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Sample GSM999870 Query DataSets for GSM999870
Status Public on Feb 02, 2015
Title 15-02-004-5_Asthmatic
Sample type RNA
 
Source name PBMC
Organism Homo sapiens
Characteristics asthma: TRUE
subtype: reversible
cell type: PBMC
Treatment protocol N/A
Growth protocol N/A
Extracted molecule total RNA
Extraction protocol Peripheral blood mononuclear cells (PBMCs) were isolated from whole blood using the Ficoll density gradient separation. DNA and RNA were isolated simultaneously from the PBMCs using the AllPrep DNA/RNA kit (Qiagen, Germantown, MD), DNA and RNA samples were quantified and purity assessed using a NanoDrop spectrophotometer (Thermo Scientific, Wilmington, DE). RNA integrity was determined using the Bioanalyzer (Agilent, Santa Clara, CA).
Label Cy3
Label protocol RNA was reverse transcribed and amplified using the TransPlex Whole Transcriptome Amplification (WTA) Kit (Sigma-Aldrich, St. Louis, MO) followed by Cy3 labeling using Nimblegen one-color labeling kits.
 
Hybridization protocol Nimblegen-recommended protocol on the Maui 12-bay hyb station.
Scan protocol Nimblegen-recommended settings on the Nimblegen’s scanner (Roche Nimblegen, Madison, WI)
Data processing Images were processed using RMA normalization with Nimblegen’s DEVA software.
 
Submission date Sep 10, 2012
Last update date Feb 02, 2015
Contact name David Schwartz
E-mail(s) DAVID.SCHWARTZ@ucdenver.edu
Phone 303-724-1783
Organization name University of Colorado, Anschutz Medical Campus
Department Medicine
Street address Anschutz Medical Campus
City Aurora
State/province CO
ZIP/Postal code 80045
Country USA
 
Platform ID GPL16025
Series (2)
GSE40732 DNA Methylation Changes and Childhood Asthma in the Inner City [gene expression]
GSE40736 DNA Methylation Changes and Childhood Asthma in the Inner City

Data table header descriptions
ID_REF
VALUE RMA signal

Data table
ID_REF VALUE
AB000409 9.7622
AB000463 9.5642
AB000781 7.0005
AB001328 7.8884
AB002294 11.0594
AB002308 11.5954
AB002311 9.3334
AB002313 10.9254
AB002360 6.8279
AB002377 9.0983
AB002381 9.9388
AB002382 8.9922
AB002384 11.1594
AB003177 10.3953
AB003333 9.7655
AB006589 6.3479
AB006590 6.23
AB006621 8.5668
AB006625 8.4681
AB007457 11.609

Total number of rows: 45033

Table truncated, full table size 746 Kbytes.




Supplementary file Size Download File type/resource
GSM999870_534619A09_532.pair.gz 2.9 Mb (ftp)(http) PAIR
GSM999870_534619A09_532_norm_RMA.pair.gz 2.4 Mb (ftp)(http) PAIR
Processed data included within Sample table
Processed data provided as supplementary file

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