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Sample GSM1277382 Query DataSets for GSM1277382
Status Public on Jul 01, 2014
Title 30 min after onset CO2 depletion (2.3) vs CO2 supplemented culture (1.3) 1st of duplicate time series
Sample type RNA
 
Channel 1
Source name 2.3
Organism Lactobacillus johnsonii
Characteristics strain: LA-1
culture condition: 30 min after onset CO2 depletion (2.3)
Treatment protocol Cells were harvested at 0.15 OD600 from 50 ml of growth medium by cold centrifugation (5', 2600 * g, 4 C)
Growth protocol Cultures were grown in 400 ml batches with MRS at 37˚C under constant pH of 6.5, sparged with gas mixtures 750 ml/min, stirring of ca. 200 rpm
Extracted molecule total RNA
Extraction protocol Cultures were lysed by beat-beating and total RNA was isolated by subsequent phenol-chloroform extraction, followed by RNA purification
Label Cy5
Label protocol The Cyscribe Post-labeling kit was used to synthesize cDNA out of 5 µg of total RNA, which was subsequently labeled according to the manufacturer's protocol (Amersham Biosciences, Amersham, Uk).
 
Channel 2
Source name 1.3
Organism Lactobacillus johnsonii
Characteristics strain: LA-1
culture condition: CO2 supplemented culture (1.3)
Treatment protocol Cells were harvested at 0.15 OD600 from 50 ml of growth medium by cold centrifugation (5', 2600 * g, 4 C)
Growth protocol Cultures were grown in 400 ml batches with MRS at 37˚C under constant pH of 6.5, sparged with gas mixtures 750 ml/min, stirring of ca. 200 rpm
Extracted molecule total RNA
Extraction protocol Cultures were lysed by beat-beating and total RNA was isolated by subsequent phenol-chloroform extraction, followed by RNA purification
Label Cy3
Label protocol The Cyscribe Post-labeling kit was used to synthesize cDNA out of 5 µg of total RNA, which was subsequently labeled according to the manufacturer's protocol (Amersham Biosciences, Amersham, Uk).
 
 
Hybridization protocol To the mixed cDNA's 25 µl Slidehyb #1 hybridization buffer (Ambion, Austin, USA) 2x Hi-RPM hyb. Buffer (Agilent) was added and 40 ul of the resulting solution was applied on the slides
Scan protocol Slides were scanned with a ScanArray Express 4000 scanner (Perkin Elmer)
Description 2.3 over 1.3
1st of duplicate time series
Data processing Data were normalized using Lowess normalization as available in MicroPrep and corrected for inter-slide differences. Median intensity of the different probes per gene was selected as the gene expression intensity.
 
Submission date Dec 02, 2013
Last update date Jul 01, 2014
Contact name Michiel Wels
E-mail(s) michiel.wels@nizo.com
Organization name NIZO food research
Street address Kernhemseweg 2
City Ede
ZIP/Postal code 6718 ZB
Country Netherlands
 
Platform ID GPL18009
Series (1)
GSE52876 Genome-wide transcriptome analysis of the oxygen response of L. johnsonii reveals that NADH oxidase is a secondary H2O2 source.

Data table header descriptions
ID_REF
VALUE normalized ratio (Cy5/Cy3)

Data table
ID_REF VALUE
1 0.89094482
2 2.958692689
3
4 1.914832836
5 1.128934949
6 1.272606088
7
8 1.525305934
9 0.640626346
10 0.985748709
11
12
13
14
15 1.429561883
16
17
18
19 1.410781305
20

Total number of rows: 43711

Table truncated, full table size 727 Kbytes.




Supplementary file Size Download File type/resource
GSM1277382_10024-2_1.txt.gz 1.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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