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Sample GSM2839920 Query DataSets for GSM2839920
Status Public on Nov 03, 2017
Title altitude exposure at alt7, biological rep 001 [batch2]
Sample type RNA
 
Source name alt7, PBMC
Organism Homo sapiens
Characteristics treatment: initial altitude exposure
time point: day 7
subject: 1
cell type: peripheral blood mononuclear cells (PMBCs)
age: 22
Sex: M
height (inches): 73
weight (kg): 81.55
batch: 2015-05-06
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 batch2_subject_1_alt7
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 11.92556949
hsa-let-7b_st 12.98794747
hsa-let-7c_st 10.93100127
hsa-let-7d_st 12.42799827
hsa-let-7e_st 8.849209938
hsa-let-7f_st 8.928873538
hsa-miR-15a_st 9.278420466
hsa-miR-16_st 13.42204857
hsa-miR-17_st 12.6532139
hsa-miR-18a_st 9.732899513
hsa-miR-19a_st 5.704065236
hsa-miR-19b_st 10.57004872
hsa-miR-20a_st 12.31832257
hsa-miR-21_st 7.965329669
hsa-miR-22_st 10.79830186
hsa-miR-23a_st 12.82113488
hsa-miR-24_st 13.09713834
hsa-miR-25_st 8.879188546
hsa-miR-26a_st 13.57987032
hsa-miR-26b_st 6.090796834

Total number of rows: 1531

Table truncated, full table size 42 Kbytes.




Supplementary file Size Download File type/resource
GSM2839920_batch2_subject_1_alt7.CEL.gz 848.9 Kb (ftp)(http) CEL
Processed data included within Sample table

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