|
| Status |
Public on Oct 11, 2015 |
| Title |
233106_PBS_6 |
| Sample type |
RNA |
| |
|
| Source name |
Lung sample from naive animal 233106 at 6hr time point
|
| Organism |
Mus musculus |
| Characteristics |
animal id: 233106
treatment: naive
time (h): 6
tissue: lung
genetic background: balb/c
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the mirVana RNA isolation kit (Ambion, Inc, Austin, TX, USA) according to manufacturer’s protocol. RNA was quantified using a ND-1000 spectrophotometer (Nanodrop Technology®, Cambridge, UK) and RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent technologies, Santa Clara, CA, USA). The 260/280 ratio were between 1.7 and 2.1 and the RINs (RNA Integrity Numbers) greater than 6 for all samples.
|
| Label |
Biotin
|
| Label protocol |
Total RNA (100ng) was transcribed and labeled into amplified RNA (aRNA) using the 3’IVT express kit (Affymetrix Inc., Santa Clara, CA) according to manufacturer’s instruction on a GCAS (Gene Chip Array Station).
|
| |
|
| Hybridization protocol |
Fragmented and labeled aRNA was hybridized to the Affymetrix Mouse Genome 430 2.0 chips according to manufacturer’s instructions. Wash and stain protocol FS450_0004.
|
| Scan protocol |
GeneChips were scanned using the GC 30007G scanner.
|
| Data processing |
Data was normalized in R/Bioconductor using the robust multi-array average (RMA) expression measure. Probesets were annotated using the latest annotation available in Bioconductor and curated using an internal Roche probe inspector tool, which updates gene annotation per probeset based on the latest genome draft release. As an additional quality measure, probesets were also curated using the tool for sequence specificity; probesets mapping to non-unique locations in the genome were flagged and ignored in subsequent analysis. Normalized data (VALUE) represents probesets that probesets passed the QC and curation processes.
|
| |
|
| Submission date |
Oct 17, 2012 |
| Last update date |
Oct 11, 2015 |
| Contact name |
Donavan Cheng |
| E-mail(s) |
donavan.cheng@gmail.com
|
| Organization name |
Hoffmann-LaRoche
|
| Department |
Translational Research Sciences
|
| Street address |
340 Kingsland Ave
|
| City |
Nutley |
| State/province |
NJ |
| ZIP/Postal code |
07110 |
| Country |
USA |
| |
|
| Platform ID |
GPL1261 |
| Series (1) |
| GSE41665 |
Effects of OVA challenge in mouse model of asthma |
|
