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

This serie has data from Notch1 and Rbpj binding in two Notch1-dependent murine T-acute lymphoblastic leukemia cell lines T6E and G4A2.

• Raw data was downloaded from: SRA
• Input file format: SRA
• Download date: 15-8-2018

From M. musculus (July 2007 NCBI37/mm9).

ChIP-seq data:

	Filename	Description	Feature	GEO-ID
1	GSM732913.sga	T6E|Notch1	Notch1	GSM732913
2	GSM732914.sga	T6E|Rbpj	Rbpj	GSM732914
3	GSM732915.sga	T6E|input	input	GSM732915
4	GSM732916.sga	G4A2|Notch1	Notch1	GSM732916
5	GSM732917.sga	G4A2|Rbpj	Rbpj	GSM732917
6	GSM732918.sga	G4A2|input	input	GSM732918

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 v2.27.0 (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