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 G. gallus (Dec 2015 Gallus_gallus-5.0/galGal5).

ChIP-seq data:

	Filename	Description	Feature	GEO-ID
1	input_liver_gga.sga	liver|input||gga	input	GSM548871
2	CEBPA_liver_gga.sga	liver|CEBPA||gga	CEBPA	GSM548872, GSM548873, GSM548874
3	input_liver_gga2.sga	liver|input||gga2	input	GSM548892
4	CEBPA_liver_gga2.sga	liver|CEBPA||gga2	CEBPA	GSM548890

Notes on samples nomenclature:

gga and gga2 referes to the two individuals from which the data were generated.

Merged samples:

Data were downloaded from ArrayExpress. For input and CEBPA ChIP-seq data corresponding to the same individual (gga and gga2), 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