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

• Raw data was downloaded from: http://hgdownload.soe.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/
• Input file format: BAM, BED (narrowPeak
• Download date: 17-10-2018

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:

• PolII: any subunit of the RNA polymerase II

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 https://genome.ucsc.edu/encode/otherTerms.html.

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.

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.

• ENCODE Project Consortium
  An integrated encyclopedia of DNA elements in the human genome. Nature. 2012 Sep 6;489(7414):57-74. doi: 10.1038/nature11247. 22955616
• GEO series GSE33213: Open Chromatin TFBS by ChIP-seq from ENCODE/Open Chrom(UT Austin)