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

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.

• Raw data was downloaded from: SRA
• Input file format: SRA
• Download date: 17-8-2017

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:

• WT H3: H3 WT from the histone substitution and deletion library (used as "WT" strain)
• WT bar1: Bar1 knockout from the yeast KO collection (used as "WT" strain)
• K18R: H3 lysin 18 replaced by arginine
• K36R: H3 lysin 36 replaced by arginine
• K4R: H3 lysine 4 replaced by arginine
• eaf3D: deletion mutant of Eaf3, a subunit of the "reduced potassium dependency" (RPD3S) complex which hypoacetylates gene-body nucleosomes of active genes
• set2D: deletion mutant of Set2 which methylates H3 lysine 36 (H3K36).

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).

• Sadeh R, Launer-Wachs R, Wandel H, Rahat A, Friedman N
  Elucidating Combinatorial Chromatin States at Single-Nucleosome Resolution. Mol Cell. 2016 Sep 15;63(6):1080-8. doi: 10.1016/j.molcel.2016.07.023. Epub 2016 Aug 2. 27496019
• GEO series GSE84240: Elucidating Combinatorial Chromatin States at Single-Nucleosome Resolution