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Status
Public on Nov 02, 2006
Title
Folate Depletion Experiment 1, p79s34
Sample type
RNA
Channel 1 Source name
Folate Depletion #1, p79s34
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
Cy3
Channel 2 Source name
Control Folate Depletion #1, p79s34
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
Cy5
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 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
52
69
69
86
79645
322.9
175.1
12
1
160.5
20.9
52
69
69
86
19698
60.6
34
4.8
1
56.9
9.9
163
0.815
6.1009
1
99
0.6608
1.5133
0.8732
0.1099
1
193
52
87
69
104
84833
348.7
181.4
13.1
1
155.8
20.5
52
87
69
104
22582
80.7
33.4
6.6
1
54.5
9.2
164
0.82
4.9503
1
99
0.6608
1.5133
0.8732
0.1099
1
5
52
105
69
122
94685
431.5
153
20.4
1
134.6
12.6
52
105
69
122
29605
120.6
46.2
9.9
1
54.5
9.1
165
0.825
4.0984
1
99
0.6608
1.5133
0.8732
0.1099
1
197
52
123
69
140
124694
546.5
146
24.4
1
134.8
14.7
52
123
69
140
57375
260.7
92.1
21.6
1
54.7
9
180
0.9
2.4011
1
99
0.6608
1.5133
0.8732
0.1099
1
9
52
141
69
158
141676
660.8
285.8
27.6
1
138.9
16.9
52
141
69
158
88574
432.4
217.1
37.9
1
52.7
8.1
172
0.86
1.7505
1
99
0.6608
1.5133
0.8732
0.1099
1
201
52
158
69
175
82580
383
129.4
16.2
1
140.1
16.5
52
158
69
175
23994
100
42
9.6
1
49.2
6.6
157
0.785
4.3841
1
99
0.6608
1.5133
0.8732
0.1099
1
13
52
176
69
193
96154
416.5
114.3
17.6
1
144.5
16.6
52
176
69
193
33478
145.5
48.8
14.2
1
49.2
6.4
170
0.85
3.2788
1
99
0.6608
1.5133
0.8732
0.1099
1
205
52
194
69
211
226375
1129.2
427.5
49.8
1
143.1
15.1
52
194
69
211
214662
1138.5
465.7
94.3
1
55.1
9
177
0.885
1.1359
1
99
0.6608
1.5133
0.8732
0.1099
1
17
52
212
69
229
86573
412.7
124.2
17.6
1
143.4
16.2
52
212
69
229
24008
99
37.2
8.2
1
53.8
8.9
158
0.79
4.774
1
99
0.6608
1.5133
0.8732
0.1099
1
209
52
230
69
247
129911
653.8
188
29.1
1
144.8
14.7
52
230
69
247
49057
243.6
76
19.6
1
55.4
9.5
165
0.825
3.0743
1
99
0.6608
1.5133
0.8732
0.1099
1
21
52
248
69
265
367399
1863.2
723.6
66.9
1
163.3
22.1
52
248
69
265
316897
1680.2
680.4
149.1
1
54.5
7.9
181
0.905
1.27
1
99
0.6608
1.5133
0.8732
0.1099
1
213
52
266
69
283
122222
526.3
163.2
19.9
1
154.6
20.2
52
266
69
283
84623
416.2
124.2
38.2
1
51.8
7.3
177
0.885
1.4482
1
99
0.6608
1.5133
0.8732
0.1099
1
385
52
284
69
301
95743
433.8
167.2
14.8
1
141.4
23.8
52
284
69
301
58329
301.2
97.7
27.8
1
51.6
7.2
163
0.815
1.6496
1
99
0.6608
1.5133
0.8732
0.1099
1
577
52
301
69
318
124074
566.9
156.2
26.9
1
124.5
12.5
52
301
69
318
120364
609.8
184.3
48.7
1
56.9
9.6
177
0.885
1.0645
1
99
0.6608
1.5133
0.8732
0.1099
1
389
52
319
69
336
117961
667
231.6
28.7
1
132.9
15.9
52
319
69
336
84695
511.3
203.2
39.9
1
57.2
9.9
149
0.745
1.4939
1
99
0.6608
1.5133
0.8732
0.1099
1
581
52
337
69
354
186518
961.4
326.7
42.9
1
123.6
14.7
52
337
69
354
197115
1075.6
429.5
92.3
1
53.7
8.4
173
0.865
1.0236
1
99
0.6608
1.5133
0.8732
0.1099
1
393
52
355
69
372
147862
642.3
220.9
28.1
1
124.6
15.3
52
355
69
372
127169
647.8
234.5
55.5
1
56
8.5
177
0.885
1.1354
1
99
0.6608
1.5133
0.8732
0.1099
1
585
52
373
69
390
90711
424.6
167.1
20.1
1
128.2
12.6
52
373
69
390
39852
183.3
74.7
15.2
1
55.5
8.9
164
0.82
2.6524
1
99
0.6608
1.5133
0.8732
0.1099
1
397
52
391
69
408
109774
529.1
143.1
23.7
1
133.2
14.5
52
391
69
408
71393
371
124.5
33
1
51.1
7.8
167
0.835
1.6332
1
99
0.6608
1.5133
0.8732
0.1099
1
589
52
409
69
426
205743
1166.9
393.1
36.7
1
133.4
26.9
52
409
69
426
184807
1106.5
424.4
95.7
1
54.7
8.3
160
0.8
1.2078
1
99
0.6608
1.5133
0.8732
0.1099
1
20000 3186 Kbytes .Supplementary data files not provided
