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Status
Public on Dec 30, 2008
Title
Strain M22-cys4::N123I, YPD media, replicate 2
Sample type
RNA
Channel 1 Source name
Strain M22-cys4::N123I, YPD media, replicate 2
Organism
Saccharomyces cerevisiae Characteristics
Allele replacement strain of M22 (CYS4-N123I)
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
Reference, YPD media, replicate 2
Organism
Saccharomyces cerevisiae Characteristics
A pool of RNA from all samples
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
PRE_VALUE Normalized log2 ratio of Ch2 (Cy5, median background subtracted)/Ch1 (Cy3, median background subtracted)
UNF_VALUE Normalized log2 ratio of Ch1 (Cy3, median background subtracted)/Ch2 (Cy5, median background subtracted)
Data table ID_REF Flags Ch1 Median Ch1 B Median Ch2 Median Ch2 B Median VALUE PRE_VALUE UNF_VALUE 1
1
276
211
165
144
1.09
-1.09
1.09
2
3
464
195
392
147
0.32
-0.32
0.32
3
3
658
226
1223
145
-1
1
-1
4
3
661
226
515
144
0.5
-0.5
0.5
5
3
1021
221
1133
142
0.02
-0.02
0.02
6
1
299
197
187
147
1
-1
1
7
3
620
199
752
147
-0.22
0.22
-0.22
8
3
2213
237
2028
155
0.35
-0.35
0.35
9
3
1670
207
2249
155
-0.24
0.24
-0.24
10
3
354
195
367
147
-0.38
0.38
-0.38
11
3
668
206
675
145
0.1
-0.1
0.1
12
3
637
190
821
142
-0.29
0.29
-0.29
13
1
261
221
206
143
-1.09
1.09
-1.09
14
3
1411
237
1306
143
0.33
-0.33
0.33
15
3
5788
214
9070
151
-0.53
0.53
-0.53
16
3
425
201
359
149
0.23
-0.23
0.23
17
3
456
198
444
142
-0.02
0.02
-0.02
18
3
382
211
395
143
-0.43
0.43
-0.43
19
3
786
231
834
143
0
0
0
20
4
277
210
238
140
0.8
-0.8
13440 508 Kbytes .Supplementary file Size Download File type/resource GSM353973.csv.gz
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(ftp) (http) CSV
Processed data included within Sample table
