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

Description

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.

Source

Samples

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.

Technical Notes

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

References

Last update: 11 Dec 2017