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Sample GSM989165 Query DataSets for GSM989165
Status Public on Sep 20, 2013
Title Subject LST022, biological rep1
Sample type RNA
 
Source name Pre
Organism Homo sapiens
Characteristics response: DR
site: Laval
allergen: Cat Pelt
Sex: F
ethnicity: Caucasian
age: 27
mch pc20 (mg/ml) at pre-challenge: 0.63
mch pc20 (mg/ml) at post-challenge: 0.12
% fall in fev1 (early): -48.3
% fall in fev1 (late): -25.8
erythrocytes (x10^12/l): 4.23
hemoglobin (g/l): 122
hematocrit (l/l): 0.357
mean cell volume (fl): 84.3
mean cell hb (pg): 28.9
mean cell hb conc. (g/l): 342
red cell distr. width (%): 13.3
platelets (x10^9/l): 270
leukocytes (x10^9/l): 5.6
neutrophils (x10^9/l): 2.8
lymphocytes (x10^9/l): 1.9
monocytes (x10^9/l): 0.5
eosinophils (x10^9/l): 0.3
basophils (x10^9/l): 0
relative.neutrophils: 0.505
relative.lymphocytes: 0.345
relative.monocytes: 0.09
relative.eosinophils: 0.053
relative.basophils: 0.007
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
E-mail(s) scott.tebbutt@hli.ubc.ca
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
ID_REF
VALUE RMA normalized

Data table
ID_REF VALUE
7892501 1.820184883
7892502 4.420509778
7892503 5.421789323
7892504 8.676945784
7892505 2.41293827
7892506 4.312933836
7892507 5.302264978
7892508 5.228121656
7892509 8.589685439
7892510 4.831243591
7892511 3.558138097
7892512 7.282880344
7892513 3.592140289
7892514 6.37164722
7892515 9.201997777
7892516 4.911904939
7892517 6.279301286
7892518 2.405613615
7892519 4.87559981
7892520 9.053579784

Total number of rows: 32321

Table truncated, full table size 627 Kbytes.




Supplementary file Size Download File type/resource
GSM989165_LST.022.Pre-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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