Kuang 2014, high-resolution view of chromatin states across distinct metabolic states.

Description

16 time points (t1 - t16) ChIP-seq of 8 histone marks (H3, H3K14ac, H3K36me3, H3K4me3, H3K56ac, H3K9ac, H4K16ac, H4K5ac) over one metabolic cycle; 14 time points (t1 - t14) ChIP-seq of 3 chromatin modifiers (Esa1, Gcn5, Set1) over one metabolic cycle

Source

Samples

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

ChIP-seq data:

Filename Description Feature GEO-ID
1 GSM1263527.sga ZKY428|Esa1|t1 Esa1 GSM1263527
2 GSM1263528.sga ZKY428|Esa1|t2 Esa1 GSM1263528
3 GSM1263529.sga ZKY428|Esa1|t3 Esa1 GSM1263529
4 GSM1263530.sga ZKY428|Esa1|t4 Esa1 GSM1263530
5 GSM1263531.sga ZKY428|Esa1|t5 Esa1 GSM1263531
6 GSM1263532.sga ZKY428|Esa1|t6 Esa1 GSM1263532
7 GSM1263533.sga ZKY428|Esa1|t7 Esa1 GSM1263533
8 GSM1263534.sga ZKY428|Esa1|t8 Esa1 GSM1263534
9 GSM1263535.sga ZKY428|Esa1|t9 Esa1 GSM1263535
10 GSM1263536.sga ZKY428|Esa1|t10 Esa1 GSM1263536
11 GSM1263537.sga ZKY428|Esa1|t11 Esa1 GSM1263537
12 GSM1263538.sga ZKY428|Esa1|t12 Esa1 GSM1263538
13 GSM1263539.sga ZKY428|Esa1|t13 Esa1 GSM1263539
14 GSM1263540.sga ZKY428|Esa1|t14 Esa1 GSM1263540
15 GSM1263499.sga ZKY428|Gcn5|t1 Gcn5 GSM1263499
16 GSM1263500.sga ZKY428|Gcn5|t2 Gcn5 GSM1263500
17 GSM1263501.sga ZKY428|Gcn5|t3 Gcn5 GSM1263501
18 GSM1263502.sga ZKY428|Gcn5|t4 Gcn5 GSM1263502
19 GSM1263503.sga ZKY428|Gcn5|t5 Gcn5 GSM1263503
20 GSM1263504.sga ZKY428|Gcn5|t6 Gcn5 GSM1263504
21 GSM1263505.sga ZKY428|Gcn5|t7 Gcn5 GSM1263505
22 GSM1263506.sga ZKY428|Gcn5|t8 Gcn5 GSM1263506
23 GSM1263507.sga ZKY428|Gcn5|t9 Gcn5 GSM1263507
24 GSM1263508.sga ZKY428|Gcn5|t10 Gcn5 GSM1263508
25 GSM1263509.sga ZKY428|Gcn5|t11 Gcn5 GSM1263509
26 GSM1263510.sga ZKY428|Gcn5|t12 Gcn5 GSM1263510
27 GSM1263511.sga ZKY428|Gcn5|t13 Gcn5 GSM1263511
28 GSM1263512.sga ZKY428|Gcn5|t14 Gcn5 GSM1263512
29 GSM1263435.sga ZKY329|H3|t1 H3 GSM1263435
30 GSM1263436.sga ZKY329|H3|t2 H3 GSM1263436
31 GSM1263437.sga ZKY329|H3|t3 H3 GSM1263437
32 GSM1263438.sga ZKY329|H3|t4 H3 GSM1263438
33 GSM1263439.sga ZKY329|H3|t5 H3 GSM1263439
34 GSM1263440.sga ZKY329|H3|t6 H3 GSM1263440
35 GSM1263441.sga ZKY329|H3|t7 H3 GSM1263441
36 GSM1263442.sga ZKY329|H3|t8 H3 GSM1263442
37 GSM1263443.sga ZKY329|H3|t9 H3 GSM1263443
38 GSM1263444.sga ZKY329|H3|t10 H3 GSM1263444
39 GSM1263445.sga ZKY329|H3|t11 H3 GSM1263445
40 GSM1263446.sga ZKY329|H3|t12 H3 GSM1263446
41 GSM1263447.sga ZKY329|H3|t13 H3 GSM1263447
42 GSM1263448.sga ZKY329|H3|t14 H3 GSM1263448
43 GSM1263449.sga ZKY329|H3|t15 H3 GSM1263449
44 GSM1263450.sga ZKY329|H3|t16 H3 GSM1263450
45 GSM1263387.sga ZKY329|H3K14ac|t1 H3K14ac GSM1263387
46 GSM1263388.sga ZKY329|H3K14ac|t2 H3K14ac GSM1263388
47 GSM1263389.sga ZKY329|H3K14ac|t3 H3K14ac GSM1263389
48 GSM1263390.sga ZKY329|H3K14ac|t4 H3K14ac GSM1263390
49 GSM1263391.sga ZKY329|H3K14ac|t5 H3K14ac GSM1263391
50 GSM1263392.sga ZKY329|H3K14ac|t6 H3K14ac GSM1263392
51 GSM1263393.sga ZKY329|H3K14ac|t7 H3K14ac GSM1263393
52 GSM1263394.sga ZKY329|H3K14ac|t8 H3K14ac GSM1263394
53 GSM1263395.sga ZKY329|H3K14ac|t9 H3K14ac GSM1263395
54 GSM1263396.sga ZKY329|H3K14ac|t10 H3K14ac GSM1263396
55 GSM1263397.sga ZKY329|H3K14ac|t11 H3K14ac GSM1263397
56 GSM1263398.sga ZKY329|H3K14ac|t12 H3K14ac GSM1263398
57 GSM1263399.sga ZKY329|H3K14ac|t13 H3K14ac GSM1263399
58 GSM1263400.sga ZKY329|H3K14ac|t14 H3K14ac GSM1263400
59 GSM1263401.sga ZKY329|H3K14ac|t15 H3K14ac GSM1263401
60 GSM1263402.sga ZKY329|H3K14ac|t16 H3K14ac GSM1263402
61 GSM1263467.sga ZKY329|H3K36me3|t1 H3K36me3 GSM1263467
62 GSM1263468.sga ZKY329|H3K36me3|t2 H3K36me3 GSM1263468
63 GSM1263469.sga ZKY329|H3K36me3|t3 H3K36me3 GSM1263469
64 GSM1263470.sga ZKY329|H3K36me3|t4 H3K36me3 GSM1263470
65 GSM1263471.sga ZKY329|H3K36me3|t5 H3K36me3 GSM1263471
66 GSM1263472.sga ZKY329|H3K36me3|t6 H3K36me3 GSM1263472
67 GSM1263473.sga ZKY329|H3K36me3|t7 H3K36me3 GSM1263473
68 GSM1263474.sga ZKY329|H3K36me3|t8 H3K36me3 GSM1263474
69 GSM1263475.sga ZKY329|H3K36me3|t9 H3K36me3 GSM1263475
70 GSM1263476.sga ZKY329|H3K36me3|t10 H3K36me3 GSM1263476
71 GSM1263477.sga ZKY329|H3K36me3|t11 H3K36me3 GSM1263477
72 GSM1263478.sga ZKY329|H3K36me3|t12 H3K36me3 GSM1263478
73 GSM1263479.sga ZKY329|H3K36me3|t13 H3K36me3 GSM1263479
74 GSM1263480.sga ZKY329|H3K36me3|t14 H3K36me3 GSM1263480
75 GSM1263481.sga ZKY329|H3K36me3|t15 H3K36me3 GSM1263481
76 GSM1263482.sga ZKY329|H3K36me3|t16 H3K36me3 GSM1263482
77 GSM1263451.sga ZKY329|H3K4me3|t1 H3K4me3 GSM1263451
78 GSM1263452.sga ZKY329|H3K4me3|t2 H3K4me3 GSM1263452
79 GSM1263453.sga ZKY329|H3K4me3|t3 H3K4me3 GSM1263453
80 GSM1263454.sga ZKY329|H3K4me3|t4 H3K4me3 GSM1263454
81 GSM1263455.sga ZKY329|H3K4me3|t5 H3K4me3 GSM1263455
82 GSM1263456.sga ZKY329|H3K4me3|t6 H3K4me3 GSM1263456
83 GSM1263457.sga ZKY329|H3K4me3|t7 H3K4me3 GSM1263457
84 GSM1263458.sga ZKY329|H3K4me3|t8 H3K4me3 GSM1263458
85 GSM1263459.sga ZKY329|H3K4me3|t9 H3K4me3 GSM1263459
86 GSM1263460.sga ZKY329|H3K4me3|t10 H3K4me3 GSM1263460
87 GSM1263461.sga ZKY329|H3K4me3|t11 H3K4me3 GSM1263461
88 GSM1263462.sga ZKY329|H3K4me3|t12 H3K4me3 GSM1263462
89 GSM1263463.sga ZKY329|H3K4me3|t13 H3K4me3 GSM1263463
90 GSM1263464.sga ZKY329|H3K4me3|t14 H3K4me3 GSM1263464
91 GSM1263465.sga ZKY329|H3K4me3|t15 H3K4me3 GSM1263465
92 GSM1263466.sga ZKY329|H3K4me3|t16 H3K4me3 GSM1263466
93 GSM1263403.sga ZKY329|H3K56ac|t1 H3K56ac GSM1263403
94 GSM1263404.sga ZKY329|H3K56ac|t2 H3K56ac GSM1263404
95 GSM1263405.sga ZKY329|H3K56ac|t3 H3K56ac GSM1263405
96 GSM1263406.sga ZKY329|H3K56ac|t4 H3K56ac GSM1263406
97 GSM1263407.sga ZKY329|H3K56ac|t5 H3K56ac GSM1263407
98 GSM1263408.sga ZKY329|H3K56ac|t6 H3K56ac GSM1263408
99 GSM1263409.sga ZKY329|H3K56ac|t7 H3K56ac GSM1263409
100 GSM1263410.sga ZKY329|H3K56ac|t8 H3K56ac GSM1263410
101 GSM1263411.sga ZKY329|H3K56ac|t9 H3K56ac GSM1263411
102 GSM1263412.sga ZKY329|H3K56ac|t10 H3K56ac GSM1263412
103 GSM1263413.sga ZKY329|H3K56ac|t11 H3K56ac GSM1263413
104 GSM1263414.sga ZKY329|H3K56ac|t12 H3K56ac GSM1263414
105 GSM1263415.sga ZKY329|H3K56ac|t13 H3K56ac GSM1263415
106 GSM1263416.sga ZKY329|H3K56ac|t14 H3K56ac GSM1263416
107 GSM1263417.sga ZKY329|H3K56ac|t15 H3K56ac GSM1263417
108 GSM1263418.sga ZKY329|H3K56ac|t16 H3K56ac GSM1263418
109 GSM1263355.sga BY5765|H3K9ac|t1 H3K9ac GSM1263355
110 GSM1263356.sga BY5765|H3K9ac|t2 H3K9ac GSM1263356
111 GSM1263357.sga BY5765|H3K9ac|t3 H3K9ac GSM1263357
112 GSM1263358.sga BY5765|H3K9ac|t4 H3K9ac GSM1263358
113 GSM1263359.sga BY5765|H3K9ac|t5 H3K9ac GSM1263359
114 GSM1263360.sga BY5765|H3K9ac|t6 H3K9ac GSM1263360
115 GSM1263361.sga BY5765|H3K9ac|t7 H3K9ac GSM1263361
116 GSM1263362.sga BY5765|H3K9ac|t8 H3K9ac GSM1263362
117 GSM1263363.sga BY5765|H3K9ac|t9 H3K9ac GSM1263363
118 GSM1263364.sga BY5765|H3K9ac|t10 H3K9ac GSM1263364
119 GSM1263365.sga BY5765|H3K9ac|t11 H3K9ac GSM1263365
120 GSM1263366.sga BY5765|H3K9ac|t12 H3K9ac GSM1263366
121 GSM1263367.sga BY5765|H3K9ac|t13 H3K9ac GSM1263367
122 GSM1263368.sga BY5765|H3K9ac|t14 H3K9ac GSM1263368
123 GSM1263369.sga BY5765|H3K9ac|t15 H3K9ac GSM1263369
124 GSM1263370.sga BY5765|H3K9ac|t16 H3K9ac GSM1263370
125 GSM1263371.sga ZKY329|H3K9ac|t1 H3K9ac GSM1263371
126 GSM1263372.sga ZKY329|H3K9ac|t2 H3K9ac GSM1263372
127 GSM1263373.sga ZKY329|H3K9ac|t3 H3K9ac GSM1263373
128 GSM1263374.sga ZKY329|H3K9ac|t4 H3K9ac GSM1263374
129 GSM1263375.sga ZKY329|H3K9ac|t5 H3K9ac GSM1263375
130 GSM1263376.sga ZKY329|H3K9ac|t6 H3K9ac GSM1263376
131 GSM1263377.sga ZKY329|H3K9ac|t7 H3K9ac GSM1263377
132 GSM1263378.sga ZKY329|H3K9ac|t8 H3K9ac GSM1263378
133 GSM1263379.sga ZKY329|H3K9ac|t9 H3K9ac GSM1263379
134 GSM1263380.sga ZKY329|H3K9ac|t10 H3K9ac GSM1263380
135 GSM1263381.sga ZKY329|H3K9ac|t11 H3K9ac GSM1263381
136 GSM1263382.sga ZKY329|H3K9ac|t12 H3K9ac GSM1263382
137 GSM1263383.sga ZKY329|H3K9ac|t13 H3K9ac GSM1263383
138 GSM1263384.sga ZKY329|H3K9ac|t14 H3K9ac GSM1263384
139 GSM1263385.sga ZKY329|H3K9ac|t15 H3K9ac GSM1263385
140 GSM1263386.sga ZKY329|H3K9ac|t16 H3K9ac GSM1263386
141 GSM1263483.sga ZKY329|H4K16ac|t1 H4K16ac GSM1263483
142 GSM1263484.sga ZKY329|H4K16ac|t2 H4K16ac GSM1263484
143 GSM1263485.sga ZKY329|H4K16ac|t3 H4K16ac GSM1263485
144 GSM1263486.sga ZKY329|H4K16ac|t4 H4K16ac GSM1263486
145 GSM1263487.sga ZKY329|H4K16ac|t5 H4K16ac GSM1263487
146 GSM1263488.sga ZKY329|H4K16ac|t6 H4K16ac GSM1263488
147 GSM1263489.sga ZKY329|H4K16ac|t7 H4K16ac GSM1263489
148 GSM1263490.sga ZKY329|H4K16ac|t8 H4K16ac GSM1263490
149 GSM1263491.sga ZKY329|H4K16ac|t9 H4K16ac GSM1263491
150 GSM1263492.sga ZKY329|H4K16ac|t10 H4K16ac GSM1263492
151 GSM1263493.sga ZKY329|H4K16ac|t11 H4K16ac GSM1263493
152 GSM1263494.sga ZKY329|H4K16ac|t12 H4K16ac GSM1263494
153 GSM1263495.sga ZKY329|H4K16ac|t13 H4K16ac GSM1263495
154 GSM1263496.sga ZKY329|H4K16ac|t14 H4K16ac GSM1263496
155 GSM1263497.sga ZKY329|H4K16ac|t15 H4K16ac GSM1263497
156 GSM1263498.sga ZKY329|H4K16ac|t16 H4K16ac GSM1263498
157 GSM1263419.sga ZKY329|H4K5ac|t1 H4K5ac GSM1263419
158 GSM1263420.sga ZKY329|H4K5ac|t2 H4K5ac GSM1263420
159 GSM1263421.sga ZKY329|H4K5ac|t3 H4K5ac GSM1263421
160 GSM1263422.sga ZKY329|H4K5ac|t4 H4K5ac GSM1263422
161 GSM1263423.sga ZKY329|H4K5ac|t5 H4K5ac GSM1263423
162 GSM1263424.sga ZKY329|H4K5ac|t6 H4K5ac GSM1263424
163 GSM1263425.sga ZKY329|H4K5ac|t7 H4K5ac GSM1263425
164 GSM1263426.sga ZKY329|H4K5ac|t8 H4K5ac GSM1263426
165 GSM1263427.sga ZKY329|H4K5ac|t9 H4K5ac GSM1263427
166 GSM1263428.sga ZKY329|H4K5ac|t10 H4K5ac GSM1263428
167 GSM1263429.sga ZKY329|H4K5ac|t11 H4K5ac GSM1263429
168 GSM1263430.sga ZKY329|H4K5ac|t12 H4K5ac GSM1263430
169 GSM1263431.sga ZKY329|H4K5ac|t13 H4K5ac GSM1263431
170 GSM1263432.sga ZKY329|H4K5ac|t14 H4K5ac GSM1263432
171 GSM1263433.sga ZKY329|H4K5ac|t15 H4K5ac GSM1263433
172 GSM1263434.sga ZKY329|H4K5ac|t16 H4K5ac GSM1263434
173 GSM1263513.sga ZKY428|Set1|t1 HA GSM1263513
174 GSM1263514.sga ZKY428|Set1|t2 HA GSM1263514
175 GSM1263515.sga ZKY428|Set1|t3 HA GSM1263515
176 GSM1263516.sga ZKY428|Set1|t4 HA GSM1263516
177 GSM1263517.sga ZKY428|Set1|t5 HA GSM1263517
178 GSM1263518.sga ZKY428|Set1|t6 HA GSM1263518
179 GSM1263519.sga ZKY428|Set1|t7 HA GSM1263519
180 GSM1263520.sga ZKY428|Set1|t8 HA GSM1263520
181 GSM1263521.sga ZKY428|Set1|t9 HA GSM1263521
182 GSM1263522.sga ZKY428|Set1|t10 HA GSM1263522
183 GSM1263523.sga ZKY428|Set1|t11 HA GSM1263523
184 GSM1263524.sga ZKY428|Set1|t12 HA GSM1263524
185 GSM1263525.sga ZKY428|Set1|t13 HA GSM1263525
186 GSM1263526.sga ZKY428|Set1|t14 HA GSM1263526

Notes on samples nomenclature:

All yeast strains were generated from the previously described strain CEN.PK with the following modifications:

With: MAT[a, alpha] the mating type locus, [X]-FLAG is the flagged version of the relative protein and SET1-3HA is the hemagglutinin version of SET1 both followed by KanMX10 or natMX drug resistance cassettes.

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: 19 Oct 2017