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Sample GSM875833 Query DataSets for GSM875833
Status Public on Apr 01, 2012
Title Control - Glucose vs. Glucose Replicate 2
Sample type RNA
 
Channel 1
Source name Mid-exponential phase cultures
Organism Rhodopirellula baltica
Characteristics strain: SH1T
growth condition: glucose
Growth protocol R. baltica SH1T was grown on marine mineral medium, supplemented with glucose as reference substrate or substrates of interest. Cultures have been grown to mid-exponential before being harvested. Collected cell material was shock-frozen and kept at -80 °C until being further processed.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using Ambion's TRI reagent and mechanical lysis following standard procedures.
Label Alexa546
Label protocol 5-10 µg of total RNA have been reverse transcribed using the SuperScript Direct cDNA labelling core kit (Applied Biosystems) following the manufacturers instructions. cDNA was purified using the QUIAEX II Gel extraction kit (Quiagen) according to the instructions described in the manual. Samples have been labelled applying the Platinum BrightTm Alexa 546 and 647 (Kreatech) nucleic acid labeling kits according to the manufacturers protocol.
 
Channel 2
Source name Mid-exponential phase cultures
Organism Rhodopirellula baltica
Characteristics strain: SH1T
growth condition: glucose
Growth protocol R. baltica SH1T was grown on marine mineral medium, supplemented with glucose as reference substrate or substrates of interest. Cultures have been grown to mid-exponential before being harvested. Collected cell material was shock-frozen and kept at -80 °C until being further processed.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using Ambion's TRI reagent and mechanical lysis following standard procedures.
Label Alexa647
Label protocol 5-10 µg of total RNA have been reverse transcribed using the SuperScript Direct cDNA labelling core kit (Applied Biosystems) following the manufacturers instructions. cDNA was purified using the QUIAEX II Gel extraction kit (Quiagen) according to the instructions described in the manual. Samples have been labelled applying the Platinum BrightTm Alexa 546 and 647 (Kreatech) nucleic acid labeling kits according to the manufacturers protocol.
 
 
Hybridization protocol The hybridisation reaction inlcuding denaturing, hybridisation, washing and drying was done in a HS400 Pro Hybridisation station controlled by respective software (Tecan). Arrays have been blocked by pre-hybridisation buffer and blocking reagent. Differently labelled cDNA was pooled in DIG Easy Hyb hybridisation solution (Roche). After blocking, sample solutions were applied to the arrays followed by denaturation and hybridisation at stringent conditions for more than 12 hrs. ULTRArray low stringency wash buffer (Applied Biosystems) was used for final washing followed by drying.
Scan protocol Scanner: ScanArray Express MicroArray scanner (Perkin Elmer)
Images were quantified using ScanArray Express Software (version 4.0)
Description Control - Biological Replicate 2
Data processing LOWESS normalisation, MADA software was used (http://www.mpi-bremen.de/en/MADA), for downstream data processing MayDay was applied (http://www-ps.informatik.uni-tuebingen.de/mayday/wp/)
 
Submission date Feb 15, 2012
Last update date Apr 01, 2012
Contact name Carl-Eric Wegner
E-mail(s) carl-eric.wegner@mpi-marburg.mpg.de
Organization name Max Planck Institute for Terrestrial Microbiology
Street address Karl von Frisch Straße 10
City Marburg (Lahn)
ZIP/Postal code 35043
Country Germany
 
Platform ID GPL7654
Series (1)
GSE35832 Combining transcriptomics with functional phylogenomics elucidates the ecophysiology of sulfatases in marine bacteria

Data table header descriptions
ID_REF
VALUE normalised log2 ratio: Alexa647/Alexa 546

Data table
ID_REF VALUE
RB2098 -1.323
RB2103 -1.204
RB2140 1.455333333
RB2147 0.499
RB2176 0.120666667
RB2188 0.108
RB203 0.123333333
RB2238 -1.006666667
RB2737 0.151
RB2745 1.788666667
RB2784 2.947333333
RB2797 -0.025
RB2832 -0.664
RB2840 0.414333333
RB2875 0.367
RB2885 -1.06
RB3423 0.012666667
RB3431 1.230666667
RB3464 0.763333333
RB3476 1.117666667

Total number of rows: 7733

Table truncated, full table size 135 Kbytes.




Supplementary file Size Download File type/resource
GSM875833_Glucose_Replicate_2.csv.gz 2.6 Mb (ftp)(http) CSV
Processed data included within Sample table

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