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GEO accession:
Sample GSM30788
Query DataSets for GSM30788
Status
Public on Sep 21, 2004
Title
ENCODE: RNA PolII-THP1 Rep2
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 THP1 cells. Replicate 2 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
0.3895673
0.1427
0.143176
532
406.66
603
658
311
70
88
72
463
471
169
176
184
79
0
1.31
0.3895673
2
0.2387873
0.0926
0.244493
674
570.19
744
779
315
69
105
263
588
616
185
187
291
2059
0
1.18
0.2387873
3
0.2868813
0.1131
0.199165
1457
1194.16
1530
1525
484
72
90
72
1015
1000
240
179
182
49
0
1.22
0.2868813
4
0.4956953
0.1875
0.080660
906
641.91
981
984
425
74
94
77
632
621
165
181
184
50
0
1.41
0.4956953
5
0.3561443
0.1349
0.156875
716
560.14
791
820
349
74
90
68
577
570
153
183
185
49
0
1.28
0.3561443
6
0.5058913
0.1910
0.076807
713
502.77
790
821
304
76
93
73
535
548
150
181
183
49
0
1.42
0.5058913
7
0.4750853
0.1730
0.098213
330
237.40
401
421
201
70
89
69
348
358
91
179
182
49
0
1.39
0.4750853
8
0.2387873
0.0946
0.239940
853
720.80
920
914
362
66
88
72
686
687
162
180
182
47
0
1.18
0.2387873
9
0.2868813
0.1014
0.224403
268
220.18
336
355
205
67
91
74
342
345
84
185
185
48
0
1.22
0.2868813
10
0.4436073
0.1621
0.113045
228
167.11
295
284
143
66
89
74
306
299
75
186
188
47
0
1.36
0.4436073
11
0.0426443
0.0155
0.453985
299
290.47
373
385
211
73
92
72
384
386
94
178
182
47
0
1.03
0.0426443
12
0.2387873
0.0952
0.238562
1108
938.83
1182
1192
311
73
91
70
843
835
157
185
188
50
0
1.18
0.2387873
13
0.2265093
0.0877
0.256239
570
486.99
642
643
267
71
91
73
528
530
124
185
188
49
0
1.17
0.2265093
14
0.5160153
0.1902
0.077771
770
540.06
847
873
399
76
93
70
563
554
171
183
184
48
0
1.43
0.5160153
15
0.3103403
0.1134
0.198416
347
279.00
425
449
255
77
93
71
382
375
94
184
189
58
0
1.24
0.3103403
16
0.3673713
0.1359
0.154976
407
314.86
483
503
252
75
94
73
414
420
121
191
192
48
0
1.29
0.3673713
17
0.0426443
0.0137
0.459223
458
446.82
525
564
246
66
87
70
505
510
120
190
191
50
0
1.03
0.0426443
18
0.2630343
0.0935
0.242452
240
200.10
312
357
184
71
88
70
325
334
87
182
185
47
0
1.20
0.2630343
19
0.2750073
0.1090
0.207748
1206
996.21
1278
1322
391
71
93
79
879
871
163
181
188
57
0
1.21
0.2750073
20
0.2509623
0.0967
0.235124
547
458.30
622
675
299
74
93
73
510
503
138
187
188
49
0
1.19
0.2509623
Total number of rows:
25392
Table truncated, full table size
2594 Kbytes
.
Supplementary file
Size
Download
File type/resource
GSM30788.tif.gz
110.9 Mb
(ftp)
(http)
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