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Sample GSM103450 Query DataSets for GSM103450
Status Public on May 30, 2006
Title S. Typhimurium wild-type LB low oxygen rep 1
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 OD600 = 0.353 in Lennox Broth 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 Channel 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 GPL3612
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
Ratio RNA/DNA Ratio F635 Median-B635 divided by F532 Median-B532
Flags Not found, empty or bad features

Data table
ID_REF VALUE F635 Median - B635 F532 Median - B532 Ratio RNA/DNA Flags
1 -0.756892481 1563 8930 0.175027996 0
2 -0.90513373 583 4686 0.124413146 0
3 -0.610744307 2884 11769 0.245050557 0
4 -1.179328492 1194 18044 0.066171581 0
5 -0.839112972 2766 19097 0.144839504 0
6 -0.047893472 3448 3850 0.895584416 0
7 -0.57992015 1841 6998 0.263075164 0
8 -0.784704515 2894 17628 0.164170638 0
9 -0.957490345 1421 12885 0.110283275 0
10 -0.597168489 4442 17569 0.252831692 0
11 -0.864386315 799 5847 0.136651274 0
12 -1.027905806 1546 16486 0.093776538 0
13 -0.391652912 5775 14230 0.405832748 0
14 -0.999842404 2205 22042 0.100036294 0
15 -0.783326223 2169 13170 0.164692483 0
16 -0.807311998 2239 14367 0.155843252 0
17 -1.154771197 764 10911 0.07002108 0
18 -0.785535471 1973 12041 0.163856823 0
19 -0.937314971 529 4579 0.115527408 0
20 -0.778725118 2647 15903 0.166446582 0

Total number of rows: 5376

Table truncated, full table size 204 Kbytes.




Supplementary file Size Download File type/resource
GSM103450.gpr.gz 388.7 Kb (ftp)(http) GPR

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