Jih 2017, mechanisms of heterochromatin assembly.

Description

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'.

Source

Samples

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:

The growing conditions are the following:

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 bed2sga.pl (ChIP-Seq v. 1.5.3).

References

Last update: 18 Oct 2017