Zentner 2015, ChEC-seq of Abf1, Rap1 and Reb1.

Description of a novel technique (ChEC-seq) for the analysis of protein-DNA complexes. This technique uses MNase enzyme (fused to the target protein of interest, as a TF) to digest DNA in the neighbouring genomic region. It is then followed by paired-end sequences. Several MNase incubation times are tested as well as controls (FLAG and no calcium) and comparison with standard ChIP-seq echnique.

• Raw data was downloaded from: GEO
• Input file format: BED
• Download date: 24-11-2017

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

	Filename	Description	Feature	GEO-ID
1	GSM1647289_noPaired.sga	W1588-4C|FLAG|no calcium cuts|	FLAG	GSM1647289
2	GSM1647289.sga	W1588-4C|FLAG|no calcium center|	FLAG	GSM1647289
3	GSM1647290_noPaired.sga	W1588-4C|FLAG|10s cuts|	FLAG	GSM1647290
4	GSM1647290.sga	W1588-4C|FLAG|10s center|	FLAG	GSM1647290
5	GSM1647291_noPaired.sga	W1588-4C|FLAG|20m cuts|	FLAG	GSM1647291
6	GSM1647291.sga	W1588-4C|FLAG|20m center|	FLAG	GSM1647291
7	GSM1647292_noPaired.sga	W1588-4C|FLAG|20s cuts|	FLAG	GSM1647292
8	GSM1647292.sga	W1588-4C|FLAG|20s center|	FLAG	GSM1647292
9	GSM1647293_noPaired.sga	W1588-4C|FLAG|30s cuts|	FLAG	GSM1647293
10	GSM1647293.sga	W1588-4C|FLAG|30s center|	FLAG	GSM1647293
11	GSM1647294_noPaired.sga	W1588-4C|FLAG|40s cuts|	FLAG	GSM1647294
12	GSM1647294.sga	W1588-4C|FLAG|40s center|	FLAG	GSM1647294
13	GSM1647295_noPaired.sga	W1588-4C|FLAG|50s cuts|	FLAG	GSM1647295
14	GSM1647295.sga	W1588-4C|FLAG|50s center|	FLAG	GSM1647295
15	GSM1647296_noPaired.sga	W1588-4C|FLAG|60s cuts|	FLAG	GSM1647296
16	GSM1647296.sga	W1588-4C|FLAG|60s center|	FLAG	GSM1647296
17	GSM1647297_noPaired.sga	W1588-4C|FLAG|2.5m cuts|	FLAG	GSM1647297
18	GSM1647297.sga	W1588-4C|FLAG|2.5m center|	FLAG	GSM1647297
19	GSM1647298_noPaired.sga	W1588-4C|FLAG|5m cuts|	FLAG	GSM1647298
20	GSM1647298.sga	W1588-4C|FLAG|5m center|	FLAG	GSM1647298
21	GSM1647299_noPaired.sga	W1588-4C|FLAG|10m cuts|	FLAG	GSM1647299
22	GSM1647299.sga	W1588-4C|FLAG|10m center|	FLAG	GSM1647299
23	GSM1647300_noPaired.sga	W1588-4C|Abf1|no calcium cuts|	Abf1	GSM1647300
24	GSM1647300.sga	W1588-4C|Abf1|no calcium center|	Abf1	GSM1647300
25	GSM1647301_noPaired.sga	W1588-4C|Abf1|10s cuts|	Abf1	GSM1647301
26	GSM1647301.sga	W1588-4C|Abf1|10s center|	Abf1	GSM1647301
27	GSM1647302_noPaired.sga	W1588-4C|Abf1|20s cuts|	Abf1	GSM1647302
28	GSM1647302.sga	W1588-4C|Abf1|20s center|	Abf1	GSM1647302
29	GSM1647303_noPaired.sga	W1588-4C|Abf1|30s cuts|Rep 1	Abf1	GSM1647303
30	GSM1647303.sga	W1588-4C|Abf1|30s center|Rep 1	Abf1	GSM1647303
31	GSM1647304_noPaired.sga	W1588-4C|Abf1|30s cuts|Rep 2	Abf1	GSM1647304
32	GSM1647304.sga	W1588-4C|Abf1|30s center|Rep 2	Abf1	GSM1647304
33	GSM1647305_noPaired.sga	W1588-4C|Abf1|30s cuts|Rep 3	Abf1	GSM1647305
34	GSM1647305.sga	W1588-4C|Abf1|30s center|Rep 3	Abf1	GSM1647305
35	GSM1647306_noPaired.sga	W1588-4C|Abf1|40s cuts|	Abf1	GSM1647306
36	GSM1647306.sga	W1588-4C|Abf1|40s center|	Abf1	GSM1647306
37	GSM1647307_noPaired.sga	W1588-4C|Abf1|50s cuts|	Abf1	GSM1647307
38	GSM1647307.sga	W1588-4C|Abf1|50s center|	Abf1	GSM1647307
39	GSM1647308_noPaired.sga	W1588-4C|Abf1|60s cuts|	Abf1	GSM1647308
40	GSM1647308.sga	W1588-4C|Abf1|60s center|	Abf1	GSM1647308
41	GSM1647309_noPaired.sga	W1588-4C|Abf1|2.5m cuts|	Abf1	GSM1647309
42	GSM1647309.sga	W1588-4C|Abf1|2.5m center|	Abf1	GSM1647309
43	GSM1647310_noPaired.sga	W1588-4C|Abf1|5m cuts|	Abf1	GSM1647310
44	GSM1647310.sga	W1588-4C|Abf1|5m center|	Abf1	GSM1647310
45	GSM1647311_noPaired.sga	W1588-4C|Abf1|10m cuts|	Abf1	GSM1647311
46	GSM1647311.sga	W1588-4C|Abf1|10m center|	Abf1	GSM1647311
47	GSM1647312_noPaired.sga	W1588-4C|Abf1|20m cuts|	Abf1	GSM1647312
48	GSM1647312.sga	W1588-4C|Abf1|20m center|	Abf1	GSM1647312
49	GSM1647313_noPaired.sga	W1588-4C|Abf1|short linker cuts|	Abf1	GSM1647313
50	GSM1647313.sga	W1588-4C|Abf1|short linker center|	Abf1	GSM1647313
51	GSM1647314_noPaired.sga	W1588-4C|Abf1|short linker cuts|	Abf1	GSM1647314
52	GSM1647314.sga	W1588-4C|Abf1|short linker center|	Abf1	GSM1647314
53	GSM1647315_noPaired.sga	W1588-4C|Rap1|no calcium cuts|	Rap1	GSM1647315
54	GSM1647315.sga	W1588-4C|Rap1|no calcium center|	Rap1	GSM1647315
55	GSM1647316_noPaired.sga	W1588-4C|Rap1|10s cuts|	Rap1	GSM1647316
56	GSM1647316.sga	W1588-4C|Rap1|10s center|	Rap1	GSM1647316
57	GSM1647317_noPaired.sga	W1588-4C|Rap1|20s cuts|	Rap1	GSM1647317
58	GSM1647317.sga	W1588-4C|Rap1|20s center|	Rap1	GSM1647317
59	GSM1647318_noPaired.sga	W1588-4C|Rap1|30s cuts|Rep 1	Rap1	GSM1647318
60	GSM1647318.sga	W1588-4C|Rap1|30s center|Rep 1	Rap1	GSM1647318
61	GSM1647319_noPaired.sga	W1588-4C|Rap1|30s cuts|Rep 2	Rap1	GSM1647319
62	GSM1647319.sga	W1588-4C|Rap1|30s center|Rep 2	Rap1	GSM1647319
63	GSM1647320_noPaired.sga	W1588-4C|Rap1|30s cuts|Rep 3	Rap1	GSM1647320
64	GSM1647320.sga	W1588-4C|Rap1|30s center|Rep 3	Rap1	GSM1647320
65	GSM1647321_noPaired.sga	W1588-4C|Rap1|40s cuts|	Rap1	GSM1647321
66	GSM1647321.sga	W1588-4C|Rap1|40s center|	Rap1	GSM1647321
67	GSM1647322_noPaired.sga	W1588-4C|Rap1|50s cuts|	Rap1	GSM1647322
68	GSM1647322.sga	W1588-4C|Rap1|50s center|	Rap1	GSM1647322
69	GSM1647323_noPaired.sga	W1588-4C|Rap1|60s cuts|	Rap1	GSM1647323
70	GSM1647323.sga	W1588-4C|Rap1|60s center|	Rap1	GSM1647323
71	GSM1647324_noPaired.sga	W1588-4C|Rap1|2.5m cuts|	Rap1	GSM1647324
72	GSM1647324.sga	W1588-4C|Rap1|2.5m center|	Rap1	GSM1647324
73	GSM1647325_noPaired.sga	W1588-4C|Rap1|5m cuts|	Rap1	GSM1647325
74	GSM1647325.sga	W1588-4C|Rap1|5m center|	Rap1	GSM1647325
75	GSM1647326_noPaired.sga	W1588-4C|Rap1|10m cuts|	Rap1	GSM1647326
76	GSM1647326.sga	W1588-4C|Rap1|10m center|	Rap1	GSM1647326
77	GSM1647327_noPaired.sga	W1588-4C|Rap1|20m cuts|	Rap1	GSM1647327
78	GSM1647327.sga	W1588-4C|Rap1|20m center|	Rap1	GSM1647327
79	GSM1647328_noPaired.sga	W1588-4C|Reb1|no cuts|Rep calcium	Reb1	GSM1647328
80	GSM1647328.sga	W1588-4C|Reb1|no center|Rep calcium	Reb1	GSM1647328
81	GSM1647329_noPaired.sga	W1588-4C|Reb1|10s cuts|	Reb1	GSM1647329
82	GSM1647329.sga	W1588-4C|Reb1|10s center|	Reb1	GSM1647329
83	GSM1647330_noPaired.sga	W1588-4C|Reb1|20s cuts|	Reb1	GSM1647330
84	GSM1647330.sga	W1588-4C|Reb1|20s center|	Reb1	GSM1647330
85	GSM1647331_noPaired.sga	W1588-4C|Reb1|30s cuts|Rep 1	Reb1	GSM1647331
86	GSM1647331.sga	W1588-4C|Reb1|30s center|Rep 1	Reb1	GSM1647331
87	GSM1647332_noPaired.sga	W1588-4C|Reb1|30s cuts|Rep 2	Reb1	GSM1647332
88	GSM1647332.sga	W1588-4C|Reb1|30s center|Rep 2	Reb1	GSM1647332
89	GSM1647333_noPaired.sga	W1588-4C|Reb1|30s cuts|Rep 3	Reb1	GSM1647333
90	GSM1647333.sga	W1588-4C|Reb1|30s center|Rep 3	Reb1	GSM1647333
91	GSM1647334_noPaired.sga	W1588-4C|Reb1|40s cuts|	Reb1	GSM1647334
92	GSM1647334.sga	W1588-4C|Reb1|40s center|	Reb1	GSM1647334
93	GSM1647335_noPaired.sga	W1588-4C|Reb1|50s cuts|	Reb1	GSM1647335
94	GSM1647335.sga	W1588-4C|Reb1|50s center|	Reb1	GSM1647335
95	GSM1647336_noPaired.sga	W1588-4C|Reb1|60s cuts|	Reb1	GSM1647336
96	GSM1647336.sga	W1588-4C|Reb1|60s center|	Reb1	GSM1647336
97	GSM1647337_noPaired.sga	W1588-4C|Reb1|2.5m cuts|	Reb1	GSM1647337
98	GSM1647337.sga	W1588-4C|Reb1|2.5m center|	Reb1	GSM1647337
99	GSM1647338_noPaired.sga	W1588-4C|Reb1|5m cuts|	Reb1	GSM1647338
100	GSM1647338.sga	W1588-4C|Reb1|5m center|	Reb1	GSM1647338
101	GSM1647339_noPaired.sga	W1588-4C|Reb1|10m cuts|	Reb1	GSM1647339
102	GSM1647339.sga	W1588-4C|Reb1|10m center|	Reb1	GSM1647339
103	GSM1647340_noPaired.sga	W1588-4C|Reb1|20m cuts|	Reb1	GSM1647340
104	GSM1647340.sga	W1588-4C|Reb1|20m center|	Reb1	GSM1647340
105	GSM1647341_noPaired.sga	W1588-4C|Reb1|short linker cuts|	Reb1	GSM1647341
106	GSM1647341.sga	W1588-4C|Reb1|short linker center|	Reb1	GSM1647341
107	GSM1647342_noPaired.sga	W1588-4C|Reb1|short linker cuts|	Reb1	GSM1647342
108	GSM1647342.sga	W1588-4C|Reb1|short linker center|	Reb1	GSM1647342
109	GSM1647343_noPaired.sga	W1588-4C|Reb1|N terminal cuts|	Reb1	GSM1647343
110	GSM1647343.sga	W1588-4C|Reb1|N terminal center|	Reb1	GSM1647343
111	GSM1647344_noPaired.sga	W1588-4C|Reb1|N terminal cuts|	Reb1	GSM1647344
112	GSM1647344.sga	W1588-4C|Reb1|N terminal center|	Reb1	GSM1647344
113	GSM1647345_noPaired.sga	W1588-4C|Abf1|ChIP_seq|	Abf1	GSM1647345
114	GSM1647345.sga	W1588-4C|Abf1|ChIP-seq|	Abf1	GSM1647345

Notes on samples nomenclature:

Samples marked as 'cuts' store MNase cutting sites and are treated as non paired.
Samples marked as 'center' instead store the central position of the sequenced fragment.

BED to SGA conversion was carried out using bed2sga.pl (ChIP-Seq v. 1.5.3).

• Zentner GE, Kasinathan S, Xin B, Rohs R, Henikoff S
  ChEC-seq kinetics discriminates transcription factor binding sites by DNA sequence and shape in vivo. Nat Commun. 2015 Oct 22;6:8733. doi: 10.1038/ncomms9733. 26490019
• GEO series GSE67453: ChEC-seq kinetics discriminates transcription factor binding sites by DNA sequence and shape in vivo