|
| Status |
Public on Mar 17, 2022 |
| Title |
bovine_LAdrenal_MIXNTE_19 |
| Sample type |
RNA |
| |
|
| Source name |
bovine left adrenal
|
| Organism |
Bos taurus |
| Characteristics |
treatment: MIXNTE
tissue: left adrenal
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Mid-cross sections of the left adrenal gland were placed in foil packs, snap-frozen in liquid nitrogen, and stored at -80° C. Total RNA was extracted from the frozen adrenal samples using TRIzol Reagent following the manufacturer's instructions. The RNA concentrations were determined using a NanoDrop ND-1000 Spectrophotometer, and the integrity of total RNA was examined by gel electrophoresis using an Agilent 2100 Bioanalyzer System.
|
| Label |
biotin
|
| Label protocol |
Three µg of RNA for each sample were reverse-transcribed to cDNA and then transcribed from cDNA to cRNA. cRNA samples were then labeled with biotin.
|
| |
|
| Hybridization protocol |
The biotinylated cRNAs were further fragmented and used as probes to hybridize the gene chips in the GeneChip Hybridization Oven 640 (Affymetrix). After hybridization, the chips were washed and stained on a GeneChip Fluidics Station 450 (Affymetrix).
|
| Scan protocol |
The reaction image and signals were read with a GeneChip Scanner (GCS 3000, 7G; Affymetrix)
|
| Data processing |
Data were collected using the GeneChip Operating Software (GCOS, version 1.2; Affymetrix). The raw expression intensity values from the GCOS were imported into Partek Genomics Suite software (PGS, version 6.6; Partek Inc., St. Louis, MO). For GeneChip background correction, the algorithm of Robust Multichip Averaging adjusted with probe length and GC oligo contents was implemented. The background-corrected data were further converted into expression values using quantile normalization across all the chips and median polish summarization of multiple probes for each probe set.
|
| |
|
| Submission date |
Mar 14, 2022 |
| Last update date |
Mar 18, 2022 |
| Contact name |
James C Matthews |
| E-mail(s) |
jmatthew@uky.edu
|
| Phone |
(859) 257-7513
|
| Organization name |
University of Kentucky
|
| Department |
Animal and Food Sciences
|
| Lab |
218
|
| Street address |
325 Cooper Drive
|
| City |
Lexington |
| State/province |
Kentucky |
| ZIP/Postal code |
40546 |
| Country |
USA |
| |
|
| Platform ID |
GPL16500 |
| Series (2) |
| GSE198583 |
Influence of form of Se supplementation and tall fescue endophyte toxicity on the adrenal gland transcriptome of grazing beef steers |
| GSE198589 |
Influence of form of Se supplementation and tall fescue endophyte toxicity on the adrenal gland and kidney transcriptome of grazing beef steers |
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