GSE99589, The Ino80 complex mediates epigenetic centromere propagation via active removal of histone H3.

Description

Genomic maps of histone H3 and centromere histon CENP-A (H3 variant) along with maps of some subunits of the Ino80 chromatin remodelling factor in wild type and mutant S. pombe strains.

Source

Samples

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

ChIP-seq data:

Filename Description Feature GEO-ID
1 GSM2648234.sga wt|Iec1-Flag|30C|rep2 Iec1-Flag GSM2648234
2 GSM2648233.sga wt|Iec1-Flag|30C|rep1 Iec1-Flag GSM2648233
3 GSM2648232.sga wt|notag|30C|rep2 notag GSM2648232
4 GSM2648231.sga wt|notag|30C|rep1 notag GSM2648231
5 GSM2648230.sga wt|Ies6-Flag|30C|rep2 Ies6-Flag GSM2648230
6 GSM2648229.sga wt|Ies6-Flag|30C|rep1 Ies6-Flag GSM2648229
7 GSM2648228.sga cnp1-1|Iec1-Flag|36C|rep2 Iec1-Flag GSM2648228
8 GSM2648227.sga cnp1-1|Iec1-Flag|36C|rep1 Iec1-Flag GSM2648227
9 GSM2648226.sga cnp1-1|notag|36C|rep2 notag GSM2648226
10 GSM2648225.sga cnp1-1|notag|36C|rep1 notag GSM2648225
11 GSM2648224.sga cnp1-1|Ies6-Flag|36C|rep2 Ies6-Flag GSM2648224
12 GSM2648223.sga cnp1-1|Ies6-Flag|36C|rep1 Ies6-Flag GSM2648223
13 GSM2648222.sga wt|Iec1-Flag|36C|rep2 Iec1-Flag GSM2648222
14 GSM2648221.sga wt|Iec1-Flag|36C|rep1 Iec1-Flag GSM2648221
15 GSM2648220.sga wt|notag|36C|rep2 notag GSM2648220
16 GSM2648219.sga wt|notag|36C|rep1 notag GSM2648219
17 GSM2648218.sga wt|Ies6-Flag|36C|rep2 Ies6-Flag GSM2648218
18 GSM2648217.sga wt|Ies6-Flag|36C|rep1 Ies6-Flag GSM2648217
19 GSM2648216.sga hrp1D|input|30C|rep2 input GSM2648216
20 GSM2648215.sga hrp1D|input|30C|rep1 input GSM2648215
21 GSM2648214.sga hrp1D|H3|30C|rep2 H3 GSM2648214
22 GSM2648213.sga hrp1D|H3|30C|rep1 H3 GSM2648213
23 GSM2648212.sga wt|input|30C|rep2 input GSM2648212
24 GSM2648211.sga wt|input|30C|rep1 input GSM2648211
25 GSM2648210.sga ies6D|input|30C|rep2 input GSM2648210
26 GSM2648209.sga ies6D|input|30C|rep1 input GSM2648209
27 GSM2648208.sga wt|H3|30C|rep2 H3 GSM2648208
28 GSM2648207.sga wt|H3|30C|rep1 H3 GSM2648207
29 GSM2648206.sga ies6D|H3|30C|rep2 H3 GSM2648206
30 GSM2648205.sga ies6D|H3|30C|rep1 H3 GSM2648205
31 GSM2648204.sga tel1R-neocen|notag|30C|rep2 notag GSM2648204
32 GSM2648203.sga tel1R-neocen|notag|30C|rep1 notag GSM2648203
33 GSM2648202.sga tel1R-neocen|Ies6-Flag|30C|rep2 Ies6-Flag GSM2648202
34 GSM2648201.sga tel1R-neocen|Ies6-Flag|30C|rep1 Ies6-Flag GSM2648201
35 GSM2648200.sga wt|notag|30C|rep2 notag GSM2648200
36 GSM2648199.sga wt|notag|30C|rep1 notag GSM2648199
37 GSM2648198.sga wt|Ies6-Flag|30C|rep2 Ies6-Flag GSM2648198
38 GSM2648197.sga wt|Ies6-Flag|30C|rep1 Ies6-Flag GSM2648197
39 GSM2648196.sga tel1R-neocen|H3|30C|rep2 H3 GSM2648196
40 GSM2648195.sga tel1R-neocen|H3|30C|rep1 H3 GSM2648195
41 GSM2648194.sga tel1R-neocen|input|30C|rep2 input GSM2648194
42 GSM2648193.sga tel1R-neocen|input|30C|rep1 input GSM2648193
43 GSM2648192.sga tel1R-neocen|Cnp1|30C|rep2 Cnp1 GSM2648192
44 GSM2648191.sga tel1R-neocen|Cnp1|30C|rep1 Cnp1 GSM2648191
45 GSM2648190.sga mis18-262|input|36C|rep2 input GSM2648190
46 GSM2648189.sga mis18-262|input|36C|rep1 input GSM2648189
47 GSM2648188.sga mis18-262|Cnp1|36C|rep2 Cnp1 GSM2648188
48 GSM2648187.sga mis18-262|Cnp1|36C|rep1 Cnp1 GSM2648187
49 GSM2648186.sga wt|input|36C|rep2 input GSM2648186
50 GSM2648185.sga wt|input|36C|rep1 input GSM2648185
51 GSM2648184.sga wt|Cnp1|36C|rep2 Cnp1 GSM2648184
52 GSM2648183.sga wt|Cnp1|36C|rep1 Cnp1 GSM2648183
53 GSM2648182.sga TetR-Flag-Iec1|H3|AHT-30C|rep2 H3 GSM2648182
54 GSM2648181.sga TetR-Flag-Iec1|H3|AHT-30C|rep1 H3 GSM2648181
55 GSM2648180.sga TetR-Flag-Iec1|H3|30C|rep2 H3 GSM2648180
56 GSM2648179.sga TetR-Flag-Iec1|H3|30C|rep1 H3 GSM2648179
57 GSM2648178.sga TetR-Flag|H3|30C|rep2 H3 GSM2648178
58 GSM2648177.sga TetR-Flag|H3|30C|rep1 H3 GSM2648177
59 GSM2648176.sga TetR-Flag-Iec1|input|AHT-30C|rep2 input GSM2648176
60 GSM2648175.sga TetR-Flag-Iec1|input|AHT-30C|rep1 input GSM2648175
61 GSM2648174.sga TetR-Flag-Iec1|Cnp1|AHT-30C|rep2 Cnp1 GSM2648174
62 GSM2648173.sga TetR-Flag-Iec1|Cnp1|AHT-30C|rep1 Cnp1 GSM2648173
63 GSM2648172.sga TetR-Flag-Iec1|input|30C|rep2 input GSM2648172
64 GSM2648171.sga TetR-Flag-Iec1|input|30C|rep1 input GSM2648171
65 GSM2648170.sga TetR-Flag-Iec1|Cnp1|30C|rep2 Cnp1 GSM2648170
66 GSM2648169.sga TetR-Flag-Iec1|Cnp1|30C|rep1 Cnp1 GSM2648169
67 GSM2648168.sga TetR-Flag|input|30C|rep2 input GSM2648168
68 GSM2648167.sga TetR-Flag|input|30C|rep1 input GSM2648167
69 GSM2648166.sga TetR-Flag|Cnp1|30C|rep2 Cnp1 GSM2648166
70 GSM2648165.sga TetR-Flag|Cnp1|30C|rep1 Cnp1 GSM2648165
71 GSM2648164.sga ino80-11|input|20C|rep2 input GSM2648164
72 GSM2648163.sga ino80-11|input|20C|rep1 input GSM2648163
73 GSM2648162.sga ino80-11|Cnp1|20C|rep2 Cnp1 GSM2648162
74 GSM2648161.sga ino80-11|Cnp1|20C|rep1 Cnp1 GSM2648161
75 GSM2648160.sga hrp1D|input|20C|rep2 input GSM2648160
76 GSM2648159.sga hrp1D|input|20C|rep1 input GSM2648159
77 GSM2648158.sga hrp1D|Cnp1|20C|rep2 Cnp1 GSM2648158
78 GSM2648157.sga hrp1D|Cnp1|20C|rep1 Cnp1 GSM2648157
79 GSM2648156.sga ino80-11|input|20C|rep2 input GSM2648156
80 GSM2648155.sga ino80-11|input|20C|rep1 input GSM2648155
81 GSM2648154.sga ino80-11|Cnp1|20C|rep2 Cnp1 GSM2648154
82 GSM2648153.sga ino80-11|Cnp1|20C|rep1 Cnp1 GSM2648153
83 GSM2648152.sga wt|input|20C|rep2 input GSM2648152
84 GSM2648151.sga wt|input|20C|rep1 input GSM2648151
85 GSM2648150.sga wt|Cnp1|20C|rep2 Cnp1 GSM2648150
86 GSM2648149.sga wt|Cnp1|20C|rep1 Cnp1 GSM2648149
87 GSM2648148.sga hrp1D|input|30C|rep2 input GSM2648148
88 GSM2648147.sga hrp1D|input|30C|rep1 input GSM2648147
89 GSM2648146.sga hrp1D|Cnp1|30C|rep2 Cnp1 GSM2648146
90 GSM2648145.sga hrp1D|Cnp1|30C|rep1 Cnp1 GSM2648145
91 GSM2648144.sga ies6D|input|30C|rep2 input GSM2648144
92 GSM2648143.sga ies6D|input|30C|rep1 input GSM2648143
93 GSM2648142.sga ies6D|Cnp1|30C|rep2 Cnp1 GSM2648142
94 GSM2648141.sga ies6D|Cnp1|30C|rep1 Cnp1 GSM2648141
95 GSM2648140.sga wt|input|30C|rep2 input GSM2648140
96 GSM2648139.sga wt|input|30C|rep1 input GSM2648139
97 GSM2648138.sga wt|Cnp1|30C|rep2 Cnp1 GSM2648138
98 GSM2648137.sga wt|Cnp1|30C|rep1 Cnp1 GSM2648137

Notes on samples nomenclature:

The ChIP-seq targets are the following:

For the following mutants: And conditions / treatments:

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: 16 Oct 2017