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Sample GSM1000042 Query DataSets for GSM1000042
Status Public on Feb 02, 2015
Title 15-08-025-8_Nonasthmatic
Sample type RNA
 
Source name PBMC
Organism Homo sapiens
Characteristics asthma: FALSE
subtype: non
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 10.4675
AB000463 10.8182
AB000781 7.7987
AB001328 7.5282
AB002294 10.5011
AB002308 12.0515
AB002311 9.6281
AB002313 11.3782
AB002360 6.5482
AB002377 9.2577
AB002381 10.4734
AB002382 9.1822
AB002384 7.401
AB003177 9.9547
AB003333 9.9697
AB006589 6.2949
AB006590 6.181
AB006621 8.8162
AB006625 7.3375
AB007457 11.9935

Total number of rows: 45033

Table truncated, full table size 746 Kbytes.




Supplementary file Size Download File type/resource
GSM1000042_534621A05_532.pair.gz 2.9 Mb (ftp)(http) PAIR
GSM1000042_534621A05_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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