Koch 2011, Maps of pre-initiation complex components in T-cells.


Map of pre-initiation complex (PIC) components in mouse primary T-cells. Note that the original dataset contains more samples that are not present here due to missing raw data. The list of missing samples is detailed in the section 'Notes on samples nomenclature'.



From Mouse Jul. 2007 (NCBI37/mm9) Assembly.

ChIP-seq data:

Filename Description Feature GEO-ID
1 GSM726990.sga Primary T-cells|CBP CBP GSM726990
2 GSM726992.sga Primary T-cells|ETS1 ETS1 GSM726992
3 GSM726991.sga Primary T-cells|PolII PolII GSM726991
4 GSM727001.sga Primary T-cells|TFIIA TFIIA GSM727001
5 GSM727002.sga Primary T-cells|TFIIB TFIIB GSM727002
6 GSM727003.sga Primary T-cells|TFIIE TFIIE GSM727003
7 GSM727004.sga Primary T-cells|TFIIF TFIIF GSM727004
8 GSM727005.sga Primary T-cells|TFIIH TFIIH GSM727005
9 GSM727000.sga Primary T-cells|Taf1 Taf1 GSM727000

RNA-seq data:

Filename Description Feature GEO-ID
1 GSM727007.sga Primary T-cells|POLYA POLYA GSM727007
2 GSM727006.sga Primary T-cells|TOTAL TOTAL GSM727006

Notes on samples nomenclature:

Technical Notes

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


Last update: 24 Mar 2016