Re: UCSC Genome Browser microarray probesets
Dong, Jianli
Jianli Dong, MD, PhD, FACMG
Professor, Department of Pathology
Director, Molecular Diagnostics Division
University of Texas Medical Branch
Office: Clinical Services Wing 5.140
Lab: Clinical Services Wing 4.100
301 University Boulevard
Galveston, Texas 77555-0422
On Dec 13, 2023, at 3:38 PM, Rudner, Xiaowen <xiaowen.ru...@thermofisher.com> wrote:
Hi Dr. Dong,
Can you send the request to gen...@soe.ucsc.edu? I will send them an email as well.
Xiaowen
From: Dong, Jianli <jid...@UTMB.EDU>
Sent: Wednesday, December 6, 2023 3:36 PM
To: Rudner, Xiaowen <xiaowen.ru...@thermofisher.com>; Van Valkenburgh, Clint <clint.vanv...@thermofisher.com>
Subject: RE: UCSC Genome Browser microarray probesets
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Xiaowen,
Is it possible that ChAS works with UCSC to fix this? May affect other labs.
Thanks,
Jianli
From: Rudner, Xiaowen <xiaowen.ru...@thermofisher.com>
Sent: Wednesday, December 6, 2023 3:32 PM
To: Van Valkenburgh, Clint <clint.vanv...@thermofisher.com>; Dong, Jianli <jid...@UTMB.EDU>
Subject: RE: UCSC Genome Browser microarray probesets
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HI Dr. Dong,
I can see you are using hg38, differed from what Clint is looking at. I am not sure why UCSC doesn’t have CytoScan probes listed at their hg38 anymore. This is a request needed to be made to UCSC .
Regards,
Xiaowen
From: Van Valkenburgh, Clint <clint.vanv...@thermofisher.com>
Sent: Wednesday, December 6, 2023 8:21 AM
To: Dong, Jianli <jid...@UTMB.EDU>; Rudner, Xiaowen <xiaowen.ru...@thermofisher.com>
Subject: RE: UCSC Genome Browser microarray probesets
Dear Dr. Dong,
I just opened my version of ChAS 4.4 and was able to access the USCS browser and find the Affymetrix CytoScan tracks under the array probesets tab in the variation section. I only selected the Affymetrix CytoScan of the 28 available tracks and unchecked the other array types.
I picked a segment from a test sample - Human hg19 chr17:43941317-45103602 UCSC Genome Browser v457 – and linked out to the USCS browser:
Clint VanValkenburgh, Ph.D.
Senior Clinical Microarray Sales Specialist, Central USA
Life Sciences Solutions
Thermo Fisher Scientific
3450 Central Expressway, Santa Clara, CA 95051
Cell: 314-540-7612
From: Van Valkenburgh, Clint <clint.vanv...@thermofisher.com>
Sent: Tuesday, December 5, 2023 5:46 PM
To: Dong, Jianli <jid...@UTMB.EDU>; Rudner, Xiaowen <xiaowen.ru...@thermofisher.com>
Subject: Re: UCSC Genome Browser microarray probesets
Hi Dr. Dong,
I am not sure and will need to discuss with Xiaowen her thoughts as I am not clear on what might have changed for the track not to appear.
Have a great evening,
Clint
Clint VanValkenburgh, Ph.D.
Sr. Clinical Microarray Sales Specialist, Central USA
Life Sciences Solutions
Thermo Fisher Scientific
3450 Central Expressway, Santa Clara, CA
Cell: 314-540-7612
From: Dong, Jianli <jid...@UTMB.EDU>
Sent: Tuesday, December 5, 2023 3:23 PM
To: Van Valkenburgh, Clint <clint.vanv...@thermofisher.com>; Rudner, Xiaowen <xiaowen.ru...@thermofisher.com>
Subject: RE: UCSC Genome Browser microarray probesets
CAUTION: This email originated from outside of Thermo Fisher Scientific. If you believe it to be suspicious, report using the Report Phish button in Outlook or send to S...@thermofisher.com.
Clint,
I normally access UCSC Genome Browser directly from ChAS software.
Possible to ask ChAS to add Affy’s probesets in this setting?
Thanks,
Jianli Dong, MD, PhD, FACMG
Professor, Department of Pathology
Director, Molecular Diagnostics Division
University of Texas Medical Branch
Office: Clinical Services Wing 5.140
Lab: Clinical Services Wing 4.100
301 University Boulevard
Galveston, Texas 77555-0422
Confidentiality Notice: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, copy, use, disclosure, or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message.
From: Van Valkenburgh, Clint <clint.vanv...@thermofisher.com>
Sent: Friday, December 1, 2023 2:53 PM
To: Dong, Jianli <jid...@UTMB.EDU>; Rudner, Xiaowen <xiaowen.ru...@thermofisher.com>
Subject: RE: UCSC Genome Browser microarray probesets
External Email Warning: Do not click links or open attachments unless you recognize the sender and expect the content. UTMB Email Phishing Awareness
Hi Dr. Dong and Xiaowen,
I was able to access more array types after googling the phrase below. When linking to this table browser I found the option to add CytoScan HD as well as many other array types. I had the same issue originally just seeing the 6 tracks. Xiaowen and I are speaking now and just wanted to get this message over to you to see if you could resolve the issue.
After using the link in purple above I accessed this page.
I hope this helps and not sure what the issue was just showing the 6 tracks.
Warmest regards,
Clint
Clint VanValkenburgh, Ph.D.
Senior Clinical Microarray Sales Specialist, Central USA
Life Sciences Solutions
Thermo Fisher Scientific
3450 Central Expressway, Santa Clara, CA 95051
Cell: 314-540-7612
From: Dong, Jianli <jid...@UTMB.EDU>
Sent: Friday, December 1, 2023 1:07 PM
To: Rudner, Xiaowen <xiaowen.ru...@thermofisher.com>; Van Valkenburgh, Clint <clint.vanv...@thermofisher.com>
Subject: UCSC Genome Browser microarray probesets
CAUTION: This email originated from outside of Thermo Fisher Scientific. If you believe it to be suspicious, report using the Report Phish button in Outlook or send to S...@thermofisher.com.
Xiaowen and Clint,
We often need to check probe coverage of regions with CNVs using UCSC Genome Browser.
I used to be able to see Affy CytoScan probes, but now can only see Illumina and Agilent probes.
Please advice how to get Affy probesets in UCSC Genome Browser.
Thanks,
Jianli
Jianli Dong, MD, PhD, FACMG
Professor, Department of Pathology
Director, Molecular Diagnostics
University of Texas Medical Branch
Office: Clinical Services Wing 5.140
Lab: Clinical Services Wing 4.100
301 University Boulevard
Galveston, Texas 77555-0422
Confidentiality Notice: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, copy, use, disclosure, or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message.
Gerardo Perez
Hello, Jianli.
Thank you for your interest in the UCSC Genome Browser.
It looks like there are hg38 ChAS 4.1 files for CytoScan HD Array but no hg38 BED file (https://www.thermofisher.com/order/catalog/product/fr/en/901835). We would need a hg38 CytoScan HD BED file to add the data as a UCSC Genome Browser track. You could try emailing Thermofisher directly and ask them to make a hg38 BED file for CytoScan HD Array. Feel free to cc us in the email. If they can provide an hg38 BED file for CytoScan HD Array, we would gladly make it a track.
I hope this is helpful. Please include gen...@soe.ucsc.edu in any replies to ensure visibility by the team. All messages sent to that address are archived on our public forum. If your question includes sensitive information, you may send it instead to genom...@soe.ucsc.edu.
Gerardo Perez
UCSC Genomics Institute
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Dong, Jianli
Thanks Gerardo!
I’m sure Xiaowen and Clint will work to provide BED files for hg38 CytoScan HD and hg38 CytoScan Accel.
Happy Holidays!
Jianli Dong, MD, PhD, FACMG
Professor, Department of Pathology
Director, Molecular Diagnostics Division
University of Texas Medical Branch
Office: Clinical Services Wing 5.140
Lab: Clinical Services Wing 4.100
301 University Boulevard
Galveston, Texas 77555-0422
Confidentiality Notice: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, copy, use, disclosure, or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message.
Thanks,
Jianli Dong, MD, PhD, FACMG
Professor, Department of Pathology
Director, Molecular Diagnostics Division
University of Texas Medical Branch
Office: Clinical Services Wing 5.140
Lab: Clinical Services Wing 4.100
301 University Boulevard
Galveston, Texas 77555-0422
Confidentiality Notice: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, copy, use, disclosure, or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message.
From: Van Valkenburgh, Clint <clint.vanv...@thermofisher.com>
Sent: Friday, December 1, 2023 2:53 PM
To: Dong, Jianli <jid...@UTMB.EDU>; Rudner, Xiaowen <xiaowen.ru...@thermofisher.com>
Subject: RE: UCSC Genome Browser microarray probesets
External Email Warning: Do not click links or open attachments unless you recognize the sender and expect the content. UTMB Email Phishing Awareness
Hi Dr. Dong and Xiaowen,
I was able to access more array types after googling the phrase below. When linking to this table browser I found the option to add CytoScan HD as well as many other array types. I had the same issue originally just seeing the 6 tracks. Xiaowen and I are speaking now and just wanted to get this message over to you to see if you could resolve the issue.
After using the link in purple above I accessed this page.
I hope this helps and not sure what the issue was just showing the 6 tracks.
Warmest regards,
Clint
Clint VanValkenburgh, Ph.D.
Senior Clinical Microarray Sales Specialist, Central USA
Life Sciences Solutions
Thermo Fisher Scientific
3450 Central Expressway, Santa Clara, CA 95051
Cell: 314-540-7612
From: Dong, Jianli <jid...@UTMB.EDU>
Sent: Friday, December 1, 2023 1:07 PM
To: Rudner, Xiaowen <xiaowen.ru...@thermofisher.com>; Van Valkenburgh, Clint <clint.vanv...@thermofisher.com>
Subject: UCSC Genome Browser microarray probesets
CAUTION: This email originated from outside of Thermo Fisher Scientific. If you believe it to be suspicious, report using the Report Phish button in Outlook or send to S...@thermofisher.com.
Xiaowen and Clint,
We often need to check probe coverage of regions with CNVs using UCSC Genome Browser.
I used to be able to see Affy CytoScan probes, but now can only see Illumina and Agilent probes.
Please advice how to get Affy probesets in UCSC Genome Browser.
Thanks,
Jianli
Jianli Dong, MD, PhD, FACMG
Professor, Department of Pathology
Director, Molecular Diagnostics
University of Texas Medical Branch
Office: Clinical Services Wing 5.140
Lab: Clinical Services Wing 4.100
301 University Boulevard
Galveston, Texas 77555-0422
O 409-772-4866 F 409-772-5683
Confidentiality Notice: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, copy, use, disclosure, or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message.
Rudner, Xiaowen
HI Gerardo and Dr. Dong,
I have uploaded the hg38 bed files for both CytoScanHD and CytoScanAccel to my OneDrive folder, will be sharing it with you shortly. Let me know if you have any issues downloading the files.
Regards,
Xiaowen
Gerardo Perez
Hello, Xiaowen.
Thank you for providing the bed data. We have added the Affy CytoScan track for hg38 to the work queue. We will work on your request as time permits with consideration of other project priorities.
If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu
Gerardo Perez
UCSC Genomics Institute
Gerardo Perez
Hello, Xiaowen.
Thank you again for providing the bed data.
The Affy CytoScan HD track for hg38 is now available as part of the Array Probesets container track (https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&c=chr17&g=genotypeArrays).
Let us know if there is anything else we can help you with. Please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu
Gerardo Perez
UCSC Genomics Institute
Rudner, Xiaowen
Thank you very much!
Xiaowen
From: Gerardo Perez <gpe...@ucsc.edu>
Sent: Thursday, January 25, 2024 3:59 PM
To: Rudner, Xiaowen <xiaowen.ru...@thermofisher.com>
Cc: Dong, Jianli <jid...@utmb.edu>; gen...@soe.ucsc.edu; Van Valkenburgh, Clint <clint.vanv...@thermofisher.com>
Subject: Re: [genome] Re: UCSC Genome Browser microarray probesets
CAUTION: This email originated from outside of Thermo Fisher Scientific. If you believe it to be suspicious, report using the Report Phish button in Outlook or send to S...@thermofisher.com.
Dong, Jianli
It’s there 😊 Thanks
Jianli Dong, MD, PhD, FACMG
Professor, Department of Pathology
Director, Molecular Diagnostics Division
University of Texas Medical Branch
Office: Clinical Services Wing 5.140
Lab: Clinical Services Wing 4.100
301 University Boulevard
Galveston, Texas 77555-0422
Confidentiality Notice: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, copy, use, disclosure, or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message.
From: Rudner, Xiaowen <xiaowen.ru...@thermofisher.com>
Sent: Thursday, February 1, 2024 11:06 AM
To: Gerardo Perez <gpe...@ucsc.edu>
Cc: Dong, Jianli <jid...@UTMB.EDU>; gen...@soe.ucsc.edu; Van Valkenburgh, Clint <clint.vanv...@thermofisher.com>
Subject: RE: [genome] Re: UCSC Genome Browser microarray probesets
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