dye > comparable to Cy5 > > and saw similar fading problems. > > > > However, I recently had the opportunity to see a new > product that seems to > > completely solve the dye fade problem. Bob Getts of > Genisphere visited my > > lab last week and brought a "pre-release" can of stuff he calls "Dye > Saver." > > It's a spray that is supposed to interfere with oxidation > by ozone or > other > > radicals. Smells like organic solvents. > > > > The stuff worked perfectly. We prepared two arrays using > identical probes > > side-by-side, and Bob sprayed one of them with Dye Saver. > Within minutes, > > we could see the Cy5 fading in the unsprayed slide, and no > change in the > > sprayed slide. After a hour the difference was VERY obvious (the > unsprayed > > chip was almost totally green). Finally, we put both chips > into a box > with > > an ozone generator to blow away the rest of the Cy5. The > sprayed chips > > survived with bright reds intact. > > > > After all the troubles we've had, this finally looks like a > real solution. > > In fact, if I had seen the images in sales literature I > would have found > it > > hard to believe. But the results were indisputible. > > > > Perhaps Bob will be able to contribute a "Commercial" > response with more > > information? In the meantime, I hope my sample can of Dye > Saver doesn't > run > > out before it goes on the market. > > > > Ron Hart > > Rutgers University > > > > P.S. I have no financial interest in Genisphere. Just a > happy customer. > > > > ----- Original Message ----- > > From: "Phillips Jonathan M" > > To: > > Sent: Wednesday, August 28, 2002 11:26 AM > > Subject: Re: labelling Problems? > > > > > > > Dear List, > > > > > > I am somewhat amazed by all of the e-mail traffic with > respect to Cy5. > > > Virtually everything that I have seen (and heard) is > negative. We have > > been > > > using Alexa 546 and Alexa 647 for about a year and a half > and during > that > > > time, have never experienced any of the problems that have been > described > > in > > > subscriber e-mails. The obvious question is "Why don't > you switch to > > Alexa > > > dyes"? > > > > > > Cheers! > > > > > > Jonathan > > > > > > Jonathan M. Phillips, Ph.D. > > > > > > Molecular Pathologist > > > Life Sciences Operation > > > IIT Research Institute > > > 10 West 35th Street > > > Chicago, Il 60616-3793 > > > Tel: 312-567-4217 > > > Fax: 312-567-4852 > > > > > > _____________________________________________ > > > > > > You may leave the list at any time by sending a message- > > > > > > "SIGNOFF GENE-ARRAYS" > > > > > > To: LISTSERV@ITSSRV1.UCSF.EDU > > > > > > NOTE: The message line should be in the body of the > message and no where > > else, i.e. the subject line. > > > > > > > _____________________________________________ > > > > You may leave the list at any time by sending a message- > > > > "SIGNOFF GENE-ARRAYS" > > > > To: LISTSERV@ITSSRV1.UCSF.EDU > > > > NOTE: The message line should be in the body of the message > and no where > else, i.e. the subject line. > > > > _____________________________________________ > > You may leave the list at any time by sending a message- > > "SIGNOFF GENE-ARRAYS" > > To: LISTSERV@ITSSRV1.UCSF.EDU > > NOTE: The message line should be in the body of the message > and no where else, i.e. the subject line. > > _____________________________________________ > > You may leave the list at any time by sending a message- > > "SIGNOFF GENE-ARRAYS" > > To: LISTSERV@ITSSRV1.UCSF.EDU > > NOTE: The message line should be in the body of the message > and no where else, i.e. the subject line. > > > > --------------060702010103050802020601 > Content-Type: text/html; charset=us-ascii > Content-Transfer-Encoding: 7bit > > > > > content="text/html;charset=iso-8859-1"> > > > > Hi All,
>
> here's an interesting posting on Ozone and Cy5 and a Cy5 > anti-fade reagent. >  Does anyone know if Oklahoma has high Ozone levels > anytime of the year?
>
> Mike
>
> 
>
> All,
>
> Per Ron Hart's request I would like to share some of the
> things we have
> learned about problems with fluorescent dyes on microarrays as well as
> provide additional information about our DyeSaver product.
> Over the last
> several years our technical support group has fielded quite a
> few calls
> regarding Cy5 failure on microarrays.  This summer has been
> very active and
> we decided to take a look through our records as well as the
> archives of
> the List serv.  One of the things we noticed is that the
> number of Tech
> calls and postings is highest during the