NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM829446 Query DataSets for GSM829446
Status Public on Mar 31, 2014
Title R137_dksA_ctrl5_ch1_Cy5_670_dksA_NO5_ch2_Cy3_650
Sample type RNA
 
Channel 1
Source name DKSA_CTRL5
Organism Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S
Characteristics genotype/variation: DKSA mutant
agent: CTRL
Growth protocol dksa minus salmonella mutant grown to 0d600 0.4 in 25 ml e salts minimal medium supplemented with 0.4% glucose, 0.1% casamino acids, 10μm fecl2, and 2 μg/ml thiamine, let grow for an additional 30 min, replicate 05: 110208
Extracted molecule total RNA
Extraction protocol High Pure RNA isolation kit (Roche)
Label Cy5
Label protocol Incorporation of dye using about 1200U Superscript II reverse transcriptase (Invitrogen, Carlsbad, CA), 40ng/ul random hexamer primers, 4nmol Cy dUTP (GE Healthcare, Fairfield, CT), and 80U RNAse Inhibitor (Roche, Indianapolis, IN), in 60ul reactions. Reverse transcription was performed for 2h at 42˚C, and the pH adjusted with 50mM NaOH. After a 10min incubation at 70˚C reactions were neutralized using HCl. Labeled cDNA was purified using the QIAGEN PCR purification kit as suggested by the manufacturer (Qiagen, Valencia, CA).
 
Channel 2
Source name DKSA_NO5
Organism Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S
Characteristics genotype/variation: DKSA mutant
agent: NO
Growth protocol dksa minus salmonella mutant grown to 0d600 0.4 in 25 ml e salts minimal medium supplemented with 0.4% glucose, 0.1% casamino acids, 10μm fecl2, and 2 μg/ml thiamine, and treated with 5 mm detanonoate for 30 min, replicate 05: 110208
Extracted molecule total RNA
Extraction protocol High Pure RNA isolation kit (Roche)
Label Cy3
Label protocol Incorporation of dye using about 1200U Superscript II reverse transcriptase (Invitrogen, Carlsbad, CA), 40ng/ul random hexamer primers, 4nmol Cy dUTP (GE Healthcare, Fairfield, CT), and 80U RNAse Inhibitor (Roche, Indianapolis, IN), in 60ul reactions. Reverse transcription was performed for 2h at 42˚C, and the pH adjusted with 50mM NaOH. After a 10min incubation at 70˚C reactions were neutralized using HCl. Labeled cDNA was purified using the QIAGEN PCR purification kit as suggested by the manufacturer (Qiagen, Valencia, CA).
 
 
Hybridization protocol 42C overnight in standard hybridization buffer (Roche Nimblegen)
Scan protocol GenePix4000B scanner (Molecular Devices, Sunnyvale, CA) using Acuity 4.0 software.
Data processing Signal extraction and quantitation with Roche’s NimbleScan 2.4 package
 
Submission date Nov 07, 2011
Last update date Mar 31, 2014
Contact name Michael McClelland
E-mail(s) mcclelland.michael@gmail.com
Phone 858-336-9554
Organization name University of California, Irvine
Department Microbiology & Molecular Genetics
Street address 132 Med Surge I
City Irvine
State/province CA
ZIP/Postal code 92697
Country USA
 
Platform ID GPL14855
Series (1)
GSE33529 Role of DksA in nitrosative stress

Data table header descriptions
ID_REF
VALUE log ratios of contributions to total signal (experimental condition / control)
CH1_SIGNAL_R137_DKSA_CTRL5_Cy5_670 Cy5 signal intensity dksA Ctrl5
CH2_SIGNAL_R137_DKSA_NO5_Cy3_650 Cy3 signal intensity dksA NO5

Data table
ID_REF VALUE CH1_SIGNAL_R137_DKSA_CTRL5_Cy5_670 CH2_SIGNAL_R137_DKSA_NO5_Cy3_650
MMCCSAL07_00001 0.340685291 303.33 1234.22
MMCCSAL07_00002 0.457247175 230.78 1228.11
MMCCSAL07_00003 0.306559041 276.67 1040.67
MMCCSAL07_00004 0.202847493 392.78 1163.56
MMCCSAL07_00005 0.268643682 318.22 1096.89
MMCCSAL07_00006 0.12053769 312.67 766.33
MMCCSAL07_00007 -0.781744865 3845.89 1180.44
MMCCSAL07_00008 0.435197081 171.89 869.44
MMCCSAL07_00009 0.409770501 245.56 1171.44
MMCCSAL07_00010 0.372728772 241.78 1059.11
MMCCSAL07_00011 0.262252712 275.44 935.56
MMCCSAL07_00012 0.325377312 311.44 1223.33
MMCCSAL07_00013 0.206592049 342.33 1022.89
MMCCSAL07_00014 0.210959287 378.11 1141.22
MMCCSAL07_00015 0.24526914 281.56 919.67
MMCCSAL07_00016 0.139275219 324 829.11
MMCCSAL07_00017 0.183491417 356.56 1010.22
MMCCSAL07_00018 0.08043036 425.11 950
MMCCSAL07_00019 0.034814893 598.22 1203.56
MMCCSAL07_00020 0.159969887 351.44 943.22

Total number of rows: 392936

Table truncated, full table size 16384 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap