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Status
Public on Nov 21, 2005
Title
wt anaerobic rep 3
Sample type
RNA
Channel 1 Source name
wt anaerobic
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. 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
920
522
33
8
1164
637
96
30
-0.31
0.83
2
1487
799
33
8
1589
648
89
24
-0.22
0.97
3
31
7
32
8
95
27
88
24
null
0.00
4
225
137
31
7
814
433
87
23
-1.87
0.27
5
239
146
32
7
802
463
90
22
-1.82
0.29
6
234
142
32
7
797
471
85
23
-1.77
0.28
7
263
163
33
8
956
584
89
22
-1.66
0.27
8
715
479
33
8
410
236
85
23
1.19
2.09
9
664
472
34
8
372
191
93
25
1.25
2.26
10
710
412
33
7
408
239
88
24
1.17
2.10
11
738
472
33
8
390
233
88
24
1.38
2.32
12
3093
2240
33
8
11920
9490
87
22
-1.77
0.26
13
1830
2015
32
7
7011
7647
93
30
-1.84
0.26
14
2775
1732
33
8
10051
6522
88
23
-1.51
0.28
15
2026
2191
43
104
7702
7918
103
141
-1.73
0.26
16
34
9
32
7
93
26
86
22
-2.59
0.25
17
34
7
33
7
90
23
86
22
-1.00
0.60
18
1111
715
33
8
1097
621
88
22
0.24
1.07
19
436
99
33
8
504
150
92
23
0.02
0.98
20
473
122
32
7
535
177
89
23
-0.06
0.98
14400 604 Kbytes .Supplementary data files not provided
