McCabe 2012, Analysis of H3K27me3 in EZH2 mutant and wild type DLBCL cell lines.

Analysis of H3K27me3 in 3 diffuse large B-cell lymphoma (DLBCL) cell lines: Pfeiffer, KARPAS-422, WSU-DLCL2 after treatment with an EZH2 inibitor (GSK126).

• Raw data was downloaded from: SRA ftp server
• Input file format: SRA
• Download date: 06-01-2016

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

ChIP-seq data:

	Filename	Description	Feature	GEO-ID
1	GSM1006149.sga	Pfeiffer|H3K27me3	H3K27me3	GSM1006149
2	GSM1006150.sga	Pfeiffer|Input	Input	GSM1006150
3	GSM1006151.sga	KARPAS-422|H3K27me3	H3K27me3	GSM1006151
4	GSM1006152.sga	KARPAS-422|Input	Input	GSM1006152
5	GSM1006153.sga	WSU-DLCL2|H3K27me3	H3K27me3	GSM1006153
6	GSM1006154.sga	WSU-DLCL2|Input	Input	GSM1006154

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).

• McCabe MT, Ott HM, Ganji G, Korenchuk S, Thompson C, Van Aller GS, Liu Y, Graves AP, Della Pietra A 3rd, Diaz E, LaFrance LV, Mellinger M, Duquenne C, Tian X, Kruger RG, McHugh CF, Brandt M, Miller WH, Dhanak D, Verma SK, Tummino PJ, Creasy CL
  EZH2 inhibition as a therapeutic strategy for lymphoma with EZH2-activating mutations. Nature. 2012 Dec 6;492(7427):108-12. doi: 10.1038/nature11606. Epub 2012 Oct 10. 23051747
• GEO series GSE40970: ChIP-seq analysis of H3K27me3 histone modification in EZH2 mutant and wild type DLBCL cell lines