Venters 2013, ChIP-exo of Pol2 and TFIIB in K562 cell line.

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

Venters BJ, Pugh BF
Genomic organization of human transcription initiation complexes. Nature. 2013 Oct 3;502(7469):53-8. doi: 10.1038/nature12535. Epub 2013 Sep 18. 24048476 Warning ! This article has been retracted. Nevertheless, the autors have written here : "To the best of our knowledge, the raw and processed human TFIIB, TBP and Pol II ChIP-exo data are valid". It is also confirmed by our own analysis.
Venters BJ, Pugh BF
Genomic Organization of Human Transcription Initiation Complexes. PLoS One. 2016 Feb 11;11(2):e0149339. doi: 10.1371/journal.pone.0149339. eCollection 2016. 26866362

Last update: 1 Oct 2018

Venters 2013, ChIP-exo of Pol2 and TFIIB in K562 cell line.

Description

Source

Samples

Technical Notes

References