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Sample GSM2129862 Query DataSets for GSM2129862
Status Public on Jul 01, 2016
Title dtatC-vs-ip_26C-log_GEO_sample01
Sample type RNA
 
Channel 1
Source name Yersinia pseudotuberculosis exponential phase culture grown at 26°C
Organism Yersinia pseudotuberculosis IP 32953
Characteristics strain: IP32953 wild type
Growth protocol Y. pseudotuberculosis wild-type strain IP32953 and its isogenis tatC mutant were grown at 26°C in LB medium under aeration to exponential phase (OD600=0.8).
Extracted molecule total RNA
Extraction protocol RNA extraction was performed using the SV Total RNA Isolation System (Promega)
Label Cy5
Label protocol RNA samples were labelled either with Cy3 (mutant) or Cy5 (wild type) using the ULS fluorescent labelling kit (Kreatech, Germany)
 
Channel 2
Source name Yersinia pseudotuberculosis exponential phase culture grown at 26°C
Organism Yersinia pseudotuberculosis IP 32953
Characteristics strain: IP32953 tatC mutant
Growth protocol Y. pseudotuberculosis wild-type strain IP32953 and its isogenis tatC mutant were grown at 26°C in LB medium under aeration to exponential phase (OD600=0.8).
Extracted molecule total RNA
Extraction protocol RNA extraction was performed using the SV Total RNA Isolation System (Promega)
Label Cy3
Label protocol RNA samples were labelled either with Cy3 (mutant) or Cy5 (wild type) using the ULS fluorescent labelling kit (Kreatech, Germany)
 
 
Hybridization protocol 300ng of each Cy3- and Cy5-labelled RNA and hybridized to the microarray at 65°C for 17 hours using the Agilent Hybridization Chamber according to the Agilent instructions
Scan protocol The array were scanned at a resolution of 5μm using the Axon GenePix Personal 4100A microarray scanner (Axon instruments) and features were extracted using GenePix Pro 6
Description Biological replicate 1 of 4.
Data processing Microrarray data processing was done using the Limma package (Smyth, 2005) from the R/Bioconductor framework (Gentleman et al., 2004). Unprocessed array intensity values were read-in using function read.maimages and background corrected with the improved saddle-point approximation to maximum likelihood method (Silver et al., 2009) using an intensity offset of 50. Array intensities have been normalized within each array using loess normalization (Yang et al., 2002) and between arrays using quantile normalization (Bolstad et al., 2003, Yang and Thorne, 2003) to obtain similar distributions of expression intensities. To obtain reliable gene expression values, we averaged normalized intensities of at least three probes targeting the same gene. Differentially expressed genes were determined using the lmFit function for linear modeling and by computation of moderated t-statistics and log-odds with function eBayes (Smyth, 2004). P-values from the moderated t-tests have been corrected for multiple testing using the Benjamini-Hochberg procedure for controlling the false discovery rate. Finally the set of differentially expressed genes was filtered by fold change (|log2FC| >=0.8).
 
Submission date Apr 21, 2016
Last update date Jul 01, 2016
Contact name Ann Kathrin Heroven
E-mail(s) Annkathrin.Heroven@helmholtz-hzi.de
Phone +49-(0)53161815705
Organization name Helmholtz Centre for Infection Research
Department Molecular Infection Biology
Street address Inhoffenstr. 7
City Braunschweig
State/province Niedersachsen
ZIP/Postal code 38124
Country Germany
 
Platform ID GPL15095
Series (2)
GSE80528 Transcriptomic and phenotypic analysis reveals new functions for the Tat pathway in Yersinia pseudotuberculosis [dtatC-vs-ip_26C-log]
GSE80532 Transcriptomic and phenotypic analysis reveals new functions for the Tat pathway in Yersinia pseudotuberculosis

Data table header descriptions
ID_REF
VALUE log2 ratio (Cy3/Cy5) for mutant/wild type

Data table
ID_REF VALUE
4 0.173099545
5 0.479062824
7 0.629707575
8 0.05202271
9 0.008684642
10 0.267666892
12 0.65658645
13 0.402291423
14 0.446899102
15 -0.09481526
16 0.71433758
17 -0.148969823
19 0.117680401
20 0.409002795
21 0.552640671
22 0.561888502
23 0.318567824
24 0.011100148
25 0.450973922
26 0.172357992

Total number of rows: 12975

Table truncated, full table size 223 Kbytes.




Supplementary file Size Download File type/resource
GSM2129862_252041210019_201205241211_S01_GE2_107_Sep09_1_1.txt.gz 1.2 Mb (ftp)(http) TXT
GSM2129862_dtatC-vs-ip_26C-log_GEO_sample01.tab.gz 236.1 Kb (ftp)(http) TAB
Processed data included within Sample table
Processed data provided as supplementary file

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