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Sample GSM989176 Query DataSets for GSM989176
Status Public on Sep 20, 2013
Title Subject LST017, biological rep2
Sample type RNA
Source name Post
Organism Homo sapiens
Characteristics response: DR
site: Laval
allergen: Cat Hair (Lot)
Sex: F
ethnicity: Caucasian
age: 26
mch pc20 (mg/ml) at pre-challenge: 5.13
mch pc20 (mg/ml) at post-challenge: 1.53
% fall in fev1 (early): -31.4
% fall in fev1 (late): -14.9
erythrocytes (x10^12/l): 4.49
hemoglobin (g/l): 133
hematocrit (l/l): 0.392
mean cell volume (fl): 87.4
mean cell hb (pg): 29.6
mean cell hb conc. (g/l): 339
red cell distr. width (%): 13.2
platelets (x10^9/l): 237
leukocytes (x10^9/l): 4.9
neutrophils (x10^9/l): 2.9
lymphocytes (x10^9/l): 1.4
monocytes (x10^9/l): 0.4
eosinophils (x10^9/l): 0.2
basophils (x10^9/l): 0
relative.neutrophils: 0.595
relative.lymphocytes: 0.283
relative.monocytes: 0.079
relative.eosinophils: 0.038
relative.basophils: 0.005
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 1.820185259
7892502 4.420509726
7892503 5.421789556
7892504 8.676945302
7892505 2.412938641
7892506 4.312934263
7892507 5.302265225
7892508 5.228121521
7892509 8.589684558
7892510 4.831244132
7892511 3.558137856
7892512 7.282880637
7892513 3.592142098
7892514 6.37164804
7892515 9.201991944
7892516 4.911904996
7892517 6.279301674
7892518 2.40561404
7892519 4.875598372
7892520 9.053579417

Total number of rows: 32321

Table truncated, full table size 627 Kbytes.

Supplementary file Size Download File type/resource
GSM989176_LST.017.Pst-DR-PAXgeneRNA_HuGene-1_0-st-v1_.CEL.gz 3.8 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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