|
| Status |
Public on Sep 17, 2010 |
| Title |
Trachea Newborn biological rep 3 |
| Sample type |
RNA |
| |
|
| Source name |
NEWBORN WT PIGS
|
| Organism |
Sus scrofa |
| Characteristics |
tissue: TRACHEA
developmental stage: newborn
genome/variation: wild type
|
| Treatment protocol |
Trachea, bronchus, and distal lung tissue samples were dissected from newborn piglets within 12 h of birth. Samples were cut into ~5 mm3 pieces and stored in RNAlater RNA Stabilization Reagent (Ambion; Austin, TX) using the manufacturer’s recommended protocols.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated with TRIzol Reagent (Invitrogen; Carlsbad, CA). Only RNA samples attaining a minimum of 7.0 RNA Integrity Number on the Agilent 2100 Bioanalyzer (Agilent Technologies; Palo Alto, CA) were processed.
|
| Label |
biotin
|
| Label protocol |
5 μg of total RNA was used to generate biotinylated cRNA using the Affymetrix Gene Chip one-cycle target labeling kit (Affymetrix, Inc.; Santa Clara, CA) according to the manufacturer’s recommended protocols
|
| |
|
| Hybridization protocol |
biotinylated cRNA was hybridized to the Affymetrix Porcine GeneChip (23,937 probe sets that interrogate approximately 23,256 transcripts from 20,201 S. scrofa genes). Each tissue hybridization (trachea, bronchus, and distal lung) was performed on a separate day, with all genotypes represented in each run.
|
| Scan protocol |
The arrays were washed, stained, and scanned using the Affymetrix Model 450 Fluidics Station and Affymetrix Model 3000 scanner
|
| Data processing |
data was collected using the GeneChip Operating Software (GCOS) v.1.4, using the manufacturer’s recommended protocols and default analysis settings
|
| |
|
| Submission date |
Mar 25, 2010 |
| Last update date |
Sep 17, 2010 |
| Contact name |
Shyam Ramachandran |
| E-mail(s) |
[email protected]
|
| Phone |
3193356933
|
| Organization name |
Univ of Iowa
|
| Department |
Pediatrics
|
| Lab |
McCray Lab
|
| Street address |
240G EMRB
|
| City |
Iowa City |
| ZIP/Postal code |
52242 |
| Country |
USA |
| |
|
| Platform ID |
GPL3533 |
| Series (1) |
| GSE21071 |
Cystic Fibrosis Pigs Develop Lung Disease and Exhibit Defective Bacterial Eradication at Birth |
|
