GSE33213, Open Chromatin TFBS by ChIP-seq from ENCODE/Open Chrom(UT Austin).


ChIP-seq data against CTCF, MYC, and PolII transcription factors in different cell types. These data were produced by the UT Austin as part of the ENCODE open chromatin subproject.

The source data were downloaded from ENCODE at UCSC



From H. sapiens (Feb 2009 GRCh37/hg19).

ChIP-seq data:

Filename Description Feature GEO-ID
1 EH000532_rep1.sga GM12878|CTCF||UT-A rep1 CTCF GSM822312
2 EH000532_rep2.sga GM12878|CTCF||UT-A rep2 CTCF GSM822312
3 EH000532_rep3.sga GM12878|CTCF||UT-A rep3 CTCF GSM822312
4 EH000535_rep1.sga K562|CTCF||UT-A rep1 CTCF GSM822311
5 EH000535_rep2.sga K562|CTCF||UT-A rep2 CTCF GSM822311
6 EH000535_rep3.sga K562|CTCF||UT-A rep3 CTCF GSM822311
7 EH000541_rep1.sga HeLa-S3|CTCF||UT-A rep1 CTCF GSM822285
8 EH000541_rep2.sga HeLa-S3|CTCF||UT-A rep2 CTCF GSM822285
9 EH000543_rep1.sga HepG2|CTCF||UT-A rep1 CTCF GSM822287
10 EH000543_rep2.sga HepG2|CTCF||UT-A rep2 CTCF GSM822287
11 EH000551_rep1.sga HUVEC|CTCF||UT-A rep1 CTCF GSM822279
12 EH000551_rep2.sga HUVEC|CTCF||UT-A rep2 CTCF GSM822279
13 EH000559_rep1.sga NHEK|CTCF||UT-A rep1 CTCF GSM822271
14 EH000559_rep2.sga NHEK|CTCF||UT-A rep2 CTCF GSM822271
15 EH000560_rep1.sga H1-hESC|CTCF||UT-A rep1 CTCF GSM822297
16 EH000562_rep1.sga GM12892|CTCF||UT-A rep1 CTCF GSM822299
17 EH000562_rep2.sga GM12892|CTCF||UT-A rep2 CTCF GSM822299
18 EH000569_rep1.sga GM12891|CTCF||UT-A rep1 CTCF GSM822294
19 EH000569_rep2.sga GM12891|CTCF||UT-A rep2 CTCF GSM822294
20 EH000570_rep1.sga GM19238|CTCF||UT-A rep1 CTCF GSM822278
21 EH000570_rep2.sga GM19238|CTCF||UT-A rep2 CTCF GSM822278
22 EH000571_rep1.sga GM19239|CTCF||UT-A rep1 CTCF GSM822277
23 EH000571_rep2.sga GM19239|CTCF||UT-A rep2 CTCF GSM822277
24 EH000572_rep1.sga GM19240|CTCF||UT-A rep1 CTCF GSM822276
25 EH000572_rep2.sga GM19240|CTCF||UT-A rep2 CTCF GSM822276
26 EH000598_rep1.sga MCF-7|CTCF||UT-A rep1 CTCF GSM822305
27 EH000598_rep2.sga MCF-7|CTCF||UT-A rep2 CTCF GSM822305
28 EH000600_rep1.sga ProgFib|CTCF||UT-A rep1 CTCF GSM822272
29 EH000600_rep2.sga ProgFib|CTCF||UT-A rep2 CTCF GSM822272
30 EH001127_rep1.sga Fibrobl|CTCF||UT-A rep1 CTCF GSM822281
31 EH001127_rep2.sga Fibrobl|CTCF||UT-A rep2 CTCF GSM822281
32 EH001131_rep1.sga MCF-7|CTCF|estrogen|UT-A rep1 CTCF GSM822309
33 EH001131_rep2.sga MCF-7|CTCF|estrogen|UT-A rep2 CTCF GSM822309
34 EH001132_rep1.sga MCF-7|CTCF|vehicle|UT-A rep1 CTCF GSM822308
35 EH001132_rep2.sga MCF-7|CTCF|vehicle|UT-A rep2 CTCF GSM822308
36 EH001135_rep1.sga Gliobla|CTCF||UT-A rep1 CTCF GSM822303
37 EH001135_rep2.sga Gliobla|CTCF||UT-A rep2 CTCF GSM822303
38 EH002078_rep1.sga A549|CTCF||UT-A rep1 CTCF GSM822289
39 EH002078_rep2.sga A549|CTCF||UT-A rep2 CTCF GSM822289
40 EH003434_rep1.sga MCF-7|CTCF|serum_stimulated_media|UT-A rep1 CTCF -
41 EH003434_rep2.sga MCF-7|CTCF|serum_stimulated_media|UT-A rep2 CTCF -
42 EH003437_rep1.sga MCF-7|CTCF|serum_starved_media|UT-A rep1 CTCF -
43 EH003437_rep2.sga MCF-7|CTCF|serum_starved_media|UT-A rep2 CTCF -
44 EH003440_rep1.sga Medullo|CTCF|-|UT-A rep1 CTCF -
45 EH003440_rep2.sga Medullo|CTCF|-|UT-A rep2 CTCF -
46 EH003446_rep1.sga GM10248|CTCF|-|UT-A rep1 CTCF -
47 EH003446_rep2.sga GM10248|CTCF|-|UT-A rep2 CTCF -
48 EH003448_rep1.sga GM13976|CTCF|-|UT-A rep1 CTCF -
49 EH003448_rep2.sga GM13976|CTCF|-|UT-A rep2 CTCF -
50 EH003456_rep1.sga GM13977|CTCF|-|UT-A rep1 CTCF -
51 EH003456_rep2.sga GM13977|CTCF|-|UT-A rep2 CTCF -
52 EH003457_rep1.sga GM10266|CTCF|-|UT-A rep1 CTCF -
53 EH003457_rep2.sga GM10266|CTCF|-|UT-A rep2 CTCF -
54 EH003458_rep1.sga GM20000|CTCF|-|UT-A rep1 CTCF -
55 EH003458_rep2.sga GM20000|CTCF|-|UT-A rep2 CTCF -
56 EH003459_rep1.sga LNCaP|CTCF|-|UT-A rep1 CTCF -
57 EH003459_rep2.sga LNCaP|CTCF|-|UT-A rep2 CTCF -
58 EH003460_rep1.sga LNCaP|CTCF|androgen|UT-A rep1 CTCF -
59 EH003460_rep2.sga LNCaP|CTCF|androgen|UT-A rep2 CTCF -
60 EH003461_rep1.sga Kidney_OC|CTCF|-|UT-A rep1 CTCF -
61 EH003461_rep2.sga Kidney_OC|CTCF|-|UT-A rep2 CTCF -
62 EH003461_rep3.sga Kidney_OC|CTCF|-|UT-A rep3 CTCF -
63 EH003462_rep1.sga Lung_OC|CTCF|-|UT-A rep1 CTCF -
64 EH003462_rep2.sga Lung_OC|CTCF|-|UT-A rep2 CTCF -
65 EH003463_rep1.sga Pancreas_OC|CTCF|-|UT-A rep1 CTCF -
66 EH003463_rep2.sga Pancreas_OC|CTCF|-|UT-A rep2 CTCF -
67 EH003464_rep1.sga Spleen_OC|CTCF|-|UT-A rep1 CTCF -
68 EH003464_rep2.sga Spleen_OC|CTCF|-|UT-A rep2 CTCF -
69 EH000528.sga GM12878|Input||UT-A Input GSM822292
70 EH000529.sga K562|Input||UT-A Input GSM822293
71 EH000538.sga HepG2|Input||UT-A Input GSM822314
72 EH000539.sga HeLa-S3|Input||UT-A Input GSM822313
73 EH000550.sga HUVEC|Input||UT-A Input GSM822280
74 EH000589.sga MCF-7|Input||UT-A Input GSM822283
75 EH000593.sga ProgFib|Input||UT-A Input GSM822269
76 EH001128.sga Fibrobl|Input||UT-A Input GSM822267
77 EH001129.sga Gliobla|Input||UT-A Input GSM822268
78 EH001137.sga Monocytes-CD14+_RO01746|Input||UT-A Input GSM822296
79 EH002077.sga A549|Input||UT-A Input GSM822307
80 EH003441.sga Medullo|Input|-|UT-A Input -
81 EH003442.sga GM10248|Input|-|UT-A Input -
82 EH003443.sga GM13976|Input|-|UT-A Input -
83 EH003444.sga GM13977|Input|-|UT-A Input -
84 EH003445.sga Colon_OC|Input|-|UT-A Input -
85 EH003447.sga GM10266|Input|-|UT-A Input -
86 EH003449.sga GM20000|Input|-|UT-A Input -
87 EH003450.sga Heart_OC|Input|-|UT-A Input -
88 EH003451.sga Kidney_OC|Input|-|UT-A Input -
89 EH003452.sga LNCaP|Input|-|UT-A Input -
90 EH003453.sga Lung_OC|Input|-|UT-A Input -
91 EH003454.sga Pancreas_OC|Input|-|UT-A Input -
92 EH003455.sga Spleen_OC|Input|-|UT-A Input -
93 EH000536_rep1.sga K562|MYC||UT-A rep1 MYC GSM822310
94 EH000536_rep2.sga K562|MYC||UT-A rep2 MYC GSM822310
95 EH000536_rep3.sga K562|MYC||UT-A rep3 MYC GSM822310
96 EH000542_rep1.sga HeLa-S3|MYC||UT-A rep1 MYC GSM822286
97 EH000542_rep2.sga HeLa-S3|MYC||UT-A rep2 MYC GSM822286
98 EH000545_rep1.sga HepG2|MYC||UT-A rep1 MYC GSM822291
99 EH000545_rep2.sga HepG2|MYC||UT-A rep2 MYC GSM822291
100 EH000545_rep3.sga HepG2|MYC||UT-A rep3 MYC GSM822291
101 EH000547_rep1.sga GM12878|MYC||UT-A rep1 MYC GSM822290
102 EH000547_rep2.sga GM12878|MYC||UT-A rep2 MYC GSM822290
103 EH000561_rep1.sga HUVEC|MYC||UT-A rep1 MYC GSM822298
104 EH000596_rep1.sga H1-hESC|MYC||UT-A rep1 MYC GSM822274
105 EH001133_rep1.sga MCF-7|MYC|vehicle|UT-A rep1 MYC GSM822301
106 EH001133_rep2.sga MCF-7|MYC|vehicle|UT-A rep2 MYC GSM822301
107 EH001134_rep1.sga MCF-7|MYC|estrogen|UT-A rep1 MYC GSM822304
108 EH001134_rep2.sga MCF-7|MYC|estrogen|UT-A rep2 MYC GSM822304
109 EH003436_rep1.sga MCF-7|MYC|serum_stimulated_media|UT-A rep1 MYC -
110 EH003436_rep2.sga MCF-7|MYC|serum_stimulated_media|UT-A rep2 MYC -
111 EH003439_rep1.sga MCF-7|MYC|serum_starved_media|UT-A rep1 MYC -
112 EH003439_rep2.sga MCF-7|MYC|serum_starved_media|UT-A rep2 MYC -
113 EH000552_rep1.sga HUVEC|PolII||UT-A rep1 PolII GSM822306
114 EH000552_rep2.sga HUVEC|PolII||UT-A rep2 PolII GSM822306
115 EH000554_rep1.sga HepG2|PolII||UT-A rep1 PolII GSM822284
116 EH000554_rep2.sga HepG2|PolII||UT-A rep2 PolII GSM822284
117 EH000554_rep3.sga HepG2|PolII||UT-A rep3 PolII GSM822284
118 EH000555_rep1.sga K562|PolII||UT-A rep1 PolII GSM822275
119 EH000555_rep2.sga K562|PolII||UT-A rep2 PolII GSM822275
120 EH000563_rep1.sga H1-hESC|PolII||UT-A rep1 PolII GSM822300
121 EH000592_rep1.sga GM12878|PolII||UT-A rep1 PolII GSM822270
122 EH000592_rep2.sga GM12878|PolII||UT-A rep2 PolII GSM822270
123 EH000597_rep1.sga HeLa-S3|PolII||UT-A rep1 PolII GSM822273
124 EH000597_rep2.sga HeLa-S3|PolII||UT-A rep2 PolII GSM822273
125 EH000606_rep1.sga ProgFib|PolII||UT-A rep1 PolII GSM822282
126 EH000606_rep2.sga ProgFib|PolII||UT-A rep2 PolII GSM822282
127 EH001130_rep1.sga MCF-7|PolII||UT-A rep1 PolII GSM822295
128 EH001130_rep2.sga MCF-7|PolII||UT-A rep2 PolII GSM822295
129 EH001136_rep1.sga Gliobla|PolII||UT-A rep1 PolII GSM822302
130 EH001136_rep2.sga Gliobla|PolII||UT-A rep2 PolII GSM822302
131 EH002079_rep1.sga A549|PolII||UT-A rep1 PolII GSM822288
132 EH002079_rep2.sga A549|PolII||UT-A rep2 PolII GSM822288
133 EH003435_rep1.sga MCF-7|PolII|serum_stimulated_media|UT-A rep1 PolII -
134 EH003435_rep2.sga MCF-7|PolII|serum_stimulated_media|UT-A rep2 PolII -
135 EH003438_rep1.sga MCF-7|PolII|serum_starved_media|UT-A rep1 PolII -
136 EH003438_rep2.sga MCF-7|PolII|serum_starved_media|UT-A rep2 PolII -

ChIP-seq peaks files:

Filename Description Feature GEO-ID
1 EH000532_narrowPeak.sga GM12878|CTCF narrowPeak||UT-A CTCF_P GSM822312
2 EH000535_narrowPeak.sga K562|CTCF narrowPeak||UT-A CTCF_P GSM822311
3 EH000541_narrowPeak.sga HeLa-S3|CTCF narrowPeak||UT-A CTCF_P GSM822285
4 EH000543_narrowPeak.sga HepG2|CTCF narrowPeak||UT-A CTCF_P GSM822287
5 EH000551_narrowPeak.sga HUVEC|CTCF narrowPeak||UT-A CTCF_P GSM822279
6 EH000559_narrowPeak.sga NHEK|CTCF narrowPeak||UT-A CTCF_P GSM822271
7 EH000560_narrowPeak.sga H1-hESC|CTCF narrowPeak||UT-A CTCF_P GSM822297
8 EH000562_narrowPeak.sga GM12892|CTCF narrowPeak||UT-A CTCF_P GSM822299
9 EH000569_narrowPeak.sga GM12891|CTCF narrowPeak||UT-A CTCF_P GSM822294
10 EH000570_narrowPeak.sga GM19238|CTCF narrowPeak||UT-A CTCF_P GSM822278
11 EH000571_narrowPeak.sga GM19239|CTCF narrowPeak||UT-A CTCF_P GSM822277
12 EH000572_narrowPeak.sga GM19240|CTCF narrowPeak||UT-A CTCF_P GSM822276
13 EH000598_narrowPeak.sga MCF-7|CTCF narrowPeak||UT-A CTCF_P GSM822305
14 EH000600_narrowPeak_rep1.sga ProgFib|CTCF narrowPeak||UT-A rep1 CTCF_P GSM822272
15 EH001127_narrowPeak.sga Fibrobl|CTCF narrowPeak||UT-A CTCF_P GSM822281
16 EH001131_narrowPeak.sga MCF-7|CTCF narrowPeak|estrogen|UT-A CTCF_P GSM822309
17 EH001132_narrowPeak.sga MCF-7|CTCF narrowPeak|vehicle|UT-A CTCF_P GSM822308
18 EH001135_narrowPeak.sga Gliobla|CTCF narrowPeak||UT-A CTCF_P GSM822303
19 EH002078_narrowPeak_rep1.sga A549|CTCF narrowPeak||UT-A rep1 CTCF_P GSM822289
20 EH003434_narrowPeak_rep1.sga MCF-7|CTCF narrowPeak|serum_stimulated_media|UT-A rep1 CTCF_P GSM1006875
21 EH003437_narrowPeak_rep1.sga MCF-7|CTCF narrowPeak|serum_starved_media|UT-A rep1 CTCF_P GSM1006878
22 EH003440_narrowPeak_rep1.sga Medullo|CTCF narrowPeak|-|UT-A rep1 CTCF_P GSM1006893
23 EH003446_narrowPeak_rep1.sga GM10248|CTCF narrowPeak|-|UT-A rep1 CTCF_P GSM1006891
24 EH003448_narrowPeak_rep1.sga GM13976|CTCF narrowPeak|-|UT-A rep1 CTCF_P GSM1006885
25 EH003456_narrowPeak_rep1.sga GM13977|CTCF narrowPeak|-|UT-A rep1 CTCF_P GSM1006869
26 EH003457_narrowPeak_rep1.sga GM10266|CTCF narrowPeak|-|UT-A rep1 CTCF_P GSM1006870
27 EH003458_narrowPeak_rep1.sga GM20000|CTCF narrowPeak|-|UT-A rep1 CTCF_P GSM1006873
28 EH003459_narrowPeak_rep1.sga LNCaP|CTCF narrowPeak|-|UT-A rep1 CTCF_P GSM1006874
29 EH003460_narrowPeak_rep1.sga LNCaP|CTCF narrowPeak|androgen|UT-A rep1 CTCF_P GSM1006887
30 EH003461_narrowPeak_rep1.sga Kidney_OC|CTCF narrowPeak|-|UT-A rep1 CTCF_P GSM1006886
31 EH003462_narrowPeak_rep1.sga Lung_OC|CTCF narrowPeak|-|UT-A rep1 CTCF_P GSM1006882
32 EH003463_narrowPeak_rep1.sga Pancreas_OC|CTCF narrowPeak|-|UT-A rep1 CTCF_P GSM1006881
33 EH003464_narrowPeak_rep1.sga Spleen_OC|CTCF narrowPeak|-|UT-A rep1 CTCF_P GSM1006883
34 EH000536_narrowPeak.sga K562|MYC narrowPeak||UT-A MYC_P GSM822310
35 EH000542_narrowPeak.sga HeLa-S3|MYC narrowPeak||UT-A MYC_P GSM822286
36 EH000545_narrowPeak.sga HepG2|MYC narrowPeak||UT-A MYC_P GSM822291
37 EH000547_narrowPeak.sga GM12878|MYC narrowPeak||UT-A MYC_P GSM822290
38 EH000561_narrowPeak.sga HUVEC|MYC narrowPeak||UT-A MYC_P GSM822298
39 EH000596_narrowPeak.sga H1-hESC|MYC narrowPeak||UT-A MYC_P GSM822274
40 EH001133_narrowPeak.sga MCF-7|MYC narrowPeak|vehicle|UT-A MYC_P GSM822301
41 EH001134_narrowPeak_rep1.sga MCF-7|MYC narrowPeak|estrogen|UT-A rep1 MYC_P GSM822304
42 EH003436_narrowPeak_rep1.sga MCF-7|MYC narrowPeak|serum_stimulated_media|UT-A rep1 MYC_P GSM1006877
43 EH003439_narrowPeak_rep1.sga MCF-7|MYC narrowPeak|serum_starved_media|UT-A rep1 MYC_P GSM1006866
44 EH000552_narrowPeak.sga HUVEC|PolII narrowPeak||UT-A PolII_P GSM822306
45 EH000554_narrowPeak.sga HepG2|PolII narrowPeak||UT-A PolII_P GSM822284
46 EH000555_narrowPeak.sga K562|PolII narrowPeak||UT-A PolII_P GSM822275
47 EH000563_narrowPeak.sga H1-hESC|PolII narrowPeak||UT-A PolII_P GSM822300
48 EH000592_narrowPeak.sga GM12878|PolII narrowPeak||UT-A PolII_P GSM822270
49 EH000597_narrowPeak.sga HeLa-S3|PolII narrowPeak||UT-A PolII_P GSM822273
50 EH000606_narrowPeak_rep1.sga ProgFib|PolII narrowPeak||UT-A rep1 PolII_P GSM822282
51 EH001130_narrowPeak.sga MCF-7|PolII narrowPeak||UT-A PolII_P GSM822295
52 EH001136_narrowPeak.sga Gliobla|PolII narrowPeak||UT-A PolII_P GSM822302
53 EH002079_narrowPeak_rep1.sga A549|PolII narrowPeak||UT-A rep1 PolII_P GSM822288
54 EH003435_narrowPeak_rep1.sga MCF-7|PolII narrowPeak|serum_stimulated_media|UT-A rep1 PolII_P GSM1006876
55 EH003438_narrowPeak_rep1.sga MCF-7|PolII narrowPeak|serum_starved_media|UT-A rep1 PolII_P GSM1006865

Notes on samples nomenclature: Notes on samples nomenclature:

All sample information was derived from a file named "files.txt" downloaded from the above-indicated URL. This file contains a list of filenames long with annotation (metadata). The sample descriptions provided here include cell type, ChIP-seq target (transcription factor), treatment and replicate. Cell types and treatments were transferred from ENCODE annotation as such. Some of the original ChIP-seq target names were modified in order to conform to the naming conventions of the MGA repository. In general, transcription factors are identified by the HGNC gene symbol of the targeted protein, with the following exception:

The sample descriptions provided here were required to be unique across all ENCODE data series of the MGA repository. For this reason, the name of the data contributing lab is always indicated in the replicate field. extracted from the ENCODE annotation file. This identifier makes it possible to match a data file from this series to the corresponding peak list in hg19/encode/Uniform_TFBS.

More information about cell lines, antibodies, treatments, protocols, etc. can be found at

Optional fields in SGA files:

The peak files contain in the optional sixth field a positive real number reflecting the overall enrichment of the ChIP-seq signal in the peak region.

Technical Notes

Files with a non-empty objectStatus in the file list provided by UCSC were not considered. BAM files were converted into BED using bamToBed (bedtools v2.27.0) and subsequently converted into SGA using bed2sga ( ChIP-Seq v. 1.5.3). Peak files in narrowPeak format were converted into SGA using bed2sga with options --narrowPeak -e 7.