Joh 2016, histone modifications maps during cellular quiescence.

Description

ChIP-seq maps of two histone modifications (H3k9me2 and H3k9me3) during 3 time points (0, 1 and 24 hours) after induction of Cellular quiescence (G0) by phosphate starvation (N starvation) in wild type and RNAi pathway mutants strains.

Source

Samples

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

ChIP-seq data:

Filename Description Feature GEO-ID
1 GSM2359580.sga ago1D|H3K9me2|N starvation, 24h after -N|rep1 H3K9me2 GSM2359580
2 GSM2359582.sga ago1D|H3K9me2|N starvation, 24h after -N|rep2 H3K9me2 GSM2359582
3 GSM2359579.sga ago1D|H3K9me2|control, 0h after -N|rep1 H3K9me2 GSM2359579
4 GSM2359581.sga ago1D|H3K9me2|control, 0h after -N|rep2 H3K9me2 GSM2359581
5 GSM2359606.sga ago1D|none|N starvation, 24h after -N|rep1 none GSM2359606
6 GSM2359608.sga ago1D|none|N starvation, 24h after -N|rep2 none GSM2359608
7 GSM2359605.sga ago1D|none|control, 0h after -N|rep1 none GSM2359605
8 GSM2359607.sga ago1D|none|control, 0h after -N|rep2 none GSM2359607
9 GSM2359574.sga clr4D|H3K9me2|N starvation, 1h after -N|rep1 H3K9me2 GSM2359574
10 GSM2359577.sga clr4D|H3K9me2|N starvation, 1h after -N|rep2 H3K9me2 GSM2359577
11 GSM2359575.sga clr4D|H3K9me2|N starvation, 24h after -N|rep1 H3K9me2 GSM2359575
12 GSM2359578.sga clr4D|H3K9me2|N starvation, 24h after -N|rep2 H3K9me2 GSM2359578
13 GSM2359573.sga clr4D|H3K9me2|control, 0h after -N|rep1 H3K9me2 GSM2359573
14 GSM2359576.sga clr4D|H3K9me2|control, 0h after -N|rep2 H3K9me2 GSM2359576
15 GSM2359587.sga clr4D|H3K9me3|N starvation, 1h after -N|rep1 H3K9me3 GSM2359587
16 GSM2359588.sga clr4D|H3K9me3|N starvation, 24h after -N|rep1 H3K9me3 GSM2359588
17 GSM2359586.sga clr4D|H3K9me3|control, 0h after -N|rep1 H3K9me3 GSM2359586
18 GSM2359600.sga clr4D|none|N starvation, 1h after -N|rep1 none GSM2359600
19 GSM2359613.sga clr4D|none|N starvation, 1h after -N|rep1 none GSM2359613
20 GSM2359603.sga clr4D|none|N starvation, 1h after -N|rep2 none GSM2359603
21 GSM2359601.sga clr4D|none|N starvation, 24h after -N|rep1 none GSM2359601
22 GSM2359614.sga clr4D|none|N starvation, 24h after -N|rep1 none GSM2359614
23 GSM2359604.sga clr4D|none|N starvation, 24h after -N|rep2 none GSM2359604
24 GSM2359599.sga clr4D|none|control, 0h after -N|rep1 none GSM2359599
25 GSM2359612.sga clr4D|none|control, 0h after -N|rep1 none GSM2359612
26 GSM2359602.sga clr4D|none|control, 0h after -N|rep2 none GSM2359602
27 GSM2359560.sga wt|H3K9me2|N starvation, 1h after -N|rep1 H3K9me2 GSM2359560
28 GSM2359563.sga wt|H3K9me2|N starvation, 1h after -N|rep2 H3K9me2 GSM2359563
29 GSM2359561.sga wt|H3K9me2|N starvation, 24h after -N|rep1 H3K9me2 GSM2359561
30 GSM2359564.sga wt|H3K9me2|N starvation, 24h after -N|rep2 H3K9me2 GSM2359564
31 GSM2359566.sga wt|H3K9me2|N starvation, 24h after -N|rep3 H3K9me2 GSM2359566
32 GSM2359568.sga wt|H3K9me2|N starvation, 24h after -N|rep4 H3K9me2 GSM2359568
33 GSM2359570.sga wt|H3K9me2|N starvation, 24h after -N|rep5 H3K9me2 GSM2359570
34 GSM2359572.sga wt|H3K9me2|N starvation, 24h after -N|rep6 H3K9me2 GSM2359572
35 GSM2359559.sga wt|H3K9me2|control, 0h after -N|rep1 H3K9me2 GSM2359559
36 GSM2359562.sga wt|H3K9me2|control, 0h after -N|rep2 H3K9me2 GSM2359562
37 GSM2359565.sga wt|H3K9me2|control, 0h after -N|rep3 H3K9me2 GSM2359565
38 GSM2359567.sga wt|H3K9me2|control, 0h after -N|rep4 H3K9me2 GSM2359567
39 GSM2359569.sga wt|H3K9me2|control, 0h after -N|rep5 H3K9me2 GSM2359569
40 GSM2359571.sga wt|H3K9me2|control, 0h after -N|rep6 H3K9me2 GSM2359571
41 GSM2359584.sga wt|H3K9me3|N starvation, 1h after -N|rep1 H3K9me3 GSM2359584
42 GSM2359585.sga wt|H3K9me3|N starvation, 24h after -N|rep1 H3K9me3 GSM2359585
43 GSM2359583.sga wt|H3K9me3|control, 0h after -N|rep1 H3K9me3 GSM2359583
44 GSM2359590.sga wt|none|N starvation, 1h after -N|rep1 none GSM2359590
45 GSM2359610.sga wt|none|N starvation, 1h after -N|rep1 none GSM2359610
46 GSM2359593.sga wt|none|N starvation, 1h after -N|rep2 none GSM2359593
47 GSM2359591.sga wt|none|N starvation, 24h after -N|rep1 none GSM2359591
48 GSM2359611.sga wt|none|N starvation, 24h after -N|rep1 none GSM2359611
49 GSM2359594.sga wt|none|N starvation, 24h after -N|rep2 none GSM2359594
50 GSM2359596.sga wt|none|N starvation, 24h after -N|rep5 none GSM2359596
51 GSM2359598.sga wt|none|N starvation, 24h after -N|rep6 none GSM2359598
52 GSM2359589.sga wt|none|control, 0h after -N|rep1 none GSM2359589
53 GSM2359609.sga wt|none|control, 0h after -N|rep1 none GSM2359609
54 GSM2359592.sga wt|none|control, 0h after -N|rep2 none GSM2359592
55 GSM2359595.sga wt|none|control, 0h after -N|rep5 none GSM2359595
56 GSM2359597.sga wt|none|control, 0h after -N|rep6 none GSM2359597

Notes on samples nomenclature:

Mutant strain used:

Technical Notes

FASTQ files were extracted from SRA files using fastq-dump (SRA toolkit v2.5.0) and mapped to the genome using Bowtie2 v 2.2.9. 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).

References

Last update: 24 Oct 2017