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GEO accession:
Sample GSM30781
Query DataSets for GSM30781
Status
Public on Sep 21, 2004
Title
ENCODE: RNA PolII-HCT116 Rep1
Sample type
genomic
Channel 1
Source name
Chromatin immunoprecipitated DNA using RNA polymerase II antibody
Organism
Homo sapiens
Extracted molecule
genomic DNA
Channel 2
Source name
input DNA
Organism
Homo sapiens
Extracted molecule
genomic DNA
Description
Genome-wide location analysis of RNA polymerase II binding at ENCODE regions in HCT116 cells. Replicate 1 of 3.
Submission date
Sep 17, 2004
Last update date
Nov 22, 2005
Contact name
Chunxu Qu
E-mail(s)
qchunxu@ucsd.edu
Phone
(858)822-5767
Organization name
Ludwig Institute for Cancer Research
Department
Gene Regulation
Lab
RenLab
Street address
City
San Diego
State/province
CA
ZIP/Postal code
92093
Country
USA
Platform ID
GPL1454
Series (1)
GSE1778
ENCODE: GWLA of TAF1, RNA PolII binding in four cell lines
Data table header descriptions
ID_REF
VALUE
same as UNF_VALUE but with flagged values removed
SIGNIFICANCE
significance
P-VAL
p-value calculated using single array error model
F635_INT
F635 intensity with background intensity subtracted
F532_INT
F532 intensity with background intensity subtracted
F635_MEDIAN
F635 mdian intensity
F635_MEAN
F635 mean intensity
F635_SD
F635 standard deviation
B635_MEDIAN
B635 median intensity
B635_MEAN
B635 mean intensity
B635_SD
B635 standard deviation
F532_MEDIAN
F532 median intensity
F532_MEAN
F532 mean intensity
F532_SD
F532 standard deviation
B532_MEDIAN
B532 median intensity
B532_MEAN
B532 mean intensity
B532_SD
B532 standard deviation
FLAG
flag from GenePro, 0 is useful
PRE_VALUE
enrichment value (F635/F532)
UNF_VALUE
log ratio (log2 of PRE_VALUE)
Data table
ID_REF
VALUE
SIGNIFICANCE
P-VAL
F635_INT
F532_INT
F635_MEDIAN
F635_MEAN
F635_SD
B635_MEDIAN
B635_MEAN
B635_SD
F532_MEDIAN
F532_MEAN
F532_SD
B532_MEDIAN
B532_MEAN
B532_SD
FLAG
PRE_VALUE
UNF_VALUE
1
0.5260693
0.2020
0.096377
1084.5
752.67
1181
1183
315
96
114
79
1068
1013
300
130
131
27
0
1.44
0.5260693
2
0.5459683
0.2130
0.084831
1481.5
1011.61
1565
1533
356
83
96
68
1386
1303
327
126
128
30
0
1.46
0.5459683
3
0.2141253
0.0842
0.293583
2263.5
1951.65
2366
2292
559
102
119
83
2558
2478
736
129
131
28
0
1.16
0.2141253
4
0.5058913
0.1972
0.101744
1607.5
1133.84
1710
1708
354
102
134
124
1540
1587
266
128
161
296
0
1.42
0.5058913
5
0.6135323
0.2369
0.063282
1403.5
915.11
1488
1576
353
84
105
77
1267
1341
286
127
130
28
0
1.53
0.6135323
6
0.5160153
0.1974
0.101542
1426.5
995.52
1511
1558
457
84
99
64
1364
1245
448
124
126
28
0
1.43
0.5160153
7
0.6690273
0.2449
0.057180
757.5
476.05
850
873
368
92
107
72
721
703
182
127
127
29
0
1.59
0.6690273
8
-0.5994623
-0.2295
0.930506
849.5
1289.04
952
1034
342
102
117
83
1730
1685
347
125
127
29
0
0.66
-0.5994623
9
0.1110313
0.0424
0.392299
410.5
379.55
494
485
218
83
102
75
599
590
188
125
127
39
0
1.08
0.1110313
10
1.0071963
0.3360
0.015138
414.5
205.86
511
492
252
96
114
81
381
378
117
123
124
28
0
2.01
1.0071963
11
0.3448283
0.1325
0.196429
588.5
464.79
683
696
230
94
110
75
706
699
94
126
127
30
0
1.27
0.3448283
12
-0.4150373
-0.1450
0.825036
232.5
310.40
338
342
176
105
123
90
497
516
203
109
111
48
0
0.75
-0.4150373
13
0.2265093
0.0878
0.285586
1180.5
1012.41
1271
1302
333
90
106
67
1368
1331
263
107
110
36
0
1.17
0.2265093
14
0.5459683
0.2046
0.093561
1296.5
885.36
1397
1202
477
100
114
69
1228
1169
512
125
127
27
0
1.46
0.5459683
15
0.8073553
0.2951
0.028538
923.5
529.12
1022
1064
318
98
116
80
793
738
232
133
133
31
0
1.75
0.8073553
16
0.3334243
0.1312
0.198830
976.5
773.58
1062
1116
307
85
108
72
1094
1072
253
130
131
31
0
1.26
0.3334243
17
-0.1520033
-0.0606
0.651987
840.5
934.41
946
944
319
105
125
87
1293
1304
161
129
132
27
0
0.90
-0.1520033
18
0.8237493
0.2962
0.028088
693.5
391.62
792
775
294
98
117
82
617
632
198
128
131
27
0
1.77
0.8237493
19
0.4750853
0.1808
0.121812
2724.5
1964.51
2826
2678
849
101
117
80
2574
2405
835
129
130
29
0
1.39
0.4750853
20
0.4956953
0.1932
0.106387
1592.5
1132.23
1684
1658
344
91
110
77
1538
1527
240
128
129
27
0
1.41
0.4956953
Total number of rows:
25392
Table truncated, full table size
2724 Kbytes
.
Supplementary file
Size
Download
File type/resource
GSM30781_cy3.tif.gz
13.0 Mb
(ftp)
(http)
TIFF
GSM30781_cy5.tif.gz
14.5 Mb
(ftp)
(http)
TIFF
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