|
| Status |
Public on Oct 23, 2015 |
| Title |
Sputum_R31 |
| Sample type |
RNA |
| |
|
| Source name |
Sputum sample from R31 (group:Control)
|
| Organism |
Homo sapiens |
| Characteristics |
age: 65
Sex: Male
disease: Control
tissue: Sputum
subtype: pauci
|
| 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 U133 Plus 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 human 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.
|
| |
|
| Submission date |
Oct 26, 2012 |
| Last update date |
Oct 23, 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 |
GPL570 |
| Series (1) |
| GSE41863 |
Sputum gene expression profiling in asthmatics |
|
