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Sample GSM103763 Query DataSets for GSM103763
Status Public on May 30, 2006
Title S. Typhimurium relAspoT LB low oxygen rep 4
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 SL1344 relAspoT mutant grown to OD600 = 0.328 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 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 07, 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 -0.94843589 1280 11367 0.112606668 0
2 -0.981654977 573 5493 0.104314582 0
3 -0.693907776 3072 15182 0.202344882 0
4 -1.281203573 1349 25776 0.052335506 0
5 -0.875033991 3185 23886 0.133341706 0
6 -0.346093725 2506 5560 0.450719424 0
7 -0.578630763 2442 9255 0.263857374 0
8 -0.921859957 2383 19906 0.119712649 0
9 -0.984482604 1661 16027 0.103637612 0
10 -0.619469982 5397 22471 0.240176227 0
11 -0.816221912 1197 7840 0.152678571 0
12 -1.065372648 2069 24051 0.086025529 0
13 -0.357342411 7400 16849 0.439195204 0
14 -1.076995562 2158 25766 0.083753784 0
15 -0.791483067 2593 16043 0.161628124 0
16 -0.890884427 2147 16700 0.128562874 0
17 -1.089524799 1096 13469 0.081372039 0
18 -0.784696111 2316 14107 0.164173814 0
19 -0.958581578 675 6136 0.110006519 0
20 -0.993434913 1673 16479 0.101523151 0

Total number of rows: 5376

Table truncated, full table size 205 Kbytes.




Supplementary file Size Download File type/resource
GSM103763.gpr.gz 375.8 Kb (ftp)(http) GPR

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