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Status
Public on Dec 30, 2008
Title
Strain M22-cys4-, YPD media, replicate 2
Sample type
RNA
Channel 1 Source name
Strain M22 with CYS4 deletion, YPD media, replicate 2
Organism
Saccharomyces cerevisiae Characteristics
S. cerevisiae M22 with CYS4 deletion.
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 with CYS4 deletion 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
3
472
186
174
135
1.02
-1.02
1.02
2
3
669
180
261
130
0.13
-0.13
0.13
3
3
2647
183
1029
133
-0.17
0.17
-0.17
4
3
1456
178
462
139
0.31
-0.31
0.31
5
3
1510
190
324
136
1.12
-1.12
1.12
6
1
306
169
154
133
0.91
-0.91
0.91
7
3
1579
189
429
131
0.55
-0.55
0.55
8
3
4618
189
1392
137
0.23
-0.23
0.23
9
3
3042
190
698
141
0.72
-0.72
0.72
10
3
542
186
221
143
0.37
-0.37
0.37
11
3
1380
192
448
137
0.26
-0.26
0.26
12
3
1589
194
413
138
0.67
-0.67
0.67
13
1
256
186
168
138
-0.55
0.55
-0.55
14
3
1616
202
563
143
0.09
-0.09
0.09
15
3
15256
226
7452
137
-0.36
0.36
-0.36
16
3
655
197
195
134
1.09
-1.09
1.09
17
3
742
181
290
136
0.11
-0.11
0.11
18
3
796
192
322
136
-0.04
0.04
-0.04
19
3
1837
189
426
141
0.86
-0.86
0.86
20
4
373
169
231
145
0.6
-0.6
13440 525 Kbytes .Supplementary file Size Download File type/resource GSM353970.csv.gz
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(ftp) (http) CSV
Processed data included within Sample table
