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.



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

Technical Notes

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.


Last update: 1 Oct 2018