Thodberg 2018, Profiling of TSS activity during stress and media response.

Transcription profiling using CAGE of S. pombe wild-type cells under several growing conditions: two media (EMM and YES) and 4 stresses (none, H2O2, heat, nitrogen starvation).

• Raw data was downloaded from: SRA
• Input file format: SRA
• Download date: 22-5-2018

From S. pombe (Aug 2015 ASM294v2/spo2).

:

	Filename	Description	Feature	GEO-ID
1	GSM3019616.sga	wt|EMM|none|rep1	CAGE	GSM3019616
2	GSM3019617.sga	wt|EMM|none|rep2	CAGE	GSM3019617
3	GSM3019618.sga	wt|EMM|none|rep3	CAGE	GSM3019618
4	GSM3019625.sga	wt|YES|H2O2|rep1	CAGE	GSM3019625
5	GSM3019626.sga	wt|YES|H2O2|rep2	CAGE	GSM3019626
6	GSM3019627.sga	wt|YES|H2O2|rep3	CAGE	GSM3019627
7	GSM3019628.sga	wt|YES|heat|rep1	CAGE	GSM3019628
8	GSM3019629.sga	wt|YES|heat|rep2	CAGE	GSM3019629
9	GSM3019630.sga	wt|YES|heat|rep3	CAGE	GSM3019630
10	GSM3019622.sga	wt|YES|none|rep1	CAGE	GSM3019622
11	GSM3019623.sga	wt|YES|none|rep2	CAGE	GSM3019623
12	GSM3019624.sga	wt|YES|none|rep3	CAGE	GSM3019624
13	GSM3019619.sga	wt|EMM|nitrogen starvation|rep1	CAGE	GSM3019619
14	GSM3019620.sga	wt|EMM|nitrogen starvation|rep2	CAGE	GSM3019620
15	GSM3019621.sga	wt|EMM|nitrogen starvation|rep3	CAGE	GSM3019621

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. 1.5.3).

• GEO series GSE110976: Comprehensive profiling of the fission yeast transcription start site activity during stress and media response.