NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1535909 Query DataSets for GSM1535909
Status Public on Nov 01, 2014
Title S_meliloti_rpoH1rpoH2_37C_10min_rep2
Sample type RNA
 
Source name rpoH1 rpoH2 mutant cells, with heat shock for 10 min
Organism Sinorhizobium meliloti 1021
Characteristics genotype: rpoH1 rpoH2 double mutant
Growth protocol Sinorhizobium meliloti 1021 was grown to mid-log phase (O.D.660nm 0.3) aerobically at 25°C in LB/MC medium.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted with TRIzol reagent (Invitrogen) and further purified using a RNeasy Midi kit (Qiagen). DNA was removed by DNase digestion with the RNase-Free DNase set (Takara Bio). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer.
Label Cy3
Label protocol Labeling was performed by Roche Diagnostics Japan, following their standard operating protocol.
 
Hybridization protocol Hybridization was performed by Roche Diagnostics Japan, following their standard operating protocol.
Scan protocol Scanning was performed with GenePix 4000B Microarray Scanner by Roche Diagnostics Japan, following their standard operating protocol.
Description This sample is of a rpoH1 rpoH2 double mutant of Sinorhizobium meliloti 1021. It is the second of four biological replicates of mutant cells with heat shock for 10 min, each from separate cultures.
Data processing The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package (Roche NimbleGen, Inc.).
 
Submission date Oct 31, 2014
Last update date Nov 01, 2014
Contact name Hisayuki Mitsui
Organization name Tohoku University
Department Graduate School of Life Sciences
Street address 2-1-1, Katahira, Aoba-ku
City Sendai
ZIP/Postal code 980-8577
Country Japan
 
Platform ID GPL19375
Series (1)
GSE62900 Expression analysis of Sinorhizobium meliloti 1021rpoH1 rpoH2 mutant during heat shock

Data table header descriptions
ID_REF
VALUE RMA-normalized, averaged gene-level signal intensity

Data table
ID_REF VALUE
SMa0002 1828.0527
SMa0005 667.7072
SMa0007 519.0853
SMa0009 346.9024
SMa0011 270.8757
SMa0013 118.5583
SMa0015 190.2802
SMa0017 1399.612
SMa0018 5505.4635
SMa0020 16613.6576
SMa0021 2200.4722
SMa0025 591.5436
SMa0026 192.3497
SMa0028 316.3698
SMa0031 3539.9628
SMa0034 3174.7902
SMa0036 1115.8056
SMa0039 701.6855
SMa0041 484.9705
SMa0044 105.7757

Total number of rows: 6193

Table truncated, full table size 109 Kbytes.




Supplementary file Size Download File type/resource
GSM1535909_421292A04.pair.gz 895.9 Kb (ftp)(http) PAIR
GSM1535909_421292A04_RMA.calls.gz 66.5 Kb (ftp)(http) CALLS
Processed data included within Sample table
Processed data provided as supplementary file

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