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Sample GSM846072 Query DataSets for GSM846072
Status Public on Dec 09, 2011
Title wild type, rep2
Sample type mixed
 
Channel 1
Source name S. Typhimurium SL1344 wild type
Organism Salmonella enterica subsp. enterica serovar Typhimurium
Characteristics strain: SL1344
genotype: wild type
growth phase: early stationary
Growth protocol Cultures were grown aerobically in LB to early stationary phase (OD 600=2.3).
Extracted molecule total RNA
Extraction protocol Extraction protocols at http://www.ifr.ac.uk/safety/Microarrays/protocols.html
Label Cy5
Label protocol Labelling protocol at http://www.ifr.ac.uk/safety/Microarrays/protocols.html
 
Channel 2
Source name S. Typhimurium genomic DNA
Organism Salmonella enterica subsp. enterica serovar Typhimurium
Characteristics strain: SL1344
genotype: wild type
Growth protocol Cultures were grown aerobically in LB to early stationary phase (OD 600=2.3).
Extracted molecule genomic DNA
Extraction protocol Extraction protocols at http://www.ifr.ac.uk/safety/Microarrays/protocols.html
Label Cy3
Label protocol Labelling protocol at http://www.ifr.ac.uk/safety/Microarrays/protocols.html
 
 
Hybridization protocol Slides were blocked with DCE according to protocol at PMID 11266573. For hybridization and washing protocols, see http://www.ifr.ac.uk/safety/Microarrays/protocols.html
Scan protocol Axon GenePix4000A 10 µm resolution scan. See http://www.ifr.ac.uk/safety/Microarrays/default.html#protocols
Description SL1344 2
Data processing Intensity ratios of channel 1 (cDNA) divided by channel 2 (reference gDNA) signals are calculated using BlueFuse 3.01 (BlueGnome, Cambridge, UK). Data centering was subsequently performed using block median normalization.
 
Submission date Dec 08, 2011
Last update date Dec 09, 2011
Contact name Neil Shearer
E-mail(s) neil.shearer@ifr.ac.uk
Organization name Institute of Food Research
Department Gut Health and Food Safety
Lab Salmonella
Street address Colney Lane
City Norwich
State/province Norfolk
ZIP/Postal code NR47UA
Country United Kingdom
 
Platform ID GPL13609
Series (1)
GSE34269 Salmonella Typhimurium: Wild type SL1344 Vs. ∆relA, ∆spoT (ppGpp0) strain grown under SPI1-inducing conditions

Data table header descriptions
ID_REF
VALUE Block median normalized log2 ratio (cDNA/reference gDNA)

Data table
ID_REF VALUE
1 0.428
2 -0.43
3 0.973
4 3.091
5 -2.603
6 -2.791
7 -0.988
8 -3.846
9 -1.045
10 0.21
11 -3.24
12 -3.658
13 -0.149
14 -1.823
15 -0.139
16 2.72
17 1.53
18 -0.775
19 -4.145
20 1.18

Total number of rows: 8064

Table truncated, full table size 88 Kbytes.




Supplementary file Size Download File type/resource
GSM846072.txt.gz 564.1 Kb (ftp)(http) TXT
Processed data included within Sample table
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