Transcription Factor Data
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White, Jason
Mar 30, 2016, 1:57:05 PM3/30/16
to gen...@soe.ucsc.edu
Good Morning,
I am interested in identifying transcription factor binding sites on miRNAs. With that said, I would like to speak with someone regarding the Chip-seq data displayed on the genome browser. Specifically, I would like to correlate the samples used to acquire the chip-seq data to my target samples (prostate cancer). Additionally, I would like to know if the raw data and experimental details are publicly available? Thanks!
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Jason White
RCMI Core Lab Manager
Tuskegee University
RCMI/CBR
Tuskegee University
RCMI/CBR
Room 2011-Williams-Bowie Hall
1200 West Montgomery Road
Tuskegee, Alabama 36088
Matthew Speir
Apr 1, 2016, 2:30:47 PM4/1/16
to White, Jason, gen...@soe.ucsc.edu
Hi Jason,
Thank you for your question about ChIP-seq data in the UCSC Genome Browser.
For an overview of the ENCODE ChIP-seq experiments for which we have data at UCSC, you can review the ENCODE ChIP-seq experiment matrix: http://genome.ucsc.edu/ENCODE/dataMatrix/encodeChipMatrixHuman.html. Clicking on the green box for a given cell type and Histone Modification or Transcription Factor combination will take you to a page listing all of the tracks we have available for that combination. From there you can click the track names to see the description page for that track which contains information such as a brief overview of the experimental methods as well as contact information for the lab that produced the data. To view these tracks in the UCSC Genome Browser, check the boxes next to each track and then click "Return to Browser".
Additionally, you can use the above ChIP-seq experiment matrix to find downloads for data we have available by selecting "files" from the "search for" dialog box that's in the upper left-hand corner of the page. After selecting "files", the green boxes in the matrix will take you to a page that will allow you to download the data for that given combination.
Note that UCSC is no longer involved in the ENCODE project and that you can find all of the data described above as well as newer data at the ENCODE project's website: https://www.encodeproject.org/. For help with the new ENCODE project site and the data they provide, you can contact the ENCODE project here: https://www.encodeproject.org/help/contacts/.
I hope this is helpful. 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.
Matthew Speir
UCSC Genome Bioinformatics Group
Thank you for your question about ChIP-seq data in the UCSC Genome Browser.
For an overview of the ENCODE ChIP-seq experiments for which we have data at UCSC, you can review the ENCODE ChIP-seq experiment matrix: http://genome.ucsc.edu/ENCODE/dataMatrix/encodeChipMatrixHuman.html. Clicking on the green box for a given cell type and Histone Modification or Transcription Factor combination will take you to a page listing all of the tracks we have available for that combination. From there you can click the track names to see the description page for that track which contains information such as a brief overview of the experimental methods as well as contact information for the lab that produced the data. To view these tracks in the UCSC Genome Browser, check the boxes next to each track and then click "Return to Browser".
Additionally, you can use the above ChIP-seq experiment matrix to find downloads for data we have available by selecting "files" from the "search for" dialog box that's in the upper left-hand corner of the page. After selecting "files", the green boxes in the matrix will take you to a page that will allow you to download the data for that given combination.
Note that UCSC is no longer involved in the ENCODE project and that you can find all of the data described above as well as newer data at the ENCODE project's website: https://www.encodeproject.org/. For help with the new ENCODE project site and the data they provide, you can contact the ENCODE project here: https://www.encodeproject.org/help/contacts/.
I hope this is helpful. 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.
Matthew Speir
UCSC Genome Bioinformatics Group
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