|
| Status |
Public on Aug 08, 2013 |
| Title |
Lung-d49_SeV-3a |
| Sample type |
RNA |
| |
|
| Source name |
whole lung, SeV post-infection day 49, rep 3, array strip A
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
time: 49 days post-infection
infection: active Sendai virus
gender: Male
|
| Treatment protocol |
Sendai virus (SeV), strain 52, was obtained from American Type Culture Collection and stored at -70°C. Mice were inoculated with SeV or an equivalent amount of UV-inactivated SeV (SeV-UV) intranasally. 3-5 week old male C57BL/6J mice were obtained from Jackson Laboratory. Mice were sacrificed post-infection day 49, and lungs were harvested, right for RNA, left for histology and other studies (see Kim et al, 2008, PMID:18488036).
|
| Growth protocol |
Mice were maintained under pathogen-free conditions, and all study protocols were approved by the Washington University Animal Studies Committee.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using QIAGEN RNeasy kit per manufacturer's protocol. Quality control was performed with Agilent Bioanalyzer.
|
| Label |
biotin
|
| Label protocol |
Biotinylated aRNA were prepared using the Illumina TotalPrep Kit (Ambion) per manufacturer's protocol.
|
| |
|
| Hybridization protocol |
Standard Illumina hybridization protocol
|
| Scan protocol |
Standard Illumina scanning protocol except for adding output of raw array data for beadlevel analyses
|
| Description |
Strip A from array and sample B6.49.S.3745 each BeadChip consists of two strips (A & B).
B6.49.S.3745.1
|
| Data processing |
Hybridization and scanning of BeadChip arrays was performed according to the manufacturer’s instructions, using BeadStudio 3.0 software (Illumina). In order to perform bead-level analysis, raw data is exported from BeadStudio. Microarray normalization and statistical analysis was performed using packages from the Bioconductor project executed in the R programming environment. Raw bead-level intensity data was imported using functions from the beadarray package, including background correction. Each Mouse-WG6 v2 BeadChip array consists of two strips. Due to potential variation in the data from the two different strips (see Shi et al. (2009) [PMID:19903361]), we treated the individual strips from each sample separately through bead-summarization. Thus, for each strip, low-level analysis and quality control was performed using functions from the beadarray package (see Ritchie et al. (2011) [PMID:22144879]). The BASH algorithm was then applied to the raw data to mask beads affected by large spatial artifacts, followed by bead-type summarization, including removal of outlier beads. Summarized data were Log2-transformed, followed by quantile normalization.
|
| |
|
| Submission date |
Aug 07, 2013 |
| Last update date |
Aug 08, 2013 |
| Contact name |
Anand Champak Patel |
| E-mail(s) |
[email protected]
|
| Organization name |
Washington University School of Medicine
|
| Department |
Pulmonary/Critical Care Medicine
|
| Lab |
Patel
|
| Street address |
Campus Box 8116, 660 S. Euclid Ave.
|
| City |
St. Louis |
| State/province |
MO |
| ZIP/Postal code |
63110 |
| Country |
USA |
| |
|
| Platform ID |
GPL17543 |
| Series (1) |
| GSE49603 |
Virus-Induced Airway Disease in Mice (C57BL/6J, d49) |
|
