H3K27Ac Mark Atlas in Human Genomes

Question

[Shicheng Guo]

Hi All,

Where I can find the H3K27Ac Mark Regions (ChIP-Seq) for Human Genomes? I know UCSC browser provided H3K27AC in 7 different cells, However, I want to get the data for more cell types or conditions.

Thanks.

         GM12878     H3K27Ac Mark  on GM12878 Cells from ENCODE      schema      2009-10-05 
         H1-hESC     H3K27Ac Mark  on H1-hESC Cells from ENCODE      schema      2011-03-21 
         HSMM        H3K27Ac Mark  on HSMM Cells from ENCODE         schema      2010-09-16 
         HUVEC       H3K27Ac Mark  on HUVEC Cells from ENCODE        schema      2009-10-06 
         K562        H3K27Ac Mark  on K562 Cells from ENCODE         schema      2009-10-05 
         NHEK        H3K27Ac Mark  on NHEK Cells from ENCODE         schema      2009-10-07 
         NHLF        H3K27Ac Mark  on NHLF Cells from ENCODE         schema      2010-06-28

Sorry, I think I find the way: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeBroadHistone

Thanks all the same!

[GZ1995]

You can also use AnnotationHub package from Bioconductor if you want these data to be stored in easily manipulable GRanges object in R.

Answer 1

[EagleEye]

Try these repositories,

https://www.encodeproject.org/matrix/?type=Experiment

http://www.roadmapepigenomics.org/complete_epigenomes/

http://egg2.wustl.edu/roadmap/web_portal/

Example

Answer 2

[Shicheng Guo]

Oct/20/2016: 19 H3k27ac dataset come out as the follow:

GSM733646_hg19_wgEncodeBroadHistoneNhlfH3k27acStdPk.broadPeak.gz
GSM733656_hg19_wgEncodeBroadHistoneK562H3k27acStdPk.broadPeak.gz
GSM733660_hg19_wgEncodeBroadHistoneHmecH3k27acStdPk.broadPeak.gz
GSM733662_hg19_wgEncodeBroadHistoneNhdfadH3k27acStdPk.broadPeak.gz
GSM733666_hg19_wgEncodeBroadHistoneHsmmtH3k27acStdPk.broadPeak.gz
GSM733674_hg19_wgEncodeBroadHistoneNhekH3k27acStdPk.broadPeak.gz
GSM733684_hg19_wgEncodeBroadHistoneHelas3H3k27acStdPk.broadPeak.gz
GSM733691_hg19_wgEncodeBroadHistoneHuvecH3k27acStdPk.broadPeak.gz
GSM733718_hg19_wgEncodeBroadHistoneH1hescH3k27acStdPk.broadPeak.gz
GSM733739_hg19_wgEncodeBroadHistoneOsteoblH3k27acStdPk.broadPeak.gz
GSM733743_hg19_wgEncodeBroadHistoneHepg2H3k27acStdPk.broadPeak.gz
GSM733755_hg19_wgEncodeBroadHistoneHsmmH3k27acStdPk.broadPeak.gz
GSM733763_hg19_wgEncodeBroadHistoneNhaH3k27acStdPk.broadPeak.gz
GSM733771_hg19_wgEncodeBroadHistoneGm12878H3k27acStdPk.broadPeak.gz
GSM1003459_hg19_wgEncodeBroadHistoneCd20ro01794H3k27acPk.broadPeak.gz
GSM1003462_hg19_wgEncodeBroadHistoneDnd41H3k27acPk.broadPeak.gz
GSM1003493_hg19_wgEncodeBroadHistoneA549H3k27acDex100nmPk.broadPeak.gz
GSM1003559_hg19_wgEncodeBroadHistoneMonocd14ro1746H3k27acPk.broadPeak.gz
GSM1003578_hg19_wgEncodeBroadHistoneA549H3k27acEtoh02Pk.broadPeak.gz