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 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.

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