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.



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.

Technical Notes

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 (ChIP-Seq v. 1.5.3). SGA files containing data for the same factor, for the same individual were merged.


Last update: 1 Oct 2018