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Sample GSM989178 Query DataSets for GSM989178
Status Public on Sep 20, 2013
Title Subject LST020, biological rep2
Sample type RNA
Source name Post
Organism Homo sapiens
Characteristics response: DR
site: Laval
allergen: Cat Hair
Sex: M
ethnicity: Caucasian
age: 26
mch pc20 (mg/ml) at pre-challenge: 0.93
mch pc20 (mg/ml) at post-challenge: 1.02
% fall in fev1 (early): -31.5
% fall in fev1 (late): -15.6
erythrocytes (x10^12/l): 4.72
hemoglobin (g/l): 152
hematocrit (l/l): 0.446
mean cell volume (fl): 94.5
mean cell hb (pg): 32.2
mean cell hb conc. (g/l): 341
red cell distr. width (%): 12.5
platelets (x10^9/l): 178
leukocytes (x10^9/l): 3.9
neutrophils (x10^9/l): 1.7
lymphocytes (x10^9/l): 1.7
monocytes (x10^9/l): 0.3
eosinophils (x10^9/l): 0.2
basophils (x10^9/l): 0
relative.neutrophils: 0.439
relative.lymphocytes: 0.423
relative.monocytes: 0.077
relative.eosinophils: 0.055
relative.basophils: 0.006
tissue: whole blood
Extracted molecule total RNA
Extraction protocol Samples were stored at -80⁰C until RNA extraction
From PAXgene tube samples, total RNA was purified from 2.5 mL of whole blood using Rneasy mini kit (Qiagen, Chatsworth, CA, USA)
From EDTA tube samples, total RNA was purified from 3.0 mL of whole blood following modified TRIzol-based extraction method.
The yield and quality of RNA was assessed by NanoDrop 8000 Spectrophotometer (Thermo Scientific, Wilmington, DE, USA) and Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA)
Label biotin
Label protocol standard Affymetrix protocol
Hybridization protocol Affymetrix Human Gene 1.0 ST array (Affymetrix, Santa Clara, CA)
Scan protocol standard Affymetrix protocol
Data processing Raw data normalization using the 'farms' package consisted of RMA background correction, quantile normalization and summarization of probe-level data using Factor Analysis for Robust Microarray Summarization
Data filtering was also performed using the Informative vs. Non-Informative Calls function in the 'farms' package. Differential gene expression was determined using moderated t-tests in limma using an FDR cut-off of 10%.
All statistical analyses were performed in the statistical computing program R.
Submission date Aug 20, 2012
Last update date Sep 20, 2013
Contact name Scott Tebbutt
Organization name University of British Columbia
Department Medicine
Lab James Hogg Research Centre
Street address Room 166, 1081 Burrard Street
City Vancouver
State/province BC
ZIP/Postal code V6Z 1Y6
Country Canada
Platform ID GPL6244
Series (1)
GSE40240 Expression data from peripheral blood - blood draws at Pre and Post time points of Allergen inhalation challenge (ER and DR)

Data table header descriptions
VALUE RMA normalized

Data table
7892501 1.820183707
7892502 4.420510014
7892503 5.421789378
7892504 8.676947101
7892505 2.41293821
7892506 4.312933052
7892507 5.30226495
7892508 5.228118741
7892509 8.589685443
7892510 4.831242902
7892511 3.558137721
7892512 7.282879446
7892513 3.592139906
7892514 6.371647918
7892515 9.201997906
7892516 4.911905222
7892517 6.279301056
7892518 2.405612527
7892519 4.875599
7892520 9.05357948

Total number of rows: 32321

Table truncated, full table size 627 Kbytes.

Supplementary file Size Download File type/resource
GSM989178_LST.020.Pst-DR-PAXgene_RNA_HuGene-1_0-st-v1_.CEL.gz 3.9 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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