Joh 2016, histone modifications maps during cellular quiescence.

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.

• Raw data was downloaded from: GEO
• Input file format: SRA
• Download date: 24-10-2017

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:

• wt: strain 975 (h+) that can enter G0 using N starvation
• ago1D: strain 975 (h+) with KO of the Argonaute Ago1 (ago1D::NatMX6)
• clr4D: strain975 (h+) with KO of the H3K9 methyltransferase Clr4 (clr4D::NatMX6)

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).

• Joh RI, Khanduja JS, Calvo IA, Mistry M, Palmieri CM, Savol AJ, Ho Sui SJ, Sadreyev RI, Aryee MJ, Motamedi M
  Survival in Quiescence Requires the Euchromatic Deployment of Clr4/SUV39H by Argonaute-Associated Small RNAs. Mol Cell. 2016 Dec 15;64(6):1088-1101. doi: 10.1016/j.molcel.2016.11.020. 27984744
• GEO series GSE89142: Survival in quiescence requires the euchromatic deployment of Clr4/SUV39H by Argonaute-associated small RNAs [ChIP-Seq]