Wang 2011, Notch1 and RBPJ binding in T Lymphoblastic Leukemia Cells.

Description

This serie has data from Notch1, RBPJ and ZNF143 binding maps and several histone modifications in T Lymphoblastic Leukemia Cells (CUTLL).

Source

Samples

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

ChIP-seq data:

Filename Description Feature GEO-ID
1 GSM732903.sga CUTLL|Notch1|rep1 Notch1 SRX070881
2 GSM732904.sga CUTLL|Notch1|rep2 Notch1 SRX070882
3 GSM732905.sga CUTLL|RBPJ|rep1 RBPJ SRX070883
4 GSM732906.sga CUTLL|RBPJ|rep2 RBPJ SRX070884
5 GSM732907.sga CUTLL|ZNF143 ZNF143 SRX070885
6 GSM732908.sga CUTLL|Input|rep1 Input SRX070886
7 GSM732909.sga CUTLL|Input|rep2 Input SRX070887
8 GSM732910.sga CUTLL|H3K4me1 H3K4me1 SRX070888
9 GSM732911.sga CUTLL|H3K4me3 H3K4me3 SRX070889
10 GSM732912.sga CUTLL|H3K27me3 H3K27me3 SRX070890

Technical Notes

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

References

Last update: 30 Jan 2017