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'.

• Raw data was downloaded from GEO: GSE40668
• Input file format: SRA
• Download date: 23-03-2016

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

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

Transcription Profiling 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:

• Missing samples:
• GSM726993: H3K4me1_ChIPSeq
• GSM726994: H3K4me3_ChIPSeq
• GSM726995: FAIRE_Seq
• GSM726996: H3K36me3_ChIPSeq
• GSM726997: TBP_ChIPSeq
• GSM726998: PolII_Ser2P_ChIPSeq
• GSM726999: PolII_Ser5P_ChIPSeq
• GSM727008: Input_ChIPSeq
• GSM727009: Rabbit_IG_ChIPSeq

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).

• Koch F, Fenouil R, Gut M, Cauchy P, Albert TK, Zacarias-Cabeza J, Spicuglia S, de la Chapelle AL, Heidemann M, Hintermair C, Eick D, Gut I, Ferrier P, Andrau JC
  Transcription initiation platforms and GTF recruitment at tissue-specific enhancers and promoters. Nat Struct Mol Biol. 2011 Jul 17;18(8):956-63. doi: 10.1038/nsmb.2085. 21765417
• GEO series GSE29362: Transcription Initiation Platforms and GTF recruitment at tissue-specific enhancers and promoters