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Status
Public on Nov 02, 2006
Title
Folate Depletion Experiment 1, p79s33
Sample type
RNA
Channel 1 Source name
Folate Depletion #1, p79s33
Organism
Homo sapiens Characteristics
human fibroblast culture, GM03349, folate depleted for 7 days before harvest for gene expression
Biomaterial provider
http://locus.umdnj.edu/nigms/nigms_cgi/display.cgi?GM03349 Extracted molecule
total RNA
Label
Cy5
Channel 2 Source name
Control Folate Depletion #1, p79s33
Organism
Homo sapiens Characteristics
human fibroblast culture, GM03349, sham folate depleted for 7 days before harvest for gene expression
Biomaterial provider
http://locus.umdnj.edu/nigms/nigms_cgi/display.cgi?GM03349 Extracted molecule
total RNA
Label
Cy3
Description
25 µg of total RNA was used for cDNA synthesis. The microarray used in this study was the NIEHS Human Oligo chip containing approximately 17,000 70mer oligonucleotides from the Operon Human Oligo Set V1.1. The gene list can be found at http://dir.niehs.nih.gov/microarray/inhousearrays.htm. Fluorescent intensities were measured with an Agilent DNA Microarray scanner (Palo Alto, CA).
Data processing
The signal intensities were quantified and normalized from the spots on the image files utilizing IPLabs image-processing software (Scanalytics, Inc., Fairfax, VA) with the Array Suite 2.0 extension (National Human Genome Research Institute, NHGRI, Bethesda, MD) (Chen et al., 1997).
Submission date
Nov 02, 2005
Last update date
Mar 28, 2008
Contact name
NIEHS Microarray Core
E-mail(s)
microarray@niehs.nih.gov, liuliw@niehs.nih.gov Organization name
NIEHS
Department
DIR
Lab
Microarray Core
Street address
111 T.W. Alexander Drive
City
RTP
State/province
NC
ZIP/Postal code
27709
Country
USA
Platform ID
GPL3037 Series (1)
GSE3548 Gene expression alteration in human fibroblast cells after folate depletion
Data table header descriptions ID_REF SR_top SR_left SR_bottom SR_right SR_T. Int. SR_Mean Treated
SR_S.Dev SR_SNR SR_iQuality SR_bkMean SR_bkDev SG_top SG_left SG_bottom SG_right SG_T. Int. SG_Mean Control
SG_S.Dev SG_SNR SG_iQuality SG_bkMean SG_bkDev unionArea propArea VALUE Treated:Control divided by calibration parameter
rQuality confLevel lowerLimit upperLimit M calibration parameter
CV Flag
Data table ID_REF SR_top SR_left SR_bottom SR_right SR_T. Int. SR_Mean SR_S.Dev SR_SNR SR_iQuality SR_bkMean SR_bkDev SG_top SG_left SG_bottom SG_right SG_T. Int. SG_Mean SG_S.Dev SG_SNR SG_iQuality SG_bkMean SG_bkDev unionArea propArea VALUE rQuality confLevel lowerLimit upperLimit M CV Flag 1
60
66
77
83
39835
177.6
61.6
10.8
1
69.9
11.7
60
66
77
83
90962
489.9
69.2
34.5
1
97.7
10.7
155
0.7673
0.3377
1
99
0.6682
1.4965
1.0733
0.1071
1
193
60
84
77
101
29487
114.3
35
7.6
1
66.1
9.5
60
84
77
101
87485
464
78.1
36.6
1
91
8.6
162
0.802
0.2294
1
99
0.6682
1.4965
1.0733
0.1071
1
5
60
102
77
119
37312
132.3
38.2
8.2
1
68.8
11.2
60
102
77
119
99188
450.9
40
34.6
1
92.7
9.1
184
0.9109
0.2734
1
99
0.6682
1.4965
1.0733
0.1071
1
197
60
119
77
136
85731
388.4
73
24
1
68.8
11.3
60
119
77
136
120509
567.7
72.5
44.3
1
87.1
8.7
186
0.9208
0.6374
1
99
0.6682
1.4965
1.0733
0.1071
1
9
60
137
77
154
76294
393
130.4
25.6
1
69.1
10.2
60
137
77
154
119773
648.5
160.4
48.8
1
88
9.4
163
0.8069
0.5647
1
99
0.6682
1.4965
1.0733
0.1071
1
201
60
155
77
172
41283
144.4
47.5
8.7
1
72.6
12.1
60
155
77
172
87505
381.2
51.4
28.4
1
88.4
9.6
187
0.9257
0.353
1
99
0.6682
1.4965
1.0733
0.1071
1
13
60
173
77
190
42246
156.5
39.1
10
1
67
10.7
60
173
77
190
97367
433.5
48.9
31.9
1
90.3
9.8
187
0.9257
0.3363
1
99
0.6682
1.4965
1.0733
0.1071
1
205
60
191
77
208
170537
953.8
194.8
59.8
1
68.4
11
60
191
77
208
182768
1024.2
172.7
84.2
1
87.6
7.8
162
0.802
0.8676
1
99
0.6682
1.4965
1.0733
0.1071
1
17
60
208
77
225
31116
118.3
34.1
7.3
1
69.7
11.3
60
208
77
225
81934
413
38.4
30.6
1
88.7
9.7
165
0.8168
0.2668
1
99
0.6682
1.4965
1.0733
0.1071
1
209
60
226
77
243
44831
242.7
67
14.9
1
71.7
11.5
60
226
77
243
98952
614.4
78.9
43.9
1
90.2
10.4
142
0.703
0.368
1
99
0.6682
1.4965
1.0733
0.1071
1
21
60
244
77
261
428954
2207.5
359.3
142.2
1
68.6
10.4
60
244
77
261
401110
2052.2
327.8
145.6
1
89.5
10.5
190
0.9406
1.0022
1
99
0.6682
1.4965
1.0733
0.1071
1
213
60
262
77
279
121091
574.1
117.2
37.6
1
67.3
10
60
262
77
279
146310
698.9
59.4
53.5
1
90.1
9.1
187
0.9257
0.7653
1
99
0.6682
1.4965
1.0733
0.1071
1
385
60
280
77
297
74520
333.5
85.9
21.6
1
65.6
10.3
60
280
77
297
109984
508.2
81.4
38.1
1
90.5
9.5
186
0.9208
0.6114
1
99
0.6682
1.4965
1.0733
0.1071
1
577
60
297
77
314
126399
671
155.4
41.3
1
70.2
11.5
60
297
77
314
127977
667.6
107
45.6
1
90.4
11.2
169
0.8366
0.9365
1
99
0.6682
1.4965
1.0733
0.1071
1
389
60
315
77
332
76582
392.4
137.2
26.3
1
68.2
9.5
60
315
77
332
104791
548.7
167
38.8
1
89.2
10.6
165
0.8168
0.6664
1
99
0.6682
1.4965
1.0733
0.1071
1
581
60
333
77
350
124861
767
182.9
45.7
1
75.1
12.2
60
333
77
350
120389
731.5
167.6
57.6
1
89.1
8.6
148
0.7327
0.9769
1
99
0.6682
1.4965
1.0733
0.1071
1
393
60
351
77
368
199897
1018.7
275.2
62.8
1
72.2
11.4
60
351
77
368
168980
837.2
152.4
64.9
1
91
8.9
182
0.901
1.1336
1
99
0.6682
1.4965
1.0733
0.1071
1
585
60
369
77
386
60080
258.1
81.1
16
1
73.7
11.4
60
369
77
386
92290
433.1
75.4
34.7
1
85
8.2
179
0.8861
0.5551
1
99
0.6682
1.4965
1.0733
0.1071
1
397
60
386
77
403
59019
215.3
58.8
14.2
1
69.6
9.8
60
386
77
403
117032
506.9
43.8
37.4
1
84
9.8
200
0.9901
0.3956
1
99
0.6682
1.4965
1.0733
0.1071
1
589
60
404
77
421
119472
668.3
247.6
39.6
1
71.5
12.3
60
404
77
421
144159
818.7
264.7
64.8
1
81.3
8.5
163
0.8069
0.7605
1
99
0.6682
1.4965
1.0733
0.1071
1
20000 3150 Kbytes .Supplementary data files not provided
