|
| Status |
Public on Jul 01, 2012 |
| Title |
UTI T2 biological rep2 [GU-16.CEL] |
| Sample type |
RNA |
| |
|
| Source name |
Bladder, 24h Infection
|
| Organism |
Mus musculus |
| Characteristics |
Sex: female
strain: C57BL/6
age: 10 wk
|
| Treatment protocol |
Mice were catheterized using a sterile Teflon catheter and 40 microlitres of PBS containing 10^9 CFU was instilled transurethrally into the bladder. Whole bladders collected at 24h following infection
|
| Growth protocol |
O/N LB culture of UPEC CFT073 at 37C was collected and concentrated into PBS by centrifugation and washes in PBS
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions
|
| Label |
biotin
|
| Label protocol |
RNA that passed Bioanalyzer analysis was quantified and 100 ng used for cDNA synthesis. RNA-derived biotinylated sense-strand DNA was applied to the whole transcript Gene 1.0 ST Mouse Microarray and hybridization was performed according to the manufacturers’ instructions in an Affymetrix Fluidics Station 400.
|
| |
|
| Hybridization protocol |
Hybridization was performed according to the manufacturers’ instructions
|
| Scan protocol |
GeneChips were scanned using the Affymetrix 3000 7G scanner
|
| Description |
GU-16.CEL
amplified into double-stranded cDNA with random hexamers tagged with a T7 promoter sequence
|
| Data processing |
Raw microarray data were normalized using quantile normalization and summarized using RMA as implemented in the affy package in Bioconductor. Differentially expressed genes were identified by analyzing the data using the MAANOVA package (Wu et al., 2003) (http://www.bioconductor.org/packages/bioc/1.8/html/maanova.html)
RMA signal intensity; significant changes in gene expression identified using a shrinkage based t test together with permutation. A false discovery rate (FDR) of 0.05 was used to generate the significant gene list
|
| |
|
| Submission date |
Dec 29, 2011 |
| Last update date |
Jul 01, 2012 |
| Contact name |
Glen C Ulett |
| E-mail(s) |
[email protected]
|
| Phone |
61756780765
|
| Organization name |
Griffith University
|
| Department |
School of Medical Science
|
| Street address |
Parklands Drive
|
| City |
Gold Coast |
| State/province |
QLD |
| ZIP/Postal code |
4222 |
| Country |
Australia |
| |
|
| Platform ID |
GPL6246 |
| Series (1) |
| GSE27575 |
Expression data for UPEC and GBS cystitis in female C57BL/6 mice |
|
