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Status
Public on Dec 30, 2008
Title
Strain M22-cys4::N123I, 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-cys4::N123I, YPD media, replicate 3
Organism
Saccharomyces cerevisiae Characteristics
Allele replacement strain of M22 (CYS4-N123I)
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-CYS4::N123I 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
253
221
145
142
-3.06
-3.06
2
1
247
185
163
143
-0.9
-0.9
3
3
570
227
271
143
-1.22
-1.22
4
4
471
244
288
144
-0.4
5
4
339
213
186
143
-0.98
6
1
266
258
145
143
-1.77
-1.77
7
1
312
254
205
139
0.8
0.8
8
3
688
239
435
144
-0.58
-0.58
9
3
488
253
482
143
0.64
0.64
10
1
257
242
164
143
1.15
1.15
11
4
349
226
216
141
-0.23
12
1
235
237
183
145
0.05
0.05
13
1
265
258
154
148
0.07
0.07
14
3
454
246
458
140
0.75
0.75
15
3
3730
244
3783
144
-0.2
-0.2
16
4
398
240
214
136
-0.58
17
4
408
236
293
142
0.11
18
1
308
247
166
148
-1.02
-1.02
19
4
476
253
304
141
-0.21
20
1
332
214
158
142
-2.19
-2.19
13440 440 Kbytes .Supplementary file Size Download File type/resource GSM353974.csv.gz
1.7 Mb
(ftp) (http) CSV
Processed data included within Sample table
