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Sample GSM103761 Query DataSets for GSM103761
Status Public on May 30, 2006
Title S. Typhimurium relAspoT LB 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 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 -0.910204786 893 7262 0.122968879 0
2 -0.982271233 430 4128 0.104166667 0
3 -0.66943982 2148 10034 0.214072155 0
4 -1.204634129 1108 17749 0.062426052 0
5 -0.848535828 2966 20927 0.141730778 0
6 -0.328419421 1997 4254 0.469440527 0
7 -0.5839187 1931 7408 0.260664147 0
8 -0.887356277 1992 15369 0.129611556 0
9 -0.940623091 1364 11897 0.114650752 0
10 -0.596066321 4560 17990 0.253474152 0
11 -0.831430302 996 6756 0.147424512 0
12 -1.023106717 1356 14301 0.094818544 0
13 -0.334378904 6985 15085 0.463042758 0
14 -1.037626046 2116 23075 0.091700975 0
15 -0.752380459 2592 14656 0.176855895 0
16 -0.833254567 2071 14107 0.14680655 0
17 -1.07469764 1071 12720 0.084198113 0
18 -0.781164581 2298 13884 0.165514261 0
19 -0.943526427 620 5444 0.113886848 0
20 -0.955057755 2188 19729 0.110902732 0

Total number of rows: 5376

Table truncated, full table size 206 Kbytes.




Supplementary file Size Download File type/resource
GSM103761.gpr.gz 370.5 Kb (ftp)(http) GPR

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