|
| Status |
Public on Oct 11, 2015 |
| Title |
1096_SMK_12_LPS SMK_12_lps2_1096_R |
| Sample type |
RNA |
| |
|
| Source name |
Lung sample from smoke exposed animal 1096 (treatment: LPS) at 12h time point
|
| Organism |
Mus musculus |
| Characteristics |
animal id: 1096
prior exposure: smoke
treatment: LPS
time: 12h
tissue: lung
strain: C57BL/6
|
| 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 amplified and labeled using NuGen Ovation Chemistry (San Carlos, California) according to manufacturer’s instruction.
|
| |
|
| 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.
|
| Description |
1096_SMK_12_LPS SMK_12_lps2_1096_R SMK_12_lps2_1096_R
|
| 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 18, 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) |
| GSE41684 |
Precision Cut Lung Slices: A Novel Method for Examining Respiratory Diseases |
|
