NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2839950 Query DataSets for GSM2839950
Status Public on Nov 03, 2017
Title altitude exposure at alt16, biological rep 020 [batch1]
Sample type RNA
 
Source name alt16, PBMC
Organism Homo sapiens
Characteristics treatment: initial altitude exposure
time point: day 16
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_alt16
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)
GSE105124 AltitudeOmics
GSE106527 AltitudeOmics microRNA expression data

Data table header descriptions
ID_REF
VALUE RMA normalized and ComBat batch corrected microRNA expression value

Data table
ID_REF VALUE
hsa-let-7a_st 10.87213105
hsa-let-7b_st 13.09475323
hsa-let-7c_st 9.87507638
hsa-let-7d_st 11.73320824
hsa-let-7e_st 9.687304679
hsa-let-7f_st 5.923154958
hsa-miR-15a_st 8.247084024
hsa-miR-16_st 12.27137035
hsa-miR-17_st 12.41687015
hsa-miR-18a_st 10.35162938
hsa-miR-19a_st 2.956495243
hsa-miR-19b_st 8.882433024
hsa-miR-20a_st 11.75738067
hsa-miR-21_st 5.779613055
hsa-miR-22_st 10.52574394
hsa-miR-23a_st 11.75886019
hsa-miR-24_st 13.24281591
hsa-miR-25_st 7.839339948
hsa-miR-26a_st 12.64448555
hsa-miR-26b_st 5.298082408

Total number of rows: 1531

Table truncated, full table size 42 Kbytes.




Supplementary file Size Download File type/resource
GSM2839950_batch1_subject_20_alt16.CEL.gz 801.2 Kb (ftp)(http) CEL
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap