Venters13, ChIP-exo of Pol2 and TFIIB in K562 cell line

Description

ChIP-exo against TFIIB and Pol2 in K562 cell line and against TFIIB in HeLa cell line. Input DNA sample used as control.

Source

Samples

From Human Feb. 2009 (GRCh37/hg19) Assembly.

ChIP-seq data:

Filename Description Feature GEO-ID
1 TFIIB_1_HeLa.sga HeLa|TFIIB|rep1 TFIIB -
2 TFIIB_2_HeLa.sga HeLa|TFIIB|rep2 TFIIB -
3 TFIIB_1_HepG2.sga HepG2|TFIIB|rep1 TFIIB -
4 TFIIB_2_HepG2.sga HepG2|TFIIB|rep2 TFIIB -
5 Input_1_K562.sga K562|Input|rep1 Input -
6 Input_2_K562.sga K562|Input|rep2 Input -
7 Pol2_1_K562.sga K562|Pol2|rep1 Pol2 -
8 Pol2_2_K562.sga K562|Pol2|rep2 Pol2 -
9 TBP_1_K562.sga K562|TBP|rep1 TBP -
10 TBP_2_K562.sga K562|TBP|rep2 TBP -
11 TBP_3_K562.sga K562|TBP|rep3 TBP -
12 TFIIB_1_K562.sga K562|TFIIB|rep1 TFIIB -
13 TFIIB_2_K562.sga K562|TFIIB|rep2 TFIIB -
14 TFIIB_1_MCF7.sga MCF7|TFIIB|rep1 TFIIB -
15 TFIIB_2_MCF7.sga MCF7|TFIIB|rep2 TFIIB -

Two biological replicates were sequenced for all ChIP samples.

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 1.5.2).

References

Last update: 24 Mar 2016