Schmidt 2010, Mapping of HNF4a and CEBPA in liver.

ChIP-seq against CCAAT/enhancer-binding protein alpha (CEBPA) in livers of species representing five vertebrate orders: human (primate), mouse (rodent), dog (carnivora), short-tailed opossum (didelphimorphia), and chicken (galliformes) using 2 replicates.
ChIP-seq against hepatocyte nuclear factor 4 alpha (HNF4A) in livers from human, mouse, and dog. Liver input as control.

• Raw data was downloaded from ArrayExpress: E-TABM-722 files
• Input file format: FASTQ

From H. sapiens (March 2006 NCBI36/hg18).

ChIP-seq data:

	Filename	Description	Feature	GEO-ID
1	do199_HNF4A_liver.sga	liver|HNF4A	HNF4A	GSM548875, GSM548876
2	do204_CEBPA_liver.sga	liver|CEBPA||rep1	CEBPA	GSM548881, GSM548882
3	do206_CEBPA_liver.sga	liver|CEBPA||rep2	CEBPA	GSM548885, GSM548886
4	input_liver.sga	liver|input	input	GSM548868, GSM548883, GSM548884

Notes on samples :

Data were downloaded from ArrayExpress, FASTQ files corresponding to the same samples were merged, so one sample corresponds to several GEO entries.

FASTQ files were mapped to the hg18 genome using Bowtie v0.12.8. SAM files were then converted into bam using samtools v0.1.14 and to bed using bamToBed v2.12.0 (bedtools). SGA conversion was carried out using bed2sga.pl (ChIP-Seq v. 1.5.2).

• 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. 20378774
• GEO series GSE22078: [E-TABM-722] Transcription factor binding evolution in five vertebrates
• ArrayExpress E-TABM-722