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GEO accession:
Sample GSM60187
Query DataSets for GSM60187
Status
Public on Jun 10, 2005
Title
dimethylated K4 histone H3 in HeLa cell, 0 minute - rep3 of 4
Sample type
genomic
Channel 1
Source name
Chromatin immunoprecipitated DNA using dimethyl-H3K4 antibody
Organism
Homo sapiens
Characteristics
Chromatin immunoprecipitated DNA using dimethyl-H3K4 antibody
Extracted molecule
genomic DNA
Label
Cy5
Channel 2
Source name
input DNA
Organism
Homo sapiens
Characteristics
input DNA
Extracted molecule
genomic DNA
Label
Cy3
Description
Genome-wide location analysis of dimethyl-H3K4 binding using RenLab ENCODE PCR tiling array. Array ID is ENC684. Replicate 3 of 4.
Data processing
Single-Array Error Model
Submission date
Jun 03, 2005
Last update date
Jun 24, 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)
GSE2730
ENCODE: GWLA analysis of a few promoter and enhancer markers in HeLa cells
Data table header descriptions
ID_REF
VALUE
log2 ratio
STATISTICS
X-statistics
P-VAL
p-value calculated using single array error model
F635_INT
normalized F635 intensity with background intensity as well as blank intensity subtracted
F532_INT
normalized F532 intensity witn background intensity as well as blank intensity subtracted
F635_MEDIAN
F635 median 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
Data table
ID_REF
VALUE
STATISTICS
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
1
0.171645
6.49372103e-02
3.07950028e-01
582.4355
517.1035
806
802
242
47
57
39
945
900
283
104
106
29
2
0.372408
1.41509699e-01
1.37147135e-01
1064.0835
821.9958
1201
1181
400
46
56
37
1189
1138
404
106
106
28
3
-0.434361
-1.71917131e-01
9.07933730e-01
2246.2168
3035.3400
2132
2097
494
47
58
39
2533
2453
541
103
104
28
4
0.388503
1.50024184e-01
1.23227078e-01
1284.3211
981.1207
1363
1368
420
48
58
38
1267
1246
383
103
105
28
5
0.321022
1.26130130e-01
1.64925868e-01
1515.3883
1213.0726
1615
1557
457
45
56
40
1438
1403
332
106
106
28
6
0.404048
1.52470908e-01
1.19416835e-01
1221.6635
923.2537
1329
1312
495
47
56
37
1244
1205
457
102
103
28
7
0.964491
3.16296517e-01
7.27209365e-03
560.7697
287.3715
748
759
336
47
57
38
690
672
250
105
106
28
8
-0.371183
-1.44449004e-01
8.67774845e-01
826.1829
1068.5955
1006
998
276
47
56
36
1344
1308
336
105
107
28
9
0.088247
3.11763179e-02
4.04835215e-01
179.2941
168.6557
340
356
142
46
56
37
417
425
95
104
105
28
10
0.277612
9.32028093e-02
2.35752017e-01
191.6223
158.0799
392
401
167
52
60
39
390
391
113
104
107
31
11
0.324090
1.14538321e-01
1.88115919e-01
211.5051
168.9507
421
431
148
50
58
38
422
423
103
103
106
28
12
0.171714
6.83964220e-02
2.98613147e-01
1700.0778
1509.3075
1740
1698
421
52
62
46
1678
1587
400
106
111
34
13
0.247045
9.71478358e-02
2.26473450e-01
648.4674
546.4121
860
866
228
53
64
51
924
924
127
107
112
51
14
0.441962
1.70074925e-01
9.44389096e-02
1162.3135
855.6169
1264
1262
388
49
58
37
1190
1161
319
105
107
29
15
0.868842
2.83891871e-01
1.41467139e-02
684.5532
374.8519
921
873
438
50
60
39
792
771
348
108
110
29
16
0.432433
1.53212052e-01
1.18279243e-01
573.9731
425.3205
799
790
335
52
59
38
874
829
307
109
111
29
17
0.181993
6.93856614e-02
2.95966919e-01
552.9524
487.4191
784
782
226
53
61
39
911
884
242
109
111
28
18
0.759924
2.44663893e-01
2.93696372e-02
399.6713
236.0169
617
638
276
53
62
41
591
596
247
109
111
31
19
-0.140464
-5.63273998e-02
6.68274949e-01
1972.5696
2174.2835
1878
1882
440
52
59
38
2052
1983
469
108
110
29
20
-0.165145
-6.50740668e-02
6.92421793e-01
1139.6122
1277.8230
1281
1258
361
52
58
37
1505
1451
399
109
110
29
Total number of rows:
25392
Table truncated, full table size
2719 Kbytes
.
Supplementary file
Size
Download
File type/resource
GSM60187.gpr.gz
2.1 Mb
(ftp)
(http)
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