|
| Status |
Public on Jul 10, 2019 |
| Title |
EAT_2-week-old lamb_Untreated_Replicate 2 |
| Sample type |
RNA |
| |
|
| Source name |
Epicardial adipose tissue, 2-week-old lamb, untreated
|
| Organism |
Ovis aries |
| Characteristics |
tissue: Epicardial adipose tissue
age: Two-week-old lamb
|
| Treatment protocol |
Ewes were treated with no or 1mg/kg/day cortisol (term fetuses) or 0.5mg/kg/day cortisol (2-week-old lambs). Fetuses and lambs were not treated; their cortisol increased secondary to maternal treatment. Lambs and term fetuses were exposed to different levels of increased maternal cortisol so direct comparisons of these two groups of increased maternal cortisol could not be made.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from epicardial adipose tissue 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 One-Color Low Input Quick Amp Labeling Kit (Agilent, Newcastle DE) 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 >13.7 pmol Cy3/µg cRNA) was fragmented and hybridized to Agilent Sheep Oligo Microarrays (G4813A) design 019921 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.
|
| 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) background detrended Processed Signal. The limma package was employed to import the raw data into R (http://www.r-project.org), perform background correction and normalize the data by the quantile normalization method. Control probes and low expressed probes were filtered out, retaining for further analysis the probes that were at least 10% brighter than the negative controls on at least six arrays.
|
| |
|
| Submission date |
Aug 30, 2018 |
| Last update date |
Jul 10, 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) |
| GSE119254 |
Transcriptomic Evidence that Cortisol Alters Perinatal Epicardial Adipose Tissue Maturation |
|
