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Sample GSM103414 Query DataSets for GSM103414
Status Public on May 30, 2006
Title S. Typhimurium wild-type LB high salt low oxygen rep 2
Sample type mixed
 
Channel 1
Source name F635 Median-B635
Organism Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344
Characteristics RNA labelled with Cy5-dCTP and laser scanned at 635nm with local background subtracted from feature signal
Treatment protocol RNA labelled during reverse transcription into cDNA with Cy5-dCTP according to protocol at http://www.ifr.ac.uk/safety/Microarrays/default.html#protocols
Growth protocol S. Typhimurium SL133 wild-type grown to late-log phase OD600 = 0.478 in Lennox Broth containing 0.3M NaCl in low-oxygen conditions
Extracted molecule total RNA
Extraction protocol Total RNA isolation protocol at http://www.ifr.ac.uk/safety/Microarrays/default.html#protocols
Label Cy5-dCTP
Label protocol Labelling protocol at http://www.ifr.ac.uk/safety/Microarrays/default.html#protocols
 
Channel 2
Source name F532 Median-B532
Organism Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344
Characteristics Genomic DNA labelled with Cy3-dCTP and laser scanned at 532nm with local background subtracted from feature signal
Treatment protocol Genomic DNA labelled with Cy3-dCTP according to protocol at http://www.ifr.ac.uk/safety/Microarrays/default.html#protocols
Growth protocol S. Typhimurium SL1344 grown to stationary phase
Extracted molecule genomic DNA
Extraction protocol Genomic DNA isolated using the Qiagen 'Genomic DNA' Kit (Cat. No.: 19060 for the buffer kit; 10243 for the columns)
Label Cy3-dCTP
Label protocol Labelling protocol at http://www.ifr.ac.uk/safety/Microarrays/default.html#protocols
 
 
Hybridization protocol Slides blocked with DCE according to protocol at PMID 11266573. For hybridisation and washing protocols see http://www.ifr.ac.uk/safety/Microarrays/default.html#protocols
Scan protocol Axon GenePix4000A, 10nm resolution scan & see http://www.ifr.ac.uk/safety/Microarrays/default.html#protocols
Description Intensity ratios of RNA (channel 1) divided by DNA (channel 2) signals minus respective local background signals. Total array is 16 blocks arranged in 4X4 configuration
Data processing Data centring was performed by bringing the median ratio (Cy5/Cy3) for each of the 16 blocks to one using the following equation: (Ti) = (Cy5i/Cy3i) - c, where T is the centred ratio, i is the gene index, Cy5 and Cy3 are the red and green intensities and c is the 50th percentile of all Cy5/Cy3 ratios. Flagged features are omitted from the data centring process.
 
Submission date Apr 06, 2006
Last update date Apr 07, 2006
Contact name Arthur Thompson
E-mail(s) arthur.thompson@bbsrc.ac.uk
Phone +44 1603255181
Fax +44 1603 255288
Organization name Institute of Food Research
Department Food Safety Science
Street address Colney Lane
City Norwich
State/province Norfolk
ZIP/Postal code NR4 7UA
Country United Kingdom
 
Platform ID GPL3586
Series (1)
GSE4631 Effect of ppGpp on Salmonella Typhimurium gene expression

Data table header descriptions
ID_REF
VALUE Log base 10 of ratio F635 Median-B635 divided by F532 Median-B532
F635 Median - B635 Feature signal (labelled RNA) minus background signal
F532 Median - B532 Feature signal (labelled DNA) minus background signal
RatioRNA/DNA Ratio F635 Median-B635 (labelled RNA) divided by F532 Median-B532 (labelled DNA)
Flags Not found, empty or bad features

Data table
ID_REF VALUE F635 Median - B635 F532 Median - B532 RatioRNA/DNA Flags
1 -0.694687188 428 2119 0.201982067 0
2 0.112121882 690 533 1.294559099 0
3 -0.223286019 543 908 0.598017621 0
4 -0.189203032 522 807 0.646840149 0
5 -1.108939081 47 604 0.07781457 0
6 -0.86690741 319 2348 0.135860307 0
7 -0.020602811 247 259 0.953667954 0
8 -1.274470967 59 1110 0.053153153 0
9 -1 149 1490 0.1 0
10 -1.753673925 59 3346 0.017632995 0
11 0.312824189 2986 1453 2.0550585 0
12 -0.945743325 258 2277 0.113306983 0
13 -1.117039939 86 1126 0.076376554 0
14 -1.750177672 70 3938 0.017775521 0
15 -0.879309396 685 5188 0.132035466 0
16 -0.570034193 946 3515 0.26913229 0
17 -0.695754317 976 4844 0.201486375 0
18 -1.321278245 66 1383 0.047722343 0
19 -0.520924905 1203 3992 0.301352705 0
20 -0.054908954 1343 1524 0.881233596 0

Total number of rows: 6144

Table truncated, full table size 223 Kbytes.




Supplementary file Size Download File type/resource
GSM103414.gpr.gz 430.2 Kb (ftp)(http) GPR

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