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GEO accession:
Sample GSM30785
Query DataSets for GSM30785
Status
Public on Sep 21, 2004
Title
ENCODE: RNA PolII-HeLa 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 HeLa 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
0.7484613
0.2726
0.003588
1329
789.62
1413
1440
592
82
110
100
1061
1096
352
193
198
67
0
1.68
0.7484613
2
0.7224663
0.2637
0.004645
1542
935.10
1625
1687
639
81
110
95
1217
1262
452
190
194
62
0
1.65
0.7224663
3
0.4222333
0.1629
0.054073
3253
2432.90
3340
3317
902
85
111
94
2852
2679
880
188
193
59
0
1.34
0.4222333
4
0.5753123
0.2200
0.015006
1993
1334.94
2080
2116
708
85
109
93
1652
1659
400
188
191
57
0
1.49
0.5753123
5
0.5753123
0.2164
0.016403
1961
1315.72
2045
2033
748
82
107
90
1632
1613
549
189
193
58
0
1.49
0.5753123
6
0.7311833
0.2629
0.004753
1543
926.86
1632
1699
728
87
111
91
1209
1265
544
191
194
56
0
1.66
0.7311833
7
0.7739963
0.2710
0.003761
905
527.94
993
1049
518
86
111
93
771
818
295
189
191
56
0
1.71
0.7739963
8
0.2630343
0.1015
0.158342
2181
1821.70
2263
2223
697
80
107
90
2182
2048
642
186
190
59
0
1.20
0.2630343
9
0.2141253
0.0827
0.207333
953
820.73
1037
1062
399
82
109
91
1090
1099
348
188
191
59
0
1.16
0.2141253
10
0.6322683
0.2241
0.013548
469
301.94
552
582
290
81
109
97
521
512
154
186
190
59
0
1.55
0.6322683
11
0.3895673
0.1488
0.071150
1284
983.59
1369
1382
491
83
113
97
1272
1281
264
192
197
93
0
1.31
0.3895673
12
0.4436073
0.1751
0.042039
3308
2424.67
3390
3386
852
80
109
94
2849
2757
698
194
199
60
0
1.36
0.4436073
13
0.4329593
0.1671
0.049690
2344
1739.35
2436
2453
747
90
114
95
2097
2057
521
191
195
64
0
1.35
0.4329593
14
0.6507653
0.2288
0.012025
1296
825.30
1386
1406
746
88
111
90
1095
1133
527
188
192
58
0
1.57
0.6507653
15
0.7048723
0.2505
0.006737
1058
649.63
1147
1208
571
87
111
89
902
923
334
187
192
58
0
1.63
0.7048723
16
0.4436073
0.1685
0.048269
1365
1004.64
1450
1456
548
83
107
89
1294
1255
371
191
196
60
0
1.36
0.4436073
17
0.1243283
0.0464
0.323678
1412
1301.08
1492
1476
496
78
106
92
1617
1563
406
190
193
58
0
1.09
0.1243283
18
0.6780723
0.2417
0.008571
813
508.72
894
952
443
79
118
251
744
786
254
183
224
738
0
1.60
0.6780723
19
0.4436073
0.1723
0.044578
3316
2436.56
3397
3335
991
79
108
91
2852
2786
821
184
192
149
0
1.36
0.4436073
20
0.4956953
0.1868
0.032697
1866
1326.70
1956
1928
702
88
115
97
1647
1613
541
192
200
64
0
1.41
0.4956953
Total number of rows:
25392
Table truncated, full table size
2693 Kbytes
.
Supplementary file
Size
Download
File type/resource
GSM30785_cy3.tif.gz
59.4 Mb
(ftp)
(http)
TIFF
GSM30785_cy5.tif.gz
59.1 Mb
(ftp)
(http)
TIFF
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