|
| Status |
Public on Nov 03, 2017 |
| Title |
baseline condition at sea level, biological rep 020 [batch1] |
| Sample type |
RNA |
| |
|
| Source name |
sea level, PBMC
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: sea level
time point: baseline
subject: 20
cell type: peripheral blood mononuclear cells (PMBCs)
age: 21
Sex: F
height (inches): 65.5
weight (kg): 59.45
batch: 2013-08-19
|
| Treatment protocol |
Exposure to altitude.
|
| Growth protocol |
Not applicable
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Peripheral blood samples were collected from an antecubital vein prior to exercise on the first, seventh, and sixteenth days of initial altitude exposure (ALT1, ALT7, and ALT16) and on the re-exposure days (POST7 and POST21), and placed into a BD Vacutainer Cell Preparation Tube containing sodium citrate and Ficoll Hypaque density fluid. PBMC (peripheral blood mononuclear cell) pellets were stored at -80C until analysis.
|
| Label |
biotin
|
| Label protocol |
cDNA synthesis and amplification were performed using the Sigma-Aldrich TransPlex Complete Whole Transcriptome Amplification (WTA) Kit.
|
| |
|
| Hybridization protocol |
Hybridization to the Affymetrix GeneChip miRNA 3.0 Array was performed per manufacturer guidelines.
|
| Scan protocol |
GeneChip Scanner 3000 7G.
|
| Description |
batch1_subject_20_sealevel
|
| Data processing |
Raw expression data was normalized with the RMA algorithm using the R/Bioconductor oligo package. Hybridization and scanning took place in two batches (batch 1 on August 19, 2013 and batch 2 on May 6, 2015). Batches were combined using the ComBat function in the R/Bioconductor sva package. Probe annotation was retrieved from Affymetrix and miRBase.
Probe group file: miRNA-3_0-st-v3.pgf
|
| |
|
| Submission date |
Nov 03, 2017 |
| Last update date |
Jan 23, 2018 |
| Contact name |
Robert C Roach |
| E-mail(s) |
rroach@hypoxia.net
|
| Phone |
303-250-8195
|
| Organization name |
University of Colorado
|
| Department |
Department of Pulmonology
|
| Lab |
Altitude Research Center
|
| Street address |
Campus Box F-524, 12469 E. 17th Place
|
| City |
Aurora |
| State/province |
CO |
| ZIP/Postal code |
80045 |
| Country |
USA |
| |
|
| Platform ID |
GPL16384 |
| Series (2) |
|
