Schmidt 2010, Mapping of HNF4a and CEBPA in liver
ChIP-seq against HNF4 alpha (hepatocyte nuclear factor 4
alpha) and CEBPA (CCAAT/enhancer-binding protein alpha), replicates 1
and 2, in liver cells from human and mouse.
- Raw data was downloaded from ArrayExpress:
- Input file format: FASTQ
From Human Mar. 2006 (GRCh36/hg18) Assembly.
The following samples were merged:
- GSM548875 and GSM548876 to make liver|HNF4a
- GSM548881 and GSM548882 to make liver|CEBPA|rep1
- GSM548885 and GSM548886 to make liver|CEBPA|rep2
- GSM548868, GSM548883 and GSM548884 to make liver|Input
FASTQ files were mapped to the hg18 genome
v0.12.8. SAM files were then converted into bam
v0.1.14 and to bed using bamToBed v2.12.0
conversion was carried out using bed2sga.pl
Schmidt D, Wilson MD, Ballester B, Schwalie PC, Brown GD, Marshall A, Kutter C, Watt S, Martinez-Jimenez CP, Mackay S, Talianidis I, Flicek P, Odom DT
Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding.
Science. 2010 May 21;328(5981):1036-40. doi: 10.1126/science.1186176. Epub 2010 Apr 8.
[E-TABM-722] Transcription factor binding evolution in five vertebrates
- ArrayExpress E-TABM-722