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:
- Input file format: FASTQ
From M. musculus (July 2007 NCBI37/mm9).
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.
FASTQ files were mapped to the mm9 mouse genome using Bowtie
SAM files were then converted into bam using samtools
and to bed using bamToBed v2.12.0
conversion was carried out using bed2sga.pl
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.
[E-TABM-722] Transcription factor binding evolution in five vertebrates
- ArrayExpress E-TABM-722