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Sample GSM989174 Query DataSets for GSM989174
Status Public on Sep 20, 2013
Title Subject STS007, biological rep2
Sample type RNA
Source name Post
Organism Homo sapiens
Characteristics response: ER
site: VGH
allergen: Cat
Sex: M
ethnicity: Caucasian
age: 42
mch pc20 (mg/ml) at pre-challenge: 0.13
mch pc20 (mg/ml) at post-challenge: NA
% fall in fev1 (early): -23
% fall in fev1 (late): -9
erythrocytes (x10^12/l): 4.32
hemoglobin (g/l): 130
hematocrit (l/l): 0.35
mean cell volume (fl): 81.1
mean cell hb (pg): 30.1
mean cell hb conc. (g/l): 371
red cell distr. width (%): 12.8
platelets (x10^9/l): 193
leukocytes (x10^9/l): 4.37
neutrophils (x10^9/l): 2.44
lymphocytes (x10^9/l): 1.44
monocytes (x10^9/l): 0.33
eosinophils (x10^9/l): 0.151
basophils (x10^9/l): 0.009
relative.neutrophils: 0.559
relative.lymphocytes: 0.329
relative.monocytes: 0.0755
relative.eosinophils: 0.0345
relative.basophils: 0.00217
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 1.820184784
7892502 4.420509682
7892503 5.421789411
7892504 8.676945223
7892505 2.412938453
7892506 4.312932601
7892507 5.302264918
7892508 5.228116034
7892509 8.589684267
7892510 4.831240995
7892511 3.558137986
7892512 7.28287978
7892513 3.592139011
7892514 6.371645296
7892515 9.201994389
7892516 4.911903082
7892517 6.279300573
7892518 2.405612047
7892519 4.875600037
7892520 9.053579578

Total number of rows: 32321

Table truncated, full table size 627 Kbytes.

Supplementary file Size Download File type/resource
GSM989174_STS.007.Pst-ER-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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