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 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.

Technical Notes

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 (ChIP-Seq v. 1.5.2).


Last update: 1 Oct 2018