Beguelin 2013, EZH2 maps in Large B-Cell Lymphoma cell lines.

EZH2 and H3K27me3 ChIP sequencing of human Large B-Cell Lymphoma (DLBCL) cell lines.

• Raw data was downloaded from: SRA website
• Input file format: SRA
• Download date: 07-01-2016

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

ChIP-seq data:

	Filename	Description	Feature	GEO-ID
1	GSM1129348.sga	NB|H3K4me3||rep1	H3K4me3	GSM1129348
2	GSM1129350.sga	NB|H3K4me3||rep2	H3K4me3	GSM1129350
3	GSM1129356.sga	NB|H3K27me3	H3K27me3	GSM1129356
4	GSM1129349.sga	NB|input||rep1	input	GSM1129349
5	GSM1129351.sga	NB|input||rep2	input	GSM1129351
6	GSM1129352.sga	GCB|H3K4me3||rep1	H3K4me3	GSM1129352
7	GSM1129354.sga	GCB|H3K4me3||rep2	H3K4me3	GSM1129354
8	GSM1129357.sga	GCB|H3K27me3	H3K27me3	GSM1129357
9	GSM1129353.sga	GCB|input||rep1	input	GSM1129353
10	GSM1129355.sga	GCB|input||rep2	input	GSM1129355
11	GSM1129358.sga	OCI-Ly7|EZH2	EZH2	GSM1129358
12	GSM1129359.sga	Farage|EZH2	EZH2	GSM1129359
13	GSM1129360.sga	SUDHL5|EZH2	EZH2	GSM1129360
14	GSM1129361.sga	OCI-Ly1|EZH2	EZH2	GSM1129361
15	GSM1129362.sga	SUDHL6|EZH2	EZH2	GSM1129362
16	GSM1129363.sga	WSUDLCL2|EZH2	EZH2	GSM1129363
17	GSM1129364.sga	Pfeiffer|EZH2	EZH2	GSM1129364

Notes on samples nomenclature:

Cell lines used:

• NB: tonsillar naive B cells.
• GCB: tonsillar germinal center B cells.
• OCI-Ly7: B-cell Non-Hodgkin lymphoma.
• Farage: B-cell Non-Hodgkin lymphoma.
• SUDHL5: large cell lymphoma
• SUDHL6: large cell lymphoma
• WSUDLCL2: B cell lymphoma
• Pfeiffer: Non-Hodgkin's B cell lymphoma

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).

• Béguelin W, Popovic R, Teater M, Jiang Y, Bunting KL, Rosen M, Shen H, Yang SN, Wang L, Ezponda T, Martinez-Garcia E, Zhang H, Zheng Y, Verma SK, McCabe MT, Ott HM, Van Aller GS, Kruger RG, Liu Y, McHugh CF, Scott DW, Chung YR, Kelleher N, Shaknovich R, Creasy CL, Gascoyne RD, Wong KK, Cerchietti L, Levine RL, Abdel-Wahab O, Licht JD, Elemento O, Melnick AM
  EZH2 is required for germinal center formation and somatic EZH2 mutations promote lymphoid transformation. Cancer Cell. 2013 May 13;23(5):677-92. doi: 10.1016/j.ccr.2013.04.011. 23680150
• GEO series GSE45982: EZH2 is required for germinal center formation and somatic EZH2 mutations promote lymphoid transformation