Jih 2017, mechanisms of heterochromatin assembly.

This serie contains genomic maps of several histone modifications (H3K4me3, H3K9me2, H3K36me3, H4K16ac);, Pol-II and heterochromatin associated protein Chp1 and Swi6 and histone H3 methyltransferase Clr4 in several wild type strains and mutants. More informations about the samples can be found on section 'Notes on sample nomenclature'.

• Raw data was downloaded from: GEO
• Input file format: SRA
• Download date: 18-10-2017

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

ChIP-seq data:

	Filename	Description	Feature	GEO-ID
1	GSM2204475.sga	WT flag-chp2-SPY5378|Flag|YES	Flag	GSM2204475
2	GSM2204478.sga	WT flag-clr3-SPY5593|Flag|YES	Flag	GSM2204478
3	GSM2204458.sga	WT-SPY137|Chp1|YES	Chp1	GSM2204458
4	GSM2204452.sga	WT-SPY137|H3K36me3|YES	H3K36me3	GSM2204452
5	GSM2204449.sga	WT-SPY137|H3K4me3|YES	H3K4me3	GSM2204449
6	GSM2204484.sga	WT-SPY137|H3K9me2|YEA	H3K9me2	GSM2204484
7	GSM2204485.sga	WT-SPY137|H3K9me2|YEA - TSA 0 hr	H3K9me2	GSM2204485
8	GSM2204486.sga	WT-SPY137|H3K9me2|YEA - TSA 3 hr	H3K9me2	GSM2204486
9	GSM2204487.sga	WT-SPY137|H3K9me2|YEA - TSA 5 hr	H3K9me2	GSM2204487
10	GSM2204488.sga	WT-SPY137|H3K9me2|YEA - TSA 7 hr	H3K9me2	GSM2204488
11	GSM2204423.sga	WT-SPY137|H3K9me2|YES	H3K9me2	GSM2204423
12	GSM2204489.sga	WT-SPY137|H3K9me3|YEA	H3K9me3	GSM2204489
13	GSM2204490.sga	WT-SPY137|H3K9me3|YEA - TSA 0 hr	H3K9me3	GSM2204490
14	GSM2204491.sga	WT-SPY137|H3K9me3|YEA - TSA 3 hr	H3K9me3	GSM2204491
15	GSM2204492.sga	WT-SPY137|H3K9me3|YEA - TSA 5 hr	H3K9me3	GSM2204492
16	GSM2204493.sga	WT-SPY137|H3K9me3|YEA - TSA 7 hr	H3K9me3	GSM2204493
17	GSM2204441.sga	WT-SPY137|H3K9me3|YES	H3K9me3	GSM2204441
18	GSM2204455.sga	WT-SPY137|H4K16ac|YES	H4K16ac	GSM2204455
19	GSM2204463.sga	WT-SPY137|Pol2|YES	Pol2	GSM2204463
20	GSM2204470.sga	WT-SPY137|Swi6|YES	Swi6	GSM2204470
21	GSM2204431.sga	ago1_delta-SPY4710|H3K9me2|YES	H3K9me2	GSM2204431
22	GSM2204462.sga	chp1_delta-SPY2421|Chp1|YES	Chp1	GSM2204462
23	GSM2204428.sga	chp1_delta-SPY2421|H3K9me2|YES	H3K9me2	GSM2204428
24	GSM2204446.sga	chp1_delta-SPY2421|H3K9me3|YES	H3K9me3	GSM2204446
25	GSM2204429.sga	chp2_delta-SPY1368|H3K9me2|YES	H3K9me2	GSM2204429
26	GSM2204447.sga	chp2_delta-SPY1368|H3K9me3|YES	H3K9me3	GSM2204447
27	GSM2204468.sga	chp2_delta-SPY1368|Pol2|YES	Pol2	GSM2204468
28	GSM2204477.sga	clr4F449Y flag-chp2-SPY5382|Flag|YES	Flag	GSM2204477
29	GSM2204480.sga	clr4F449Y flag-clr3-SPY5597|Flag|YES	Flag	GSM2204480
30	GSM2204460.sga	clr4F449Y-SPY4642|Chp1|YES	Chp1	GSM2204460
31	GSM2204454.sga	clr4F449Y-SPY4642|H3K36me3|YES	H3K36me3	GSM2204454
32	GSM2204451.sga	clr4F449Y-SPY4642|H3K4me3|YES	H3K4me3	GSM2204451
33	GSM2204425.sga	clr4F449Y-SPY4642|H3K9me2|YES	H3K9me2	GSM2204425
34	GSM2204443.sga	clr4F449Y-SPY4642|H3K9me3|YES	H3K9me3	GSM2204443
35	GSM2204457.sga	clr4F449Y-SPY4642|H4K16ac|YES	H4K16ac	GSM2204457
36	GSM2204465.sga	clr4F449Y-SPY4642|Pol2|YES	Pol2	GSM2204465
37	GSM2204472.sga	clr4F449Y-SPY4642|Swi6|YES	Swi6	GSM2204472
38	GSM2204432.sga	clr4I418P ago1_delta-SPY6529|H3K9me2|YES	H3K9me2	GSM2204432
39	GSM2204433.sga	clr4I418P ago1_delta-SPY5086|H3K9me2|YES	H3K9me2	GSM2204433
40	GSM2204434.sga	clr4I418P ago1_delta-SPY5244|H3K9me2|YES	H3K9me2	GSM2204434
41	GSM2204435.sga	clr4I418P ago1_delta-SPY5245|H3K9me2|YES	H3K9me2	GSM2204435
42	GSM2204436.sga	clr4I418P ago1_delta-SPY6326|H3K9me2|YES	H3K9me2	GSM2204436
43	GSM2204437.sga	clr4I418P ago1_delta-SPY5086|H3K9me2|YES + 2.5 ug/mL tetracycline	H3K9me2	GSM2204437
44	GSM2204438.sga	clr4I418P ago1_delta-SPY5244|H3K9me2|YES + 2.5 ug/mL tetracycline	H3K9me2	GSM2204438
45	GSM2204439.sga	clr4I418P ago1_delta-SPY5245|H3K9me2|YES + 2.5 ug/mL tetracycline	H3K9me2	GSM2204439
46	GSM2204440.sga	clr4I418P ago1_delta-SPY6326|H3K9me2|YES + 2.5 ug/mL tetracycline	H3K9me2	GSM2204440
47	GSM2204461.sga	clr4I418P-SPY6537|Chp1|YES	Chp1	GSM2204461
48	GSM2204426.sga	clr4I418P-SPY6537|H3K9me2|YES	H3K9me2	GSM2204426
49	GSM2204444.sga	clr4I418P-SPY6537|H3K9me3|YES	H3K9me3	GSM2204444
50	GSM2204466.sga	clr4I418P-SPY6537|Pol2|YES	Pol2	GSM2204466
51	GSM2204427.sga	clr4W31G-SPY5562|H3K9me2|YES	H3K9me2	GSM2204427
52	GSM2204445.sga	clr4W31G-SPY5562|H3K9me3|YES	H3K9me3	GSM2204445
53	GSM2204476.sga	clr4_delta flag-chp2-SPY5380|Flag|YES	Flag	GSM2204476
54	GSM2204479.sga	clr4_delta flag-clr3-SPY5595|Flag|YES	Flag	GSM2204479
55	GSM2204459.sga	clr4_delta-SPY815|Chp1|YES	Chp1	GSM2204459
56	GSM2204453.sga	clr4_delta-SPY815|H3K36me3|YES	H3K36me3	GSM2204453
57	GSM2204450.sga	clr4_delta-SPY815|H3K4me3|YES	H3K4me3	GSM2204450
58	GSM2204424.sga	clr4_delta-SPY815|H3K9me2|YES	H3K9me2	GSM2204424
59	GSM2204442.sga	clr4_delta-SPY815|H3K9me3|YES	H3K9me3	GSM2204442
60	GSM2204456.sga	clr4_delta-SPY815|H4K16ac|YES	H4K16ac	GSM2204456
61	GSM2204464.sga	clr4_delta-SPY815|Pol2|YES	Pol2	GSM2204464
62	GSM2204471.sga	clr4_delta-SPY815|Swi6|YES	Swi6	GSM2204471
63	GSM2204481.sga	flag-clr4-SPY4636|Flag|YES	Flag	GSM2204481
64	GSM2204482.sga	flag-clr4F449Y-SPY4642|Flag|YES	Flag	GSM2204482
65	GSM2204483.sga	flag-clr4W31G-SPY5562|Flag|YES	Flag	GSM2204483
66	GSM2204469.sga	swi6_delta chp2_delta-SPY5242|Pol2|YES	Pol2	GSM2204469
67	GSM2204430.sga	swi6_delta-SPY1098|H3K9me2|YES	H3K9me2	GSM2204430
68	GSM2204448.sga	swi6_delta-SPY1098|H3K9me3|YES	H3K9me3	GSM2204448
69	GSM2204467.sga	swi6_delta-SPY1098|Pol2|YES	Pol2	GSM2204467
70	GSM2204473.sga	swi6_delta-SPY1098|Swi6|YES	Swi6	GSM2204473
71	GSM2204474.sga	untagged-SPY137|Flag|YES	Flag	GSM2204474

Notes on samples nomenclature:

The first field in the sample description contain the yeast genotype and strain separated by a '-' symbol. Yeast genotypes used are the following:

• WT: wild type
• ago1_delta: KO mutant of Ago1
• chp1_delta: KO mutant of Chp1
• chp2_delta: KO mutant of Chp2
• clr4F449Y: Clr4 carring the mutation F449Y
• clr4I418P: Clr4 carring the mutation I418P
• clr4I418P ago1_delta: Clr4 carring the mutation I418P in an Ago1 mutant background
• clr4W31G: Clr4 carring the mutation W31G
• clr4_delta: KO mutant of Clr4
• flag-chp2: Flag-tagged Chp2
• clr4_delta flag-clr3: KO mutant of Clr4 with a flag-tagged Clr3
• flag-clr4: Flag-tagged Clr4
• flag-clr4F449Y: Flag-tagged Clr4 carring the mutation F449Y
• flag-clr4W31G: Flag-tagged Clr4 carring the mutation W31G
• swi6_delta: KO mutant of Swi6
• swi6_delta chp2_delta: double mutant of Swi6 and Chp2

The growing conditions are the following:

• YES: growing medium
• YEA: Yeast Extract Agar
• TSA [0 hr to 7 hr]: cells were treated with Trichostatin A (TSA an histone deacetylase inhibitor that block heterocromatin formation) for 15 hr, resuspended in YEA to re-establish heterochromatin, and harvested at 0, 3, 5 and 7 hr.

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).

• Jih G, Iglesias N, Currie MA, Bhanu NV, Paulo JA, Gygi SP, Garcia BA, Moazed D
  Unique roles for histone H3K9me states in RNAi and heritable silencing of transcription. Nature. 2017 Jul 27;547(7664):463-467. doi: 10.1038/nature23267. Epub 2017 Jun 22. 28682306
• GEO series GSE83495: A transcriptionally permissive histone H3 lysine 9 methylation state enables RNAi-mediated heterochromatin assembly