|
| Status |
Public on Jul 01, 2016 |
| Title |
dtatC-vs-ip_37C-stat_GEO_sample03 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Yersinia pseudotuberculosis stationary phase culture grown at 37°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 for 1 hour at 26°C in LB medium supplemented with 2.5 mM CaCl2 under aeration, then shifted to 37°C and grown to stationary phase (OD600=2.0).
|
| 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 stationary phase culture grown at 37°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 for 1 hour at 26°C in LB medium supplemented with 2.5 mM CaCl2 under aeration, then shifted to 37°C and grown to stationary phase (OD600=2.0).
|
| 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 3 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) |
| GSE80531 |
Transcriptomic and phenotypic analysis reveals new functions for the Tat pathway in Yersinia pseudotuberculosis [dtatC-vs-ip_37C-stat] |
| GSE80532 |
Transcriptomic and phenotypic analysis reveals new functions for the Tat pathway in Yersinia pseudotuberculosis |
|
