|
| Status |
Public on Jan 04, 2019 |
| Title |
lamb heart Left ventricle cortisol telemetry newborn replicate 5 |
| Sample type |
RNA |
| |
|
| Source name |
newborn heart
|
| Organism |
Ovis aries |
| Characteristics |
organ: newborn heart
tissue: Left ventricle
treatment: cortisol
|
| Treatment protocol |
Ewes were infused with 1mg/kg/day cortisol or vehicle from approximately day 115 of pregnancy (n=5/group) until birth. Lamb heart (septum and left ventricle) samples were collected at or just after birth.
|
| Growth protocol |
Continuous infusions of 1mg/kg/day cortisol or vehicle to the ewe were begun at approximately day 115 of gestation and continued until birth
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with Trizol (Life Technologies, Carlsbad, CA), and purified through Qiagen Rneasy+ kits with on-column DNase digestion (QIAGEN, Valencia, CA) according to manufacturers' protocols. Total RNA concentration was measured by Nanodrop ND-1000 and RNA quality was monitored by Agilent Bioanalyzer
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the Low input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
|
| |
|
| Hybridization protocol |
600 ng of Cy3-labelled cRNA (specific activity >8.6 pmol Cy3/µg cRNA) was fragmented and hybridized to Agilent Sheep Oligo Microarrays (G4813A) by the ICBR facility at the University of Florida according to Agilent's methodology.
|
| Scan protocol |
Slides were scanned on the Agilent DNA Microarray Scanner (G2505B) using one color (green) scan setting for 8x15k array slides, by the ICBR facility at University of Florida.
|
| Description |
Gene expression at birth in left ventricle of heart of newborn lamb
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 10.1.1.1 (Agilent) using default parameters (protocol GE1-v5_10 and Grid: 019921_D_F_20100112), and were background detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers and probes with low expression (less than 10% brighter than negative control probes) were excluded. Data were normalized using the quantile method and log transformed.These files are uploaded as the Telemetry LV matrix and the Telemetry Septum Matrix. The remaining probes were analyzed using a moderated t test that employs an empirical Bayes method for small sample size (P < 0.05). This was all performed using the Limma package in R software.
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| |
|
| Submission date |
Feb 12, 2018 |
| Last update date |
Jan 04, 2019 |
| Contact name |
Elaine Mary Richards |
| E-mail(s) |
esumners@cop.ufl.edu
|
| Phone |
3522737698
|
| Organization name |
University of Florida
|
| Department |
Pharmacodynamics
|
| Lab |
Keller-Wood
|
| Street address |
PO Box 100274
|
| City |
Gainesville |
| State/province |
FL |
| ZIP/Postal code |
32610-0487 |
| Country |
USA |
| |
|
| Platform ID |
GPL14112 |
| Series (1) |
| GSE110470 |
Mechanisms of in utero cortisol effects on the newborn heart revealed by transcriptomic modeling |
|
