Watanabe 2014, Identification of beta-catenin binding regions in SW480 cells.

ChIP-seq against beta-catenin in human colon cancer SW480 cells, IgG used ascontrol.
A peak file, provided by the authors, is added to the collection.

• Raw data was downloaded from GEO series: GSE53927
• Input file format: SRA, BED

From H. sapiens (Feb 2009 GRCh37/hg19).

ChIP-seq data:

	Filename	Description	Feature	GEO-ID
1	GSM1303695_beta-catenin.sga	SW480 cells|beta-catenin	beta-catenin	GSM1303695
2	GSM1303696_IgG.sga	SW480 cells|Control IgG	IgG	GSM1303696

ChIP-seq peaks files:

	Filename	Description	Feature	GEO-ID
1	GSE53927_BetaCateninPeaks_peaks.sga	SW480 cells|beta-catenin peaks	beta-catenin_peaks	GSE53927

FASTQ files were extracted from SRA files using fastq-dump (SRA toolkit v2.5.0) and 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 bed2sga.pl (ChIP-Seq v. 1.5.2).
Peak BED file was downloaded from GEO and converted to SGA bed2sga.pl as well.

• Watanabe K, Biesinger J, Salmans ML, Roberts BS, Arthur WT, Cleary M, Andersen B, Xie X, Dai X
  Integrative ChIP-seq/microarray analysis identifies a CTNNB1 target signature enriched in intestinal stem cells and colon cancer. PLoS One. 2014 Mar 20;9(3):e92317. doi: 10.1371/journal.pone.0092317. eCollection 2014. 24651522
• GEO series GSE53927: Identification of beta-catenin binding regions in SW480 cells