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
• Download date: 06-9-2018

From C. familiaris (Sep 2011 CanFam3.1/canFam3).

ChIP-seq data:

	Filename	Description	Feature	GEO-ID
1	input_liver_cfa3.sga	liver|input||cfa3	input	GSM548893
2	CEBPA_liver_cfa3.sga	liver|CEBPA||cfa3	CEBPA	GSM548917, GSM548918, GSM548919
3	HNF4A_liver_cfa3.sga	liver|HNF4A||cfa3	HNF4A	GSM548912, GSM548913, GSM548914
4	input_liver_cfa4.sga	liver|input||cfa4	input	GSM548865, GSM548866
5	CEBPA_liver_cfa4.sga	liver|CEBPA||cfa4	CEBPA	GSM548904, GSM548905, GSM548906
6	HNF4A_liver_cfa4.sga	liver|HNF4A||cfa4	HNF4A	GSM548915, GSM548916

Notes on samples nomenclature:

cfa3 and cfa4 referes to the two individuals from which the data were generated.

Merged samples:

Data were downloaded from ArrayExpress. For input, CEBPA and HNF4A ChIP-seq data corresponding to the same individual (cfa3 and cfa4), were merged, so one sample corresponds to several GEO entries.

FASTQ files were mapped to the 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. 1.5.3). SGA files containing data for the same factor, for the same individual were merged.

• 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