[genome]Normalized data for RNA-seq and Chip-seq data for differential analysis

[xiewanchen2013]

Dear Madam/Sir,

 

I want to know if there is any available data of normalized RNA-seq and Chip-seq data for differential analysis between cell-lines such as by edgeR or DEseq.

 

Thank you for your time!

 

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xiewanchen2013

[Brian Lee]

Dear Xiewanchen,

Thank you for using the UCSC Genome Browser and your question about uniform data for different cell-lines. 

On the left side of the ENCODE portal page under Human and Mouse are links to the cell types used in all ENCODE experiments.

A quick way to view the list of cell types and corresponding transcription factors mapped by ENCODE is to view the ChIP-seq matrix for either human or mouse. Targets are listed horizontally across the top, indicating available mapped transcription factor data, cell lines vertically along the left. Clicking on the green highlighted boxes will bring you to experiment data specific to the corresponding cell type and target.

Another option is to use the Track Search or File Search tools and to search the "Cell, tissue or DNA sample" field to see if the desired transcription factor is listed.

For your question about normalized RNA-seq and ChIP-seq data, the ENCODE Analysis Working Group (AWG) performed a cross-consortium effort to do an integrated analysis of all ENCODE data types based on uniform processing. In September 2012 the results of AWG analysis of data produced from September 2007 through January 2011 were published in a series of coordinated publications. Resulting files from the uniform processing reported in these publications are hosted on the ENCODE Analysis Data Hub for download and visualization in the UCSC Browser. Visit the ENCODE Integrative Analysis and Quality Metrics pages for more information. 

You can access all the the AWG files from the ENCODE Human downloads page, http://genome.ucsc.edu/ENCODE/downloads.html.  You can click the TFBS and RNA-seq links there to arrive at the two corresponding hub track pages:

http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=hub_4607_uniformRNA&hubUrl=http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/hub.txt

http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=hub_4607_uniformTfbs&hubUrl=http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/hub.txt

Thank you again for your inquiry and using the UCSC Genome Browser. If you have further questions, please feel free to contact the mailing list again at gen...@soe.ucsc.edu.

All the best,

Brian Lee
UCSC Genome Bioinformatics Group

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