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Status
Public on Nov 21, 2005
Title
wt anaerobic plus NO3 rep 1
Sample type
RNA
Channel 1 Source name
wt anaerobic plus NO3
Organism
Escherichia coli Characteristics
Strain:E.coli K-12 MG1655
Extracted molecule
total RNA
Label
Cy5
Channel 2 Source name
aerobic reference
Organism
Escherichia coli Characteristics
Strain:E.coli K-12 MG1655
Extracted molecule
total RNA
Label
Cy3
Description
Pool RNA was isolated from four independently grown cultures of E. coli K-12 MG1655. The pool of control RNA was isolated from independent cultures of bacteria grown aerobically in the absence of nitrate or nitrite, but in the presence of TMAO. Test RNA from E.coli K-12 MG1655 wt was isolated from three independently anaerobically grown cultures plus nitrate. Samples were mixed with 2 volumes of RNA Protect (Qiagen Ltd) to stabilise the total RNA. An RNeasy kit (Qiagen Ltd) was used to extract the total RNA according to manufacturers’ instructions. Contaminating DNA was removed by using on-column DNase I digestion (Qiagen Ltd). The quality and quantity of the RNA preparations were determined with an Agilent 2100 Bioanalyzer by using the RNA 6000 nano assay Labchip (Agilent, Stockport, United Kingdom).
Data processing
Raw, not normalised
Submission date
Nov 10, 2005
Last update date
Nov 10, 2005
Contact name
Chrystala Constantinidou
E-mail(s)
[email protected] Phone
+44 (0)121 414 5564
Organization name
University of Birmingham
Department
School of Biosciences
Lab
UBEC
Street address
City
Birmingham
ZIP/Postal code
B15 2TT
Country
United Kingdom
Platform ID
GPL1246 Series (1)
GSE3591 A reassesment of the FNR regulon and the effects of nitrate,nitrite, narXL and narQP
Data table header descriptions ID_REF CH1_MEAN Cy5 Mean Foreground
CH1_SD Cy5 Foreground SD
CH1_BKD_MEAN Cy5 Mean Background
CH1_BKD_SD Cy5 Background SD
CH2_MEAN Cy3 Mean Foreground
CH2_SD Cy3 Foreground SD
CH2_BKD_MEAN Cy3 Mean Background
CH2_BKD_SD Cy3 Background SD
VALUE Log ratio (log2 of PRE_VALUE)
PRE_VALUE (Cy5 Foreground – Background) / (Cy3 Foreground – Background)
Data table ID_REF CH1_MEAN CH1_SD CH1_BKD_MEAN CH1_BKD_SD CH2_MEAN CH2_SD CH2_BKD_MEAN CH2_BKD_SD VALUE PRE_VALUE 1
2218
794
57
23
993
307
137
43
1.31
2.52
2
1927
1003
56
23
862
441
135
41
1.37
2.57
3
63
25
56
22
141
42
129
42
-0.59
0.67
4
218
285
57
22
700
1009
130
61
-1.15
0.28
5
507
288
58
24
1831
831
129
41
-2.14
0.26
6
565
270
58
28
1859
954
125
40
-1.89
0.29
7
668
274
56
24
2191
1084
130
43
-1.67
0.30
8
1171
547
59
22
664
281
129
38
0.84
2.07
9
1029
478
59
24
624
277
136
41
0.70
1.99
10
1019
472
61
24
549
223
142
39
0.98
2.34
11
1044
789
57
25
599
303
134
35
0.86
2.12
12
2387
1882
60
24
10694
8936
133
47
-2.26
0.22
13
3073
1608
63
24
11507
6983
128
40
-1.91
0.26
14
5025
5511
61
23
16073
11870
129
42
-1.70
0.31
15
3224
1739
59
20
11751
5473
129
40
-1.84
0.27
16
60
23
59
22
131
38
123
36
-3.17
0.33
17
61
22
59
23
134
35
121
36
-2.81
0.38
18
1727
476
59
22
728
199
125
34
1.51
2.75
19
307
139
56
23
334
127
137
41
0.39
1.27
20
313
107
55
23
349
115
139
44
0.22
1.21
14400 630 Kbytes .Supplementary data files not provided
