Sadeh 2016, Combinatorial Chromatin States at Single-Nucleosome Resolution.

Description

This series contains data obtained with a novel technique: combinatorial-iChIP-seq. This technique was developed to determine the genome-wide co-occurrence of histone marks on the same nucleosome resolution.
Several mutants were used to test the technique (see "Notes on samples").
Saccharomyces cerevisiae cells were grown in Yeast Extract-Peptone-Dextrose (YPD) media at 30C.

Source

Samples

From S. cerevisiae (Apr 2011 R64/sacCer3).

ChIP-seq data:

Filename Description Feature GEO-ID
1 GSM2230106.sga WT H3|H3-H3 H3-H3 GSM2230106
2 GSM2230111.sga WT H3|H3-Input H3-Input GSM2230111
3 GSM2230107.sga WT H3|H3-K18ac H3-K18ac GSM2230107
4 GSM2230108.sga WT H3|H3-K36me3 H3-K36me3 GSM2230108
5 GSM2230109.sga WT H3|H3-K4me3 H3-K4me3 GSM2230109
6 GSM2230110.sga WT H3|H3-K79me3 H3-K79me3 GSM2230110
7 GSM2230112.sga WT H3|K18ac-H3 K18ac-H3 GSM2230112
8 GSM2230117.sga WT H3|K18ac-Input||run1 K18ac-Input GSM2230117
9 GSM2230136.sga WT bar1|K18ac-Input||run2 K18ac-Input GSM2230136
10 GSM2230113.sga WT H3|K18ac-K18ac||run1 K18ac-K18ac GSM2230113
11 GSM2230137.sga WT bar1|K18ac-K18ac||run2 K18ac-K18ac GSM2230137
12 GSM2230114.sga WT H3|K18ac-K36me3||run1 K18ac-K36me3 GSM2230114
13 GSM2230138.sga WT bar1|K18ac-K36me3||run2 K18ac-K36me3 GSM2230138
14 GSM2230115.sga WT H3|K18ac-K4me3||run1 K18ac-K4me3 GSM2230115
15 GSM2230139.sga WT bar1|K18ac-K4me3||run2 K18ac-K4me3 GSM2230139
16 GSM2230116.sga WT H3|K18ac-K79me3||run1 K18ac-K79me3 GSM2230116
17 GSM2230141.sga WT bar1|K18ac-K79me3||run2 K18ac-K79me3 GSM2230141
18 GSM2230118.sga WT H3|K36me3-H3 K36me3-H3 GSM2230118
19 GSM2230123.sga WT H3|K36me3-Input||run1 K36me3-Input GSM2230123
20 GSM2230142.sga WT bar1|K36me3-Input||run2 K36me3-Input GSM2230142
21 GSM2230119.sga WT H3|K36me3-K18ac||run1 K36me3-K18ac GSM2230119
22 GSM2230143.sga WT bar1|K36me3-K18ac||run2 K36me3-K18ac GSM2230143
23 GSM2230120.sga WT H3|K36me3-K36me3||run1 K36me3-K36me3 GSM2230120
24 GSM2230144.sga WT bar1|K36me3-K36me3||run2 K36me3-K36me3 GSM2230144
25 GSM2230121.sga WT H3|K36me3-K4me3||run1 K36me3-K4me3 GSM2230121
26 GSM2230145.sga WT bar1|K36me3-K4me3||run2 K36me3-K4me3 GSM2230145
27 GSM2230122.sga WT H3|K36me3-K79me3||run1 K36me3-K79me3 GSM2230122
28 GSM2230147.sga WT bar1|K36me3-K79me3||run2 K36me3-K79me3 GSM2230147
29 GSM2230124.sga WT H3|K4me3-H3 K4me3-H3 GSM2230124
30 GSM2230129.sga WT H3|K4me3-Input||run1 K4me3-Input GSM2230129
31 GSM2230148.sga WT bar1|K4me3-Input||run2 K4me3-Input GSM2230148
32 GSM2230125.sga WT H3|K4me3-K18ac||run1 K4me3-K18ac GSM2230125
33 GSM2230149.sga WT bar1|K4me3-K18ac||run2 K4me3-K18ac GSM2230149
34 GSM2230126.sga WT H3|K4me3-K36me3||run1 K4me3-K36me3 GSM2230126
35 GSM2230150.sga WT bar1|K4me3-K36me3||run2 K4me3-K36me3 GSM2230150
36 GSM2230127.sga WT H3|K4me3-K4me3||run1 K4me3-K4me3 GSM2230127
37 GSM2230151.sga WT bar1|K4me3-K4me3||run2 K4me3-K4me3 GSM2230151
38 GSM2230128.sga WT H3|K4me3-K79me3||run1 K4me3-K79me3 GSM2230128
39 GSM2230153.sga WT bar1|K4me3-K79me3||run2 K4me3-K79me3 GSM2230153
40 GSM2230130.sga WT H3|K79me3-H3 K79me3-H3 GSM2230130
41 GSM2230135.sga WT H3|K79me3-Input||run1 K79me3-Input GSM2230135
42 GSM2230160.sga WT bar1|K79me3-Input||run2 K79me3-Input GSM2230160
43 GSM2230131.sga WT H3|K79me3-K18ac||run1 K79me3-K18ac GSM2230131
44 GSM2230161.sga WT bar1|K79me3-K18ac||run2 K79me3-K18ac GSM2230161
45 GSM2230132.sga WT H3|K79me3-K36me3||run1 K79me3-K36me3 GSM2230132
46 GSM2230162.sga WT bar1|K79me3-K36me3||run2 K79me3-K36me3 GSM2230162
47 GSM2230133.sga WT H3|K79me3-K4me3||run1 K79me3-K4me3 GSM2230133
48 GSM2230163.sga WT bar1|K79me3-K4me3||run2 K79me3-K4me3 GSM2230163
49 GSM2230134.sga WT H3|K79me3-K79me3||run1 K79me3-K79me3 GSM2230134
50 GSM2230165.sga WT bar1|K79me3-K79me3||run2 K79me3-K79me3 GSM2230165
51 GSM2230016.sga K18R|H3-H3 H3-H3 GSM2230016
52 GSM2230021.sga K18R|H3-Input H3-Input GSM2230021
53 GSM2230017.sga K18R|H3-K18ac H3-K18ac GSM2230017
54 GSM2230018.sga K18R|H3-K36me3 H3-K36me3 GSM2230018
55 GSM2230019.sga K18R|H3-K4me3 H3-K4me3 GSM2230019
56 GSM2230020.sga K18R|H3-K79me3 H3-K79me3 GSM2230020
57 GSM2230022.sga K18R|K18ac-H3 K18ac-H3 GSM2230022
58 GSM2230027.sga K18R|K18ac-Input K18ac-Input GSM2230027
59 GSM2230023.sga K18R|K18ac-K18ac K18ac-K18ac GSM2230023
60 GSM2230024.sga K18R|K18ac-K36me3 K18ac-K36me3 GSM2230024
61 GSM2230025.sga K18R|K18ac-K4me3 K18ac-K4me3 GSM2230025
62 GSM2230026.sga K18R|K18ac-K79me3 K18ac-K79me3 GSM2230026
63 GSM2230028.sga K18R|K36me3-H3 K36me3-H3 GSM2230028
64 GSM2230033.sga K18R|K36me3-Input K36me3-Input GSM2230033
65 GSM2230029.sga K18R|K36me3-K18ac K36me3-K18ac GSM2230029
66 GSM2230030.sga K18R|K36me3-K36me3 K36me3-K36me3 GSM2230030
67 GSM2230031.sga K18R|K36me3-K4me3 K36me3-K4me3 GSM2230031
68 GSM2230032.sga K18R|K36me3-K79me3 K36me3-K79me3 GSM2230032
69 GSM2230034.sga K18R|K4me3-H3 K4me3-H3 GSM2230034
70 GSM2230039.sga K18R|K4me3-Input K4me3-Input GSM2230039
71 GSM2230035.sga K18R|K4me3-K18ac K4me3-K18ac GSM2230035
72 GSM2230036.sga K18R|K4me3-K36me3 K4me3-K36me3 GSM2230036
73 GSM2230037.sga K18R|K4me3-K4me3 K4me3-K4me3 GSM2230037
74 GSM2230038.sga K18R|K4me3-K79me3 K4me3-K79me3 GSM2230038
75 GSM2230040.sga K18R|K79me3-H3 K79me3-H3 GSM2230040
76 GSM2230045.sga K18R|K79me3-Input K79me3-Input GSM2230045
77 GSM2230041.sga K18R|K79me3-K18ac K79me3-K18ac GSM2230041
78 GSM2230042.sga K18R|K79me3-K36me3 K79me3-K36me3 GSM2230042
79 GSM2230043.sga K18R|K79me3-K4me3 K79me3-K4me3 GSM2230043
80 GSM2230044.sga K18R|K79me3-K79me3 K79me3-K79me3 GSM2230044
81 GSM2230046.sga K36R|H3-H3 H3-H3 GSM2230046
82 GSM2230051.sga K36R|H3-Input H3-Input GSM2230051
83 GSM2230047.sga K36R|H3-K18ac H3-K18ac GSM2230047
84 GSM2230048.sga K36R|H3-K36me3 H3-K36me3 GSM2230048
85 GSM2230049.sga K36R|H3-K4me3 H3-K4me3 GSM2230049
86 GSM2230050.sga K36R|H3-K79me3 H3-K79me3 GSM2230050
87 GSM2230052.sga K36R|K18ac-H3 K18ac-H3 GSM2230052
88 GSM2230057.sga K36R|K18ac-Input K18ac-Input GSM2230057
89 GSM2230053.sga K36R|K18ac-K18ac K18ac-K18ac GSM2230053
90 GSM2230054.sga K36R|K18ac-K36me3 K18ac-K36me3 GSM2230054
91 GSM2230055.sga K36R|K18ac-K4me3 K18ac-K4me3 GSM2230055
92 GSM2230056.sga K36R|K18ac-K79me3 K18ac-K79me3 GSM2230056
93 GSM2230058.sga K36R|K36me3-H3 K36me3-H3 GSM2230058
94 GSM2230063.sga K36R|K36me3-Input K36me3-Input GSM2230063
95 GSM2230059.sga K36R|K36me3-K18ac K36me3-K18ac GSM2230059
96 GSM2230060.sga K36R|K36me3-K36me3 K36me3-K36me3 GSM2230060
97 GSM2230061.sga K36R|K36me3-K4me3 K36me3-K4me3 GSM2230061
98 GSM2230062.sga K36R|K36me3-K79me3 K36me3-K79me3 GSM2230062
99 GSM2230064.sga K36R|K4me3-H3 K4me3-H3 GSM2230064
100 GSM2230069.sga K36R|K4me3-Input K4me3-Input GSM2230069
101 GSM2230065.sga K36R|K4me3-K18ac K4me3-K18ac GSM2230065
102 GSM2230066.sga K36R|K4me3-K36me3 K4me3-K36me3 GSM2230066
103 GSM2230067.sga K36R|K4me3-K4me3 K4me3-K4me3 GSM2230067
104 GSM2230068.sga K36R|K4me3-K79me3 K4me3-K79me3 GSM2230068
105 GSM2230070.sga K36R|K79me3-H3 K79me3-H3 GSM2230070
106 GSM2230075.sga K36R|K79me3-Input K79me3-Input GSM2230075
107 GSM2230071.sga K36R|K79me3-K18ac K79me3-K18ac GSM2230071
108 GSM2230072.sga K36R|K79me3-K36me3 K79me3-K36me3 GSM2230072
109 GSM2230073.sga K36R|K79me3-K4me3 K79me3-K4me3 GSM2230073
110 GSM2230074.sga K36R|K79me3-K79me3 K79me3-K79me3 GSM2230074
111 GSM2230076.sga K4R|H3-H3 H3-H3 GSM2230076
112 GSM2230081.sga K4R|H3-Input H3-Input GSM2230081
113 GSM2230077.sga K4R|H3-K18ac H3-K18ac GSM2230077
114 GSM2230078.sga K4R|H3-K36me3 H3-K36me3 GSM2230078
115 GSM2230079.sga K4R|H3-K4me3 H3-K4me3 GSM2230079
116 GSM2230080.sga K4R|H3-K79me3 H3-K79me3 GSM2230080
117 GSM2230082.sga K4R|K18ac-H3 K18ac-H3 GSM2230082
118 GSM2230087.sga K4R|K18ac-Input K18ac-Input GSM2230087
119 GSM2230083.sga K4R|K18ac-K18ac K18ac-K18ac GSM2230083
120 GSM2230084.sga K4R|K18ac-K36me3 K18ac-K36me3 GSM2230084
121 GSM2230085.sga K4R|K18ac-K4me3 K18ac-K4me3 GSM2230085
122 GSM2230086.sga K4R|K18ac-K79me3 K18ac-K79me3 GSM2230086
123 GSM2230088.sga K4R|K36me3-H3 K36me3-H3 GSM2230088
124 GSM2230093.sga K4R|K36me3-Input K36me3-Input GSM2230093
125 GSM2230089.sga K4R|K36me3-K18ac K36me3-K18ac GSM2230089
126 GSM2230090.sga K4R|K36me3-K36me3 K36me3-K36me3 GSM2230090
127 GSM2230091.sga K4R|K36me3-K4me3 K36me3-K4me3 GSM2230091
128 GSM2230092.sga K4R|K36me3-K79me3 K36me3-K79me3 GSM2230092
129 GSM2230094.sga K4R|K4me3-H3 K4me3-H3 GSM2230094
130 GSM2230099.sga K4R|K4me3-Input K4me3-Input GSM2230099
131 GSM2230095.sga K4R|K4me3-K18ac K4me3-K18ac GSM2230095
132 GSM2230096.sga K4R|K4me3-K36me3 K4me3-K36me3 GSM2230096
133 GSM2230097.sga K4R|K4me3-K4me3 K4me3-K4me3 GSM2230097
134 GSM2230098.sga K4R|K4me3-K79me3 K4me3-K79me3 GSM2230098
135 GSM2230100.sga K4R|K79me3-H3 K79me3-H3 GSM2230100
136 GSM2230105.sga K4R|K79me3-Input K79me3-Input GSM2230105
137 GSM2230101.sga K4R|K79me3-K18ac K79me3-K18ac GSM2230101
138 GSM2230102.sga K4R|K79me3-K36me3 K79me3-K36me3 GSM2230102
139 GSM2230103.sga K4R|K79me3-K4me3 K79me3-K4me3 GSM2230103
140 GSM2230104.sga K4R|K79me3-K79me3 K79me3-K79me3 GSM2230104
141 GSM2230166.sga eaf3D|K18ac-Input K18ac-Input GSM2230166
142 GSM2230167.sga eaf3D|K18ac-K18ac K18ac-K18ac GSM2230167
143 GSM2230168.sga eaf3D|K18ac-K36me3 K18ac-K36me3 GSM2230168
144 GSM2230169.sga eaf3D|K18ac-K4me3 K18ac-K4me3 GSM2230169
145 GSM2230171.sga eaf3D|K18ac-K79me3 K18ac-K79me3 GSM2230171
146 GSM2230172.sga eaf3D|K36me3-Input K36me3-Input GSM2230172
147 GSM2230173.sga eaf3D|K36me3-K18ac K36me3-K18ac GSM2230173
148 GSM2230174.sga eaf3D|K36me3-K36me3 K36me3-K36me3 GSM2230174
149 GSM2230175.sga eaf3D|K36me3-K4me3 K36me3-K4me3 GSM2230175
150 GSM2230177.sga eaf3D|K36me3-K79me3 K36me3-K79me3 GSM2230177
151 GSM2230178.sga eaf3D|K4me3-Input K4me3-Input GSM2230178
152 GSM2230179.sga eaf3D|K4me3-K18ac K4me3-K18ac GSM2230179
153 GSM2230180.sga eaf3D|K4me3-K36me3 K4me3-K36me3 GSM2230180
154 GSM2230181.sga eaf3D|K4me3-K4me3 K4me3-K4me3 GSM2230181
155 GSM2230183.sga eaf3D|K4me3-K79me3 K4me3-K79me3 GSM2230183
156 GSM2230190.sga eaf3D|K79me3-Input K79me3-Input GSM2230190
157 GSM2230191.sga eaf3D|K79me3-K18ac K79me3-K18ac GSM2230191
158 GSM2230192.sga eaf3D|K79me3-K36me3 K79me3-K36me3 GSM2230192
159 GSM2230193.sga eaf3D|K79me3-K4me3 K79me3-K4me3 GSM2230193
160 GSM2230195.sga eaf3D|K79me3-K79me3 K79me3-K79me3 GSM2230195
161 GSM2230196.sga set2D|K18ac-Input K18ac-Input GSM2230196
162 GSM2230197.sga set2D|K18ac-K18ac K18ac-K18ac GSM2230197
163 GSM2230198.sga set2D|K18ac-K36me3 K18ac-K36me3 GSM2230198
164 GSM2230199.sga set2D|K18ac-K4me3 K18ac-K4me3 GSM2230199
165 GSM2230201.sga set2D|K18ac-K79me3 K18ac-K79me3 GSM2230201
166 GSM2230202.sga set2D|K36me3-Input K36me3-Input GSM2230202
167 GSM2230203.sga set2D|K36me3-K18ac K36me3-K18ac GSM2230203
168 GSM2230204.sga set2D|K36me3-K36me3 K36me3-K36me3 GSM2230204
169 GSM2230205.sga set2D|K36me3-K4me3 K36me3-K4me3 GSM2230205
170 GSM2230207.sga set2D|K36me3-K79me3 K36me3-K79me3 GSM2230207
171 GSM2230208.sga set2D|K4me3-Input K4me3-Input GSM2230208
172 GSM2230209.sga set2D|K4me3-K18ac K4me3-K18ac GSM2230209
173 GSM2230210.sga set2D|K4me3-K36me3 K4me3-K36me3 GSM2230210
174 GSM2230211.sga set2D|K4me3-K4me3 K4me3-K4me3 GSM2230211
175 GSM2230213.sga set2D|K4me3-K79me3 K4me3-K79me3 GSM2230213
176 GSM2230220.sga set2D|K79me3-Input K79me3-Input GSM2230220
177 GSM2230221.sga set2D|K79me3-K18ac K79me3-K18ac GSM2230221
178 GSM2230222.sga set2D|K79me3-K36me3 K79me3-K36me3 GSM2230222
179 GSM2230223.sga set2D|K79me3-K4me3 K79me3-K4me3 GSM2230223
180 GSM2230225.sga set2D|K79me3-K79me3 K79me3-K79me3 GSM2230225

Notes on samples :

Sevral mutants were used for this study:

Technical Notes

Following authors methods, FASTQ files were extracted from SRA files using fastq-dump (SRA toolkit v2.5.0). The resulting paired-end reads were mapped to the genome using Bowtie2 v2.2.9 with maximum fragment length of 1000 bp. 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