|
| Status |
Public on Jun 01, 2024 |
| Title |
H04 |
| Sample type |
RNA |
| |
|
| Source name |
The pup was cared for in >90% oxygen chamber (HOX) from postnatal day 1 to day 10 (P1-P10), rat4
|
| Organism |
Rattus norvegicus |
| Characteristics |
tissue: Lung
strain: Sprague-Dawley
age: 10 days old
|
| Treatment protocol |
Nursing dams were cared for in a 12-h dark-light cycle and had free access to chow and water. According to the study design, two or four pregnant rats were used for each experiment. The dam and pups were cared for in either >90% oxygen chamber (HOX) or room air (NOX) from postnatal day 1 to day 10 (P1-P10), and then all of them were caged in room air between P11 and P21. Oxygen concentrations were continuously monitored with an oxygen sensor (Reming Bioinstruments Co., Redfield, NY). Pups were caged with nursing dams while the dams were alternated between oxygen environments to diminish oxygen toxicity. Taurine 100 mg/kg/d was given i.p. between P1 and P10. One dose of tunicamycin 0.3 mg/kg was given at P3 i.p. TUDCA 100 mg/kg was given i.p. between P1 and P10.
|
| Growth protocol |
Time-dated-pregnant Sprague-Dawley rats were obtained from Envigo (Madison, WI) and were acclimated to our animal facility for 7 days. The use of animals was approved by the Medical College of Wisconsin Institutional Animal Care and Use Committee and conformed to the National Institute of Health Guide for the Care and Use of Laboratory Animals.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted Trizol (Invitrogen, Carlsbad, CA, USA). RNA was amplified/labeled using Affymetrix 3' IVT Express Kit (Affymetrix, Santa Clara, CA).
|
| Label |
biotin
|
| Label protocol |
cRNA was synthesized, labeled, fragmented, and hybridized to an array in accordance to the Affymetrix GeneChip expression analysis technical manual.
|
| |
|
| Hybridization protocol |
The Affymetrix GeneChip rat genome RG230 2.0 array was selected for these studies for its overall comprehensive coverage.
|
| Scan protocol |
After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001 and scanned with a 7G Affymetrix GeneChip Scanner
|
| Description |
Time-dated-pregnant Sprague-Dawley rats were obtained from Envigo
Gene expression interrogating 31099 transcripts
|
| Data processing |
Array images were quantified with Affymetrix Expression Console Software and normalized with Robust Multichip Analysis (Bioconductor - www.bioconductor.org) to determine signal log ratios [26]. Gene expression differences were also evaluated by principle component analyses, and the statistical significance of differential gene expression and false discovery rates (FDR) were derived through Partek GS ANOVA statistic and ToppCluster.
|
| |
|
| Submission date |
Dec 08, 2023 |
| Last update date |
Jun 01, 2024 |
| Contact name |
Martin Hessner |
| E-mail(s) |
mhessner@mcw.edu
|
| Organization name |
Medical College of Wisconsin
|
| Department |
Pediatrics
|
| Lab |
Max McGee National Research Center for Juvenile Diabetes
|
| Street address |
8701 Watertown Plank Road
|
| City |
Milwaukee |
| State/province |
WI |
| ZIP/Postal code |
53226 |
| Country |
USA |
| |
|
| Platform ID |
GPL1355 |
| Series (1) |
| GSE249767 |
The juxtaposition of Taurine in Bronchopulmonary Dysplasia |
|
