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 M. musculus (July 2007 NCBI37/mm9).

ChIP-seq data:

Filename Description Feature GEO-ID
1 do70_CEBPA_liver.sga liver CEBPA rep1 CEBPA -
2 do73_CEBPA_liver.sga liver CEBPA rep2 CEBPA -
3 do96_HNF4a_liver.sga liver HNF4a rep1 HNF4a -
4 Input_liver.sga liver Input all Input -

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 mm9 mouse 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: 28 Feb 2017