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Status
Public on Dec 30, 2008
Title
Strain M22, YPD media, replicate 3
Sample type
RNA
Channel 1 Source name
Reference, YPD media, replicate 3
Organism
Saccharomyces cerevisiae Characteristics
A pool of RNA from all samples
Extracted molecule
total RNA
Extraction protocol
RNeasy mini kit (Qiagen)
Label
Cy3
Label protocol
Genisphere Array 350 Expression Array Detection Kit, http://www.genisphere.com/array_detection_protocols.html
Channel 2 Source name
Strain M22, YPD media, replicate 3
Organism
Saccharomyces cerevisiae Characteristics
S. cerevisiae M22 (wine, Italy).
Extracted molecule
total RNA
Extraction protocol
RNeasy mini kit (Qiagen)
Label
Cy5
Label protocol
Genisphere Array 350 Expression Array Detection Kit, http://www.genisphere.com/array_detection_protocols.html
Hybridization protocol
Hybridization was performed in the microarray core facility in Washington University in St. Louis. http://www.genisphere.com/pdf/Array350_10-02-06.pdf
Scan protocol
Arrays were scanned using a ScanArray Express laser scanner (Perkin Elmer).
Description
Overnight cultures of M22 were diluted in fresh YPD to 10% v/v and grown for 3 hours at 30'C. Total RNA was isolated using an RNeasy mini kit (Qiagen), reverse transcribed, labeled, and hybridized to epoxy-coated slides (MWG Biotech).
Data processing
Individual array is normalized using the LOWESS algorithm.
Submission date
Dec 22, 2008
Last update date
Dec 29, 2008
Contact name
Hyun Seok Kim
E-mail(s)
Hyun.Kim@UTsouthwestern.edu Organization name
UT Southwestern Medical Center
Street address
Harry Hines Blvd.
City
Dallas
State/province
TX
ZIP/Postal code
75063
Country
USA
Platform ID
GPL7882 Series (1)
GSE14102 Gene expression change caused by CYS4 alleles
Data table header descriptions ID_REF Flags 1: Not found, 2: Absent, 3: Found & good, 4: Bad
Ch1 Median Median feature pixel intensity for ch1
Ch1 B Median Median feature background intensity for ch1
Ch2 Median Median feature pixel intensity for ch2
Ch2 B Median Median feature background intensity for ch2
VALUE same as UNF_VALUE but with flagged values removed
UNF_VALUE Normalized log2 ratio of Ch2 (Cy5, median background subtracted)/Ch1 (Cy3, median background subtracted)
Data table ID_REF Flags Ch1 Median Ch1 B Median Ch2 Median Ch2 B Median VALUE UNF_VALUE 1
1
290
235
166
144
0.16
0.16
2
4
390
237
267
147
0.71
3
3
819
250
436
140
-0.19
-0.19
4
3
542
231
334
140
0.19
0.19
5
3
629
253
446
146
0.47
0.47
6
1
304
237
155
144
-1.1
-1.1
7
4
480
233
261
145
-0.11
8
3
1065
261
726
143
0.21
0.21
9
3
715
263
495
141
0.4
0.4
10
1
333
265
195
145
0.91
0.91
11
4
540
267
274
147
-0.15
12
3
1045
263
514
147
-0.39
-0.39
13
1
315
229
185
145
0.24
0.24
14
3
578
256
288
146
-0.27
-0.27
15
3
2456
238
1630
141
-0.01
-0.01
16
1
276
253
181
144
2.19
2.19
17
4
423
243
262
145
0.41
18
1
292
239
168
138
0.63
0.63
19
4
481
243
219
145
-0.62
20
3
361
244
207
147
0.27
0.27
13440 428 Kbytes .Supplementary file Size Download File type/resource GSM353968.csv.gz
1.6 Mb
(ftp) (http) CSV
Processed data included within Sample table
