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Sample GSM1576384 Query DataSets for GSM1576384
Status Public on Jan 06, 2015
Title tam44_41_15min_rep1
Sample type RNA
 
Source name tam44 cells, 41 ℃, 15 minute, replicate 1
Organism Corynebacterium glutamicum
Characteristics strain: tam44
sampling time: 15 minutes
Treatment protocol When OD610 of the cultures reached around 7, the growth temperature increased to 41 ℃, and the cultures were incubated for additional 1 hour.
Growth protocol All strains were grown in 10 ml A medium supplemented with 4 % glucose at 33 ℃ with agitation (200 rpm).
Extracted molecule total RNA
Extraction protocol Total RNA was extacted from each sample with NucleoSpin RNA (TaKaRa Bio Inc., JAPAN), according to the manufacturer's recommendations.
Label Cy3
Label protocol The cDNAs were synthesized from RNA by using reverse transcriptase from 10 μg of total RNAs and labeled with cyanine 3 (Cy3) using the SuperScript Indirect cDNA Labeling system (Life Technologies).
 
Hybridization protocol Hybridization was performed using Gene Expression Hybridization Kit according to the manufacture’s manual (Agilent). The labeled cDNA was hybridized to microarrays in an Agilent Technologies Microarray chamber at 65˚C for 17 h in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent), and 1 minute with 37˚C GE Wash buffer 2 (Agilent).
Scan protocol Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) at a resolution of 5 µm using single color scan setting for 4x44k array slides. PMT is set to 100% for Cy3 channels.
Description gene expression 15 minutes after growth temperature upshift
Data processing The scanned images were analyzed quantified with Feature Extraction Software 10.5.5.1 (Agilent) using default parameters (protocol GE1_105_Dec08). Feature extracted data were analyzed using GeneSpring GX v 12.0 software from Agilent. Normalization of the data was done in GeneSpring GX using the recommended Percentile shift normalization (50th percentile).
 
Submission date Jan 05, 2015
Last update date Jan 06, 2015
Contact name Shinichi Oide
E-mail(s) soide@rite.or.jp
Organization name Research institute of Innovative Technology for the Earth (RITE)
Street address 9-2 Kizugawadai, Kizugawa
City Kyoto
ZIP/Postal code 619-0292
Country Japan
 
Platform ID GPL17881
Series (1)
GSE64654 Transcriptome analyses of the Corynebacterium glutamicum strains adapted to supraoptimal growth temperatures

Data table header descriptions
ID_REF
VALUE Normalized log2 value

Data table
ID_REF VALUE
GE_BrightCorner -3.747729219
DarkCorner -6.467101661
CGRfwd12996 -0.226177222
CGRfwd02925 1.266219101
CGRrev10208 2.294559482
CGRfwd05513 3.44550795
CGRfwd02214 -1.005438799
CGRrev03511 5.296581271
CGR2323 5.493815289
CGRic10 6.122019702
CGRrev12095 -1.184155533
CGRrev07327 3.46805759
CGRfwd09606 -1.04288724
CGRrev13276 -1.33613786
CGRfwd01345 -0.189757372
CGRfwd15546 2.905754926
CGRrev07226 -0.894013454
CGRrev01475 5.477497991
CGRrev11415 -1.818423789
CGRfwd11558 -3.172311887

Total number of rows: 40264

Table truncated, full table size 943 Kbytes.




Supplementary file Size Download File type/resource
GSM1576384_tam44_15min.txt.gz 2.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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