|
| Status |
Public on Nov 14, 2006 |
| Title |
Normoxic adrenal rep2 |
| Sample type |
RNA |
| |
|
| Source name |
rat normoxic adrenals at PD7
|
| Organism |
Rattus norvegicus |
| Characteristics |
adrenal subcapsules; Hsd:SD rats; male/female; PD7
|
| Treatment protocol |
hypoxia @ 12 % O2 from birth to PD7 (or control at room air); adrenals quickly removed and decapsulated; frozen on dry ice and pooled (24 glands/sample)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
TRIzol reagent and column purified. RNA quality was assessed spectrophotometrically on the basis of the A260/A280 ratio. All RNA samples were checked for integrity of 18S and 28S RNA by gel electrophoresis.
|
| Label |
biotin
|
| Label protocol |
double-stranded DNA was synthesized from 10 mg total RNA using a Superscript cDNA Synthesis Kit (Invitrogen). Biotin-labeled cRNA was generated by transcription with T7 polymerase and purified on RNeasy affinity columns (Qiagen).
|
| |
|
| Hybridization protocol |
Fragmented, biotinylated cRNA (10 mg), along with hybrid controls (Affymetrix; Santa Clara, CA), were hybridized to the Affymetrix Rat Genome U34A GeneChip array containing probes for 15,923 transcripts.
|
| Scan protocol |
Arrays were washed and stained and then scanned at 488 nm in a G2500A GeneArray Scanner (Agilent; Palo Alto, CA).
|
| Description |
PD7 adrenal subcapsule
|
| Data processing |
Evaluation of data from microarray analysis was performed as described in detail previously (15). Briefly, scanned images were quantified by GeneChip Operating Software 1.1 (Affymetrix). Signal intensities were used to determine overall expression level and a detection confidence score. Fold-change in expression was calculated from the average signal intensity of each group. A modified version of the false-discovery rate (FDR) method was used to assess significance of results (15). To identify genes significantly affected by hypoxia, genes with a FDR £ 0.25 and a minimum fold-change of ± 1.3 were selected. Functional categories used to sort genes according to biological function were derived from the Expression Analysis Systematic Explorer (EASE) software. More specific descriptions of gene function were obtained from the National Center for Biotechnology Information Entrez Gene Database (http://www.ncbi.nlm.nih.gov).
|
| |
|
| Submission date |
Nov 08, 2006 |
| Last update date |
Nov 14, 2006 |
| Contact name |
Eric David Bruder |
| E-mail(s) |
eric.bruder@aurora.org
|
| Organization name |
Aurora St. Luke's Medical Center
|
| Department |
Endocrine Research
|
| Street address |
2801 W. KK River Parkway, Suite 245
|
| City |
Milwaukee |
| State/province |
WI |
| ZIP/Postal code |
53215 |
| Country |
USA |
| |
|
| Platform ID |
GPL341 |
| Series (1) |
| GSE6249 |
Expression data from adrenal glands from normoxic and hypoxic neonatal rats |
|
