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Status
Public on Sep 01, 2004
Title
Sporulation gerE mutant Hour 6.5 exp. 3
Sample type
RNA
Channel 1
Source name
wild type (strain PY79)
Organism
Bacillus subtilis
Extracted molecule
total RNA
Channel 2
Source name
gerE mutant (strain PE454)
Organism
Bacillus subtilis
Extracted molecule
total RNA
Description
Strains PY79 and PE454 were grown in parallel in hydrolysed casein medium at 37°C to an OD600 of 0.6. Sporulation was induced by resuspension in Sterlini-Mandelstam medium at 37C. Six hour and thirty minutes after resuspension, 25 ml of each culture were collected for RNA isolation and immediately mixed with an equal volume of methanol at –20C. RNA was isolated with a Hot Phenol/Trizol procedure. cDNA was prepared from 50 ug tot RNA and fluorescently labeled using Superscript Reverse Transcriptase and Cy5-dUTP for the RNA sample from strain PY79 and Cy3-dUTP for the RNA sample from strain PE454. Protocols for RNA isolation, cDNA preparation and labeling, hybridization to the microarrays and washing procedure can be found at http://mcb.harvard.edu/losick This is the third repetition of the experiment at this time point.
Submission date
Jul 22, 2004
Last update date
Oct 28, 2005
Contact name
Patrick Yves Eichenberger
E-mail(s)
peichenb@mcb.harvard.edu
Phone
617-495-0532
Fax
617-496-4642
URL
http://mcb.harvard.edu/losick
Organization name
Harvard University
Department
Molecular and Cellular Biology
Lab
Losick
Street address
16 Divinity Avenue
City
Cambridge
State/province
MA
ZIP/Postal code
02138
Country
USA
Platform ID
GPL1353
Series (1)
GSE1620
Sporulation in Bacillus subtilis (mother cell)
Data table header descriptions
ID_REF
CH1_MEDIAN
channel1 median signal
CH1_MEAN
channel1 mean signal
CH1_SD
channel1 signal standard deviation
CH1_BKD_MEDIAN
channel1 median background
CH1_BKD_MEAN
channel1 mean background
CH1_BKD_SD
channel1 background standard deviation
CH2_MEDIAN
channel2 median signal
CH2_MEAN
channel2 mean signal
CH2_SD
channel2 signal standard deviation
CH2_BKD_MEDIAN
channel2 median background
CH2_BKD_MEAN
channel2 mean background
CH2_BKD_SD
channel2 background standard deviation
VALUE
log ratio (log2 of PRE_VALUE)
FLAGS
user defined flag (default=0, bad=-100, empty=-75)
PRE_VALUE
ratio channel1 median signal minus median background and channel2 median signal minus median background, not normalized
Data table
ID_REF
CH1_MEDIAN
CH1_MEAN
CH1_SD
CH1_BKD_MEDIAN
CH1_BKD_MEAN
CH1_BKD_SD
CH2_MEDIAN
CH2_MEAN
CH2_SD
CH2_BKD_MEDIAN
CH2_BKD_MEAN
CH2_BKD_SD
VALUE
FLAGS
PRE_VALUE
1
534
549
126
148
155
68
563
576
137
152
159
67
-0.0938793
0
0.937
2
253
262
83
153
156
53
307
307
88
159
162
40
-0.5563933
0
0.68
3
485
513
141
153
158
52
483
502
118
156
159
39
0.0243203
0
1.017
4
679
708
225
156
163
74
563
591
197
162
163
42
0.3829443
0
1.304
5
685
699
298
158
163
54
744
784
315
161
163
50
-0.1472023
0
0.903
6
351
361
123
160
168
55
428
420
95
167
169
43
-0.4560093
0
0.729
7
296
320
96
161
164
51
368
378
84
163
166
41
-0.6038413
0
0.658
8
210
217
62
168
171
54
270
271
60
169
175
42
-100
9
276
275
80
168
171
54
285
292
69
168
171
39
-100
10
1298
1269
333
181
189
73
1011
1008
224
180
183
43
0.4276063
0
1.345
11
389
400
112
180
183
55
515
540
109
176
180
41
-0.6989983
0
0.616
12
516
514
105
177
183
56
636
661
176
180
181
42
-0.4266253
0
0.744
13
228
244
76
184
187
54
296
301
58
183
186
42
-100
14
207
221
71
187
190
55
249
245
49
186
189
42
-100
15
332
343
119
184
190
60
397
409
95
186
188
41
-0.5145733
0
0.7
16
260
263
78
187
193
57
293
298
64
187
190
46
-0.5311563
0
0.692
17
540
526
132
195
201
63
625
650
146
190
195
46
-0.3364283
0
0.792
18
200
210
75
155
159
55
234
234
51
155
160
44
-100
19
206
196
64
155
158
55
218
236
121
164
166
39
-100
20
414
472
216
156
161
53
422
464
192
159
162
40
-0.0276753
0
0.981
Total number of rows: 4623 Table truncated, full table size 299 Kbytes .Supplementary file
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