|
| Status |
Public on Nov 12, 2013 |
| Title |
Day 3 post-MRSA wild type infection, sample 2 |
| Sample type |
RNA |
| |
|
| Source name |
male C57BL/6 mouse, day 3 post-MRSA infection
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
gender: male
tissue: lung
treatment: methicillin-resistant Staphylococcus aureus (MRSA) infection
time post-mrsa infection: 3 day
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Standard protocol as recommended by Illumina.
|
| Label |
Biotin
|
| Label protocol |
Standard protocol as recommended by Illumina.
|
| |
|
| Hybridization protocol |
Standard protocol as recommended by Illumina.
|
| Scan protocol |
Standard protocol as recommended by Illumina using the Illumina iScan.
|
| Description |
Day 3 post-MRSA wild type infection.
|
| Data processing |
Raw signal intensities of each probe were obtained using data analysis software (Illumina BeadStudio) and imported to the Lumi package of Bioconductor for data transformation and normalization (Du et al. 2008 [PMID 18467348], Lin et al. 2008 [PMID 18178591], Du et al. 2007 [PMID 17540033]). A/P call detection was performed based on detection p-value. The probes with less than 0.01 were considered as valid signals. The data for these probes were normalized by the quantile method. Differentially expressed genes were identified using an Analysis of Variance (ANOVA) model with empirical Bayesian variance estimation (Wettenhall et al. 2004 [PMID 15297296]). The problem of multiple comparisons was corrected using the false discovery rate (FDR). Initially, genes were identified as being differentially expressed on the basis of a statistically significant (raw p-value < 0.01 and fdr < 0.05 and 1.5-fold change (up or down) in expression level in different treatment samples.
|
| |
|
| Submission date |
Dec 02, 2011 |
| Last update date |
Nov 12, 2013 |
| Contact name |
Jiwang Chen |
| E-mail(s) |
chenjw@uic.edu
|
| Organization name |
University of Illinois at Chicago
|
| Street address |
840 S Wood Street
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60612 |
| Country |
USA |
| |
|
| Platform ID |
GPL6885 |
| Series (1) |
| GSE36587 |
Transcriptional events during lung recovery from MRSA infection: a mouse pneumonia model |
|
