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Sample GSM2552929 Query DataSets for GSM2552929
Status Public on Mar 29, 2017
Title SL1344_Exponential_BR1
Sample type mixed
 
Channel 1
Source name SL1344 cells
Organism Salmonella enterica subsp. enterica serovar Typhimurium
Characteristics strain: SL1344
Growth protocol Cultures of S. Typhimurium SL1344 were inoculated 1:100 into 25 mls fresh Lennox broth and grown at 37oC until OD600 0.2 (Late exponential phase) or OD600 2.0 (Early stationary phase) was reached
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from the cells using the SV total RNA isolation kit from promega as described (www.ifr.ac.uk/safety/molmicro). Sonicated genomic DNA was used as a reference in these experiments and was purified by standard phenol-chloroform extraction followed by sodium acetate/ethanol precipitation.
Label Cy3
Label protocol cDNA synthesis was performed with the Superscript double-stranded cDNA synthesis kit (Invitrogen), following the random-priming method outlined by the manufacturer. Fluorescent labeling of DNA samples for transcriptomic experiments were carried out using the BioPrime Random Labeling kit (Invitrogen) as follows: 60 ml of 2.5 x random primer solution, x* ul DNA, and (70.5-x) ul sterile water were heated at 100oC for 10 minutes, snap chilled on ice and following were then added – 15 ul dNTP mix (1mM dCTP, 2mM dGTP, dTTP, dATP), 1.5 ul 1 mM Cy3/Cy5 labeled dCTP (GE healthcare) and 3 ul Klenow fragment (40 U/ ml). *[1000 ng of cDNA and 1000 ng of sonicated genomic DNA were fluorescently labeled with Cy3 d-CTP and Cy5-dCTP respectively]. The Labeling reactions wereas carried out at 37 oC overnight and 15 ul of stop buffer added to terminate the reaction.
 
Channel 2
Source name SL1344 control DNA
Organism Salmonella enterica subsp. enterica serovar Typhimurium
Characteristics strain: SL1344
Growth protocol Cultures of S. Typhimurium SL1344 were inoculated 1:100 into 25 mls fresh Lennox broth and grown at 37oC until OD600 0.2 (Late exponential phase) or OD600 2.0 (Early stationary phase) was reached
Extracted molecule genomic DNA
Extraction protocol Total RNA was extracted from the cells using the SV total RNA isolation kit from promega as described (www.ifr.ac.uk/safety/molmicro). Sonicated genomic DNA was used as a reference in these experiments and was purified by standard phenol-chloroform extraction followed by sodium acetate/ethanol precipitation.
Label Cy5
Label protocol cDNA synthesis was performed with the Superscript double-stranded cDNA synthesis kit (Invitrogen), following the random-priming method outlined by the manufacturer. Fluorescent labeling of DNA samples for transcriptomic experiments were carried out using the BioPrime Random Labeling kit (Invitrogen) as follows: 60 ml of 2.5 x random primer solution, x* ul DNA, and (70.5-x) ul sterile water were heated at 100oC for 10 minutes, snap chilled on ice and following were then added – 15 ul dNTP mix (1mM dCTP, 2mM dGTP, dTTP, dATP), 1.5 ul 1 mM Cy3/Cy5 labeled dCTP (GE healthcare) and 3 ul Klenow fragment (40 U/ ml). *[1000 ng of cDNA and 1000 ng of sonicated genomic DNA were fluorescently labeled with Cy3 d-CTP and Cy5-dCTP respectively]. The Labeling reactions wereas carried out at 37 oC overnight and 15 ul of stop buffer added to terminate the reaction.
 
 
Hybridization protocol Cy3 labeled cDNA and Cy5 labeled control genomic DNAs were co-precipitated using standard sodium acetate/ethanol procedures and resuspended in hybridization buffer (Oxford Gene Technologies), and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers and hybridiized for 24 hours at 55oC in an Agilent hybiridization oven at 5 rpm. After hybridization, slides were washed according to instructions provided by Oxford Gene Technologies
Scan protocol The microarray slides were scanned using an Agilent G2505C scanner. Cy3 and Cy5 images were acquired at 5 micron resolution. Scanned images were analyzed using Feature extraction software (Agilent).
Description biological replicate 1
Data processing median normalization of background subtracted Cy3/Cy5 ratios
 
Submission date Mar 28, 2017
Last update date Mar 29, 2017
Contact name Shane Dillon
E-mail(s) [email protected]
Organization name Dublin Institute of Technology
Department School of Biological Sciences
Street address Kevin Street
City Dublin
ZIP/Postal code Dublin 8
Country Ireland
 
Platform ID GPL11416
Series (1)
GSE97161 Salmonella enterica serovar Typhimurium gene expression in exponential and stationary phase cultures

Data table header descriptions
ID_REF
VALUE median normalized Log2 Cy3/Cy5 ratios representing test/reference samples

Data table
ID_REF VALUE
1 5.017218744
2 5.009064239
3 4.191286112
4 3.670542608
5 -1.475375634
6 -4.679816047
7 4.709416963
8 -3.253910663
9 1.09424284
10 -0.755693714
11 -0.156283948
12 -1.052496776
13 2.001483723
14 -1.037575514
15 1.013872578
16 1.203799741
17 -3.646296457
18 1.255399467
19 1.161543488
20 0.758697781

Total number of rows: 15738

Table truncated, full table size 270 Kbytes.




Supplementary file Size Download File type/resource
GSM2552929_US91303661_SLOT01_S01_GE2_105_Dec08_1_1_Transcriptome_Exp_BR1.txt.gz 1.6 Mb (ftp)(http) TXT
Processed data included within Sample table

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