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Status
Public on Nov 02, 2006
Title
Folate Depletion Experiment 2, p103s85
Sample type
RNA
Channel 1 Source name
Folate Depletion #2, p103s85
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 #2, p103s85
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)
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
GPL3036 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 the 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
86
91
104
109
38433
176.3
81.2
4.1
1
109.8
29.5
86
91
104
109
46777
277.2
101.6
18.8
1
81.8
11.6
132
0.8516
0.9198
1
99
0.6326
1.5807
0.6915
0.1205
1
193
86
109
104
127
35152
152
73.2
3.5
1
109.7
29.4
86
109
104
127
38196
203.4
82.5
15.2
1
82
9.9
133
0.8581
1.0807
1
99
0.6326
1.5807
0.6915
0.1205
1
5
86
127
104
145
112460
698.3
235
15.7
1
115
31.6
86
127
104
145
124713
828
258.1
71.1
1
75.6
7.2
140
0.9032
1.2196
1
99
0.6326
1.5807
0.6915
0.1205
1
197
86
145
104
163
101246
540.9
292.6
11.8
1
113.3
33.4
86
145
104
163
117454
702.1
319.9
50.3
1
76.9
10.6
151
0.9742
1.1141
1
99
0.6326
1.5807
0.6915
0.1205
1
9
86
163
104
181
130226
795.6
379.3
17.4
1
113.8
33.3
86
163
104
181
119788
758.9
339
51.8
1
78.9
11.5
145
0.9355
1.5161
1
99
0.6326
1.5807
0.6915
0.1205
1
201
86
182
104
200
57669
298.5
117.4
6.9
1
110.7
29.8
86
182
104
200
71722
442.6
152.3
33.8
1
79.1
9.4
141
0.9097
0.9753
1
99
0.6326
1.5807
0.6915
0.1205
1
13
86
200
104
218
99391
605.5
175.9
13.6
1
118.3
31.6
86
200
104
218
105866
703.6
163.4
52.6
1
78.9
9.8
138
0.8903
1.2445
1
99
0.6326
1.5807
0.6915
0.1205
1
205
86
218
104
236
222060
1352.5
856.1
31.6
1
109
29.1
86
218
104
236
210678
1338.6
755.2
95.2
1
80.2
10.7
147
0.9484
1.4611
1
99
0.6326
1.5807
0.6915
0.1205
1
17
86
236
104
254
26394
93.1
55.6
2.2
1
108.5
28.5
86
236
104
254
39776
240.9
58.1
18.7
1
76.7
9.2
127
0.8194
0.5587
1
99
0.6326
1.5807
0.6915
0.1205
1
209
86
254
104
272
67193
367.7
188.7
8.5
1
118.1
30.1
86
254
104
272
88557
577.6
230.5
42.9
1
76.5
9.9
138
0.8903
0.9208
1
99
0.6326
1.5807
0.6915
0.1205
1
21
86
272
104
290
810190
5207.9
2401.3
114.6
1
130
32.8
86
272
104
290
817791
5307.1
2430.9
166.2
1
113.2
30.6
154
0.9935
1.4192
1
99
0.6326
1.5807
0.6915
0.1205
1
213
86
290
104
308
209110
1267.6
471
28
1
126.7
32.5
86
290
104
308
257018
1614.9
552.9
55.8
1
127.3
27.5
150
0.9677
1.1351
1
99
0.6326
1.5807
0.6915
0.1205
1
385
86
308
104
326
94003
679.4
334.6
14.8
1
126.5
33.4
86
308
104
326
115707
877.2
411.1
32.2
1
115.5
25.7
119
0.7677
1.1202
1
99
0.6326
1.5807
0.6915
0.1205
1
577
86
327
104
345
186456
1233.1
538.5
26.7
1
117.6
33.8
86
327
104
345
230846
1605.3
682.2
133.8
1
71.5
7.8
141
0.9097
1.1109
1
99
0.6326
1.5807
0.6915
0.1205
1
389
86
345
104
363
112292
717.8
500.7
16.3
1
116.8
30.8
86
345
104
363
114924
802.5
526
68
1
70.6
7.5
132
0.8516
1.2935
1
99
0.6326
1.5807
0.6915
0.1205
1
581
86
363
104
381
259684
1732
844.4
38.4
1
121.5
32.4
86
363
104
381
272431
1885.9
886.3
142.2
1
73.4
9.6
142
0.9161
1.3282
1
99
0.6326
1.5807
0.6915
0.1205
1
393
87
381
105
399
167424
1071.6
690.2
24
1
116.4
31.8
87
381
105
399
206510
1414
871.6
120.8
1
66.8
7.4
138
0.8903
1.096
1
99
0.6326
1.5807
0.6915
0.1205
1
585
87
399
105
417
54236
306.4
147.9
6.8
1
113.3
32.3
87
399
105
417
55679
370.4
177
31.5
1
66.7
7.4
129
0.8323
1.1963
1
99
0.6326
1.5807
0.6915
0.1205
1
397
87
417
105
435
76305
468.5
187.2
10.4
1
113.9
32.3
87
417
105
435
87735
619.4
199.7
50
1
69.1
8.4
132
0.8516
1.0938
1
99
0.6326
1.5807
0.6915
0.1205
1
589
87
435
105
453
267582
1926.7
1089.1
43.1
1
117
31.8
87
435
105
453
227560
1678.5
910.8
125.5
1
73.1
9.8
131
0.8452
1.6601
1
99
0.6326
1.5807
0.6915
0.1205
1
17664 2845 Kbytes .Supplementary data files not provided
