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).



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

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 (ChIP-Seq v. 1.5.3).


Last update: 1 Oct 2018