Wang 2011, Notch1 and RBPJ binding in human and murine T-lymphoblastic leukemia cells.

This serie has data from Notch1, RBPJ and ZNF143 binding and several histone modifications in Notch1-dependent human TLL (T-Lymphoblastic Leukemia) cell line CUTLL1.

• Raw data was downloaded from: SRA
• Input file format: SRA
• Download date: 24-1-2017

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

ChIP-seq data:

	Filename	Description	Feature	GEO-ID
1	GSM732903.sga	CUTLL1|Notch1||rep1	Notch1	GSM732903
2	GSM732904.sga	CUTLL1|Notch1||rep2	Notch1	GSM732904
3	GSM732905.sga	CUTLL1|RBPJ||rep1	RBPJ	GSM732905
4	GSM732906.sga	CUTLL1|RBPJ||rep2	RBPJ	GSM732906
5	GSM732907.sga	CUTLL1|ZNF143	ZNF143	GSM732907
6	GSM732908.sga	CUTLL1|input||rep1	input	GSM732908
7	GSM732909.sga	CUTLL1|input||rep2	input	GSM732909
8	GSM732910.sga	CUTLL1|H3K4me1	H3K4me1	GSM732910
9	GSM732911.sga	CUTLL1|H3K4me3	H3K4me3	GSM732911
10	GSM732912.sga	CUTLL1|H3K27me3	H3K27me3	GSM732912

FASTQ files were extracted from SRA files using fastq-dump (SRA toolkit v2.5.0) and mapped to the hg19 genome using Bowtie2 version 2.2.9. 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. 1.5.3).

• Wang H, Zou J, Zhao B, Johannsen E, Ashworth T, Wong H, Pear WS, Schug J, Blacklow SC, Arnett KL, Bernstein BE, Kieff E, Aster JC
  Genome-wide analysis reveals conserved and divergent features of Notch1/RBPJ binding in human and murine T-lymphoblastic leukemia cells. Proc Natl Acad Sci U S A. 2011 Sep 6;108(36):14908-13. doi: 10.1073/pnas.1109023108. Epub 2011 Jul 7. 21737748
• GEO series GSE29600: Genome-wide Analysis Reveals Conserved and Divergent Features of Notch1/RBPJ Binding in Human and Murine T Lymphoblastic Leukemia Cells