Lee 2017, Histone H3, Pol2 and various chromatin remodelers in wild type and mutant S. pombe strains

Description

ChIP-seq experiments on S. pombe growing in rich media for These factors were asseyed in wild type (WT) cells, in sevral mutants (see "Notes on samples") and examinated under three growing conditions 22C, 33C, 37C.

Source

Samples

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

ChIP-seq data:

Filename Description Feature GEO-ID
1 GSM2210714.sga fft2-5xFLAG|Fft2-FLAG|30C|rep1 Fft2 GSM2210714
2 GSM2210715.sga fft2-5xFLAG|Fft2-FLAG|30C|rep2 Fft2 GSM2210715
3 GSM2210716.sga fft3-5xFLAG|Fft2-FLAG|30C|rep1 Fft2 GSM2210716
4 GSM2210717.sga fft3-5xFLAG|Fft2-FLAG|30C|rep2 Fft2 GSM2210717
5 GSM2210767.sga H3H4DD|H3|22C|rep1 H3 GSM2210767
6 GSM2210768.sga H3H4DD|H3|22C|rep2 H3 GSM2210768
7 GSM2210751.sga H3H4DD|RNAPII-CTDS2P|22C|rep1 RNAPII-CTDS2P GSM2210751
8 GSM2210752.sga H3H4DD|RNAPII-CTDS2P|22C|rep2 RNAPII-CTDS2P GSM2210752
9 GSM2210759.sga H3H4DD|RNAPII-CTDun|22C|rep1 RNAPII-CTDun GSM2210759
10 GSM2210760.sga H3H4DD|RNAPII-CTDun|22C|rep2 RNAPII-CTDun GSM2210760
11 GSM2210718.sga ino80-5xFLAG|Ino80-FLAG|30C|rep1 Ino80 GSM2210718
12 GSM2210719.sga ino80-5xFLAG|Ino80-FLAG|30C|rep2 Ino80 GSM2210719
13 GSM2210720.sga snf21-5xFLAG|Snf21-FLAG|30C|rep1 Snf21 GSM2210720
14 GSM2210721.sga snf21-5xFLAG|Snf21-FLAG|30C|rep2 Snf21 GSM2210721
15 GSM2210694.sga spt16-18|RNAPII-CTDS2P|37C|rep1 RNAPII-CTDS2P GSM2210694
16 GSM2210695.sga spt16-18|RNAPII-CTDS2P|37C|rep2 RNAPII-CTDS2P GSM2210695
17 GSM2210710.sga spt16-18|RNAPII-CTDun|37C|rep1 RNAPII-CTDun GSM2210710
18 GSM2210711.sga spt16-18|RNAPII-CTDun|37C|rep2 RNAPII-CTDun GSM2210711
19 GSM2210723.sga spt16-GFP|Spt16-GFP|30C|rep1 Spt16 GSM2210723
20 GSM2210724.sga spt16-GFP|Spt16-GFP|30C|rep2 Spt16 GSM2210724
21 GSM2210763.sga WT|H3|22C|rep1 H3 GSM2210763
22 GSM2210764.sga WT|H3|22C|rep2 H3 GSM2210764
23 GSM2210741.sga WT|H3|37C|rep1 H3 GSM2210741
24 GSM2210742.sga WT|H3|37C|rep2 H3 GSM2210742
25 GSM2210747.sga WT|RNAPII-CTDS2P|22C|rep1 RNAPII-CTDS2P GSM2210747
26 GSM2210748.sga WT|RNAPII-CTDS2P|22C|rep2 RNAPII-CTDS2P GSM2210748
27 GSM2210660.sga WT|RNAPII-CTDS2P|30C|rep1 RNAPII-CTDS2P GSM2210660
28 GSM2210661.sga WT|RNAPII-CTDS2P|30C|rep2 RNAPII-CTDS2P GSM2210661
29 GSM2210725.sga fft3Dxspt16-1|RNAPII-CTDS2P|37C|rep1 RNAPII-CTDS2P GSM2210725
30 GSM2210726.sga fft3Dxspt16-1|RNAPII-CTDS2P|37C|rep2 RNAPII-CTDS2P GSM2210726
31 GSM2432124.sga fft2Dfft3D|RNAPII-CTDS2P|37C|rep1 RNAPII-CTDS2P GSM2432124
32 GSM2432125.sga fft2Dfft3D|RNAPII-CTDS2P|37C|rep2 RNAPII-CTDS2P GSM2432125
33 GSM2210686.sga WT|RNAPII-CTDS2P|37C|rep1 RNAPII-CTDS2P GSM2210686
34 GSM2210687.sga WT|RNAPII-CTDS2P|37C|rep2 RNAPII-CTDS2P GSM2210687
35 GSM2210755.sga WT|RNAPII-CTDun|22C|rep1 RNAPII-CTDun GSM2210755
36 GSM2210756.sga WT|RNAPII-CTDun|22C|rep2 RNAPII-CTDun GSM2210756
37 GSM2210670.sga WT|RNAPII-CTDun|30C|rep1 RNAPII-CTDun GSM2210670
38 GSM2210671.sga WT|RNAPII-CTDun|30C|rep2 RNAPII-CTDun GSM2210671
39 GSM2210733.sga fft3Dxspt16-1|RNAPII-CTDun|37C|rep1 RNAPII-CTDun GSM2210733
40 GSM2210734.sga fft3Dxspt16-1|RNAPII-CTDun|37C|rep2 RNAPII-CTDun GSM2210734
41 GSM2432126.sga fft2Dfft3D|RNAPII-CTDun|37C|rep1 RNAPII-CTDun GSM2432126
42 GSM2432127.sga fft2Dfft3D|RNAPII-CTDun|37C|rep2 RNAPII-CTDun GSM2432127
43 GSM2210702.sga WT|RNAPII-CTDun|37C|rep1 RNAPII-CTDun GSM2210702
44 GSM2210703.sga WT|RNAPII-CTDun|37C|rep2 RNAPII-CTDun GSM2210703
45 GSM2210773.sga WT|input|22C input GSM2210773
46 GSM2210771.sga WT|input|30C|rep1 input GSM2210771
47 GSM2210772.sga WT|input|30C|rep2 input GSM2210772
48 GSM2210774.sga WT|input|37C|rep1 input GSM2210774
49 GSM2210775.sga WT|input|37C|rep2 input GSM2210775
50 GSM2210662.sga fft1D|RNAPII-CTDS2P|30C|rep1 RNAPII-CTDS2P GSM2210662
51 GSM2210663.sga fft1D|RNAPII-CTDS2P|30C|rep2 RNAPII-CTDS2P GSM2210663
52 GSM2210672.sga fft1D|RNAPII-CTDun|30C|rep1 RNAPII-CTDun GSM2210672
53 GSM2210673.sga fft1D|RNAPII-CTDun|30C|rep2 RNAPII-CTDun GSM2210673
54 GSM2210668.sga fft2Dfft3D|RNAPII-CTDS2P|30C|rep1 RNAPII-CTDS2P GSM2210668
55 GSM2210669.sga fft2Dfft3D|RNAPII-CTDS2P|30C|rep2 RNAPII-CTDS2P GSM2210669
56 GSM2432121.sga fft2Dfft3D|RNAPII-CTDS2P|37C|rep1 RNAPII-CTDS2P GSM2432121
57 GSM2432122.sga fft2Dfft3D|RNAPII-CTDS2P|37C|rep2 RNAPII-CTDS2P GSM2432122
58 GSM2210678.sga fft2Dfft3D|RNAPII-CTDun|30C|rep1 RNAPII-CTDun GSM2210678
59 GSM2210679.sga fft2Dfft3D|RNAPII-CTDun|30C|rep2 RNAPII-CTDun GSM2210679
60 GSM2432123.sga fft2Dfft3D|RNAPII-CTDun|37C RNAPII-CTDun GSM2432123
61 GSM2210664.sga fft2D|RNAPII-CTDS2P|30C|rep1 RNAPII-CTDS2P GSM2210664
62 GSM2210665.sga fft2D|RNAPII-CTDS2P|30C|rep2 RNAPII-CTDS2P GSM2210665
63 GSM2210674.sga fft2D|RNAPII-CTDun|30C|rep1 RNAPII-CTDun GSM2210674
64 GSM2210675.sga fft2D|RNAPII-CTDun|30C|rep2 RNAPII-CTDun GSM2210675
65 GSM2210769.sga fft3DH3H4DD|H3|22C|rep1 H3 GSM2210769
66 GSM2210770.sga fft3DH3H4DD|H3|22C|rep2 H3 GSM2210770
67 GSM2210753.sga fft3DH3H4DD|RNAPII-CTDS2P|22C|rep1 RNAPII-CTDS2P GSM2210753
68 GSM2210754.sga fft3DH3H4DD|RNAPII-CTDS2P|22C|rep2 RNAPII-CTDS2P GSM2210754
69 GSM2210761.sga fft3DH3H4DD|RNAPII-CTDun|22C|rep1 RNAPII-CTDun GSM2210761
70 GSM2210762.sga fft3DH3H4DD|RNAPII-CTDun|22C|rep2 RNAPII-CTDun GSM2210762
71 GSM2210731.sga fft3Dspt16-1|RNAPII-CTDS2P|37C|rep1 RNAPII-CTDS2P GSM2210731
72 GSM2210732.sga fft3Dspt16-1|RNAPII-CTDS2P|37C|rep2 RNAPII-CTDS2P GSM2210732
73 GSM2210739.sga fft3Dspt16-1|RNAPII-CTDun|37C|rep1 RNAPII-CTDun GSM2210739
74 GSM2210740.sga fft3Dspt16-1|RNAPII-CTDun|37C|rep2 RNAPII-CTDun GSM2210740
75 GSM2210765.sga fft3D|H3|22C|rep1 H3 GSM2210765
76 GSM2210766.sga fft3D|H3|22C|rep2 H3 GSM2210766
77 GSM2210743.sga fft3D|H3|37C|rep1 H3 GSM2210743
78 GSM2210744.sga fft3D|H3|37C|rep2 H3 GSM2210744
79 GSM2210749.sga fft3D|RNAPII-CTDS2P|22C|rep1 RNAPII-CTDS2P GSM2210749
80 GSM2210750.sga fft3D|RNAPII-CTDS2P|22C|rep2 RNAPII-CTDS2P GSM2210750
81 GSM2210666.sga fft3D|RNAPII-CTDS2P|30C|rep1 RNAPII-CTDS2P GSM2210666
82 GSM2210667.sga fft3D|RNAPII-CTDS2P|30C|rep2 RNAPII-CTDS2P GSM2210667
83 GSM2210727.sga fft3D|RNAPII-CTDS2P|37C|rep1 RNAPII-CTDS2P GSM2210727
84 GSM2210728.sga fft3D|RNAPII-CTDS2P|37C|rep2 RNAPII-CTDS2P GSM2210728
85 GSM2210757.sga fft3D|RNAPII-CTDun|22C|rep1 RNAPII-CTDun GSM2210757
86 GSM2210758.sga fft3D|RNAPII-CTDun|22C|rep2 RNAPII-CTDun GSM2210758
87 GSM2210676.sga fft3D|RNAPII-CTDun|30C|rep1 RNAPII-CTDun GSM2210676
88 GSM2210677.sga fft3D|RNAPII-CTDun|30C|rep2 RNAPII-CTDun GSM2210677
89 GSM2210735.sga fft3D|RNAPII-CTDun|37C|rep1 RNAPII-CTDun GSM2210735
90 GSM2210736.sga fft3D|RNAPII-CTDun|37C|rep2 RNAPII-CTDun GSM2210736
91 GSM2210680.sga hrp1D|RNAPII-CTDS2P|30C|rep1 RNAPII-CTDS2P GSM2210680
92 GSM2210681.sga hrp1D|RNAPII-CTDS2P|30C|rep2 RNAPII-CTDS2P GSM2210681
93 GSM2210696.sga hrp1D|RNAPII-CTDun|30C|rep1 RNAPII-CTDun GSM2210696
94 GSM2210697.sga hrp1D|RNAPII-CTDun|30C|rep2 RNAPII-CTDun GSM2210697
95 GSM2210682.sga hrp3D|RNAPII-CTDS2P|30C|rep1 RNAPII-CTDS2P GSM2210682
96 GSM2210683.sga hrp3D|RNAPII-CTDS2P|30C|rep2 RNAPII-CTDS2P GSM2210683
97 GSM2210698.sga hrp3D|RNAPII-CTDun|30C|rep1 RNAPII-CTDun GSM2210698
98 GSM2210699.sga hrp3D|RNAPII-CTDun|30C|rep2 RNAPII-CTDun GSM2210699
99 GSM2210684.sga ies6D|RNAPII-CTDS2P|30C|rep1 RNAPII-CTDS2P GSM2210684
100 GSM2210685.sga ies6D|RNAPII-CTDS2P|30C|rep2 RNAPII-CTDS2P GSM2210685
101 GSM2210700.sga ies6D|RNAPII-CTDun|30C|rep1 RNAPII-CTDun GSM2210700
102 GSM2210701.sga ies6D|RNAPII-CTDun|30C|rep2 RNAPII-CTDun GSM2210701
103 GSM2210712.sga WT|FLAG|30C mock|rep1 mock GSM2210712
104 GSM2210713.sga WT|FLAG|30C mock|rep2 mock GSM2210713
105 GSM2210722.sga WT|IgG|30C mock IgG GSM2210722
106 GSM2210688.sga snf21-36|RNAPII-CTDS2P|37C|rep1 RNAPII-CTDS2P GSM2210688
107 GSM2210689.sga snf21-36|RNAPII-CTDS2P|37C|rep2 RNAPII-CTDS2P GSM2210689
108 GSM2210704.sga snf21-36|RNAPII-CTDun|37C|rep1 RNAPII-CTDun GSM2210704
109 GSM2210705.sga snf21-36|RNAPII-CTDun|37C|rep2 RNAPII-CTDun GSM2210705
110 GSM2210690.sga snf22D|RNAPII-CTDS2P|30C|rep1 RNAPII-CTDS2P GSM2210690
111 GSM2210691.sga snf22D|RNAPII-CTDS2P|30C|rep2 RNAPII-CTDS2P GSM2210691
112 GSM2210706.sga snf22D|RNAPII-CTDun|30C|rep1 RNAPII-CTDun GSM2210706
113 GSM2210707.sga snf22D|RNAPII-CTDun|30C|rep2 RNAPII-CTDun GSM2210707
114 GSM2210745.sga spt16-18|H3|37C|rep1 H3 GSM2210745
115 GSM2210746.sga spt16-18|H3|37C|rep2 H3 GSM2210746
116 GSM2210729.sga spt16-1|RNAPII-CTDS2P|37C|rep1 RNAPII-CTDS2P GSM2210729
117 GSM2210730.sga spt16-1|RNAPII-CTDS2P|37C|rep2 RNAPII-CTDS2P GSM2210730
118 GSM2210737.sga spt16-1|RNAPII-CTDun|37C|rep1 RNAPII-CTDun GSM2210737
119 GSM2210738.sga spt16-1|RNAPII-CTDun|37C|rep2 RNAPII-CTDun GSM2210738
120 GSM2210692.sga swr1D|RNAPII-CTDS2P|30C|rep1 RNAPII-CTDS2P GSM2210692
121 GSM2210693.sga swr1D|RNAPII-CTDS2P|30C|rep2 RNAPII-CTDS2P GSM2210693
122 GSM2210708.sga swr1D|RNAPII-CTDun|30C|rep1 RNAPII-CTDun GSM2210708
123 GSM2210709.sga swr1D|RNAPII-CTDun|30C|rep2 RNAPII-CTDun GSM2210709

Notes on samples:

Sevral mutants were used for this study:

GFP- (green fluorescent protein) and FLAG-tags were added to proteins when specific antibodies against the target proteins were not available.

Technical Notes

FASTQ files were extracted from SRA files using fastq-dump (SRA toolkit v2.5.0) and mapped to the genome using Bowtie2 v2.2.9. 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: 29 Aug 2017