Bottomly 2010, Beta-catenin binding region in colon cancer

ChIP-seq experiment investigating the binding of β-catenin in HCT116 human colon cancer cells.

• Raw data was downloaded from: SRA series: SRA012054
  Input file format: SRA

From H. sapiens (March 2006 NCBI36/hg18).

ChIP-seq data:

	Filename	Description	Feature	GEO-ID
1	SRR038620.sga	HCT116 colon cancer cells|b-canenin	betaCATENIN	-

FASTQ files were extracted from SRA files using fastq-dump (SRA toolkit v2.5.0) and mapped to 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 bed2sga.pl (ChIP-seq).

• Bottomly D, Kyler SL, McWeeney SK, Yochum GS
  Identification of {beta}-catenin binding regions in colon cancer cells using ChIP-Seq. Nucleic Acids Res. 2010 Sep;38(17):5735-45. doi: 10.1093/nar/gkq363. Epub 2010 May 11. 20460455