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Sample GSM989175 Query DataSets for GSM989175
Status Public on Sep 20, 2013
Title Subject LST013, biological rep2
Sample type RNA
 
Source name Post
Organism Homo sapiens
Characteristics response: DR
site: Laval
allergen: Cat Hair
Sex: F
ethnicity: Caucasian
age: 23
mch pc20 (mg/ml) at pre-challenge: 0.3
mch pc20 (mg/ml) at post-challenge: 0.18
% fall in fev1 (early): -38.9
% fall in fev1 (late): -31.8
erythrocytes (x10^12/l): 4.49
hemoglobin (g/l): 127
hematocrit (l/l): 0.373
mean cell volume (fl): 83.1
mean cell hb (pg): 28.2
mean cell hb conc. (g/l): 340
red cell distr. width (%): 13.8
platelets (x10^9/l): 164
leukocytes (x10^9/l): 7.4
neutrophils (x10^9/l): 4.2
lymphocytes (x10^9/l): 2.7
monocytes (x10^9/l): 0.3
eosinophils (x10^9/l): 0.3
basophils (x10^9/l): 0
relative.neutrophils: 0.559
relative.lymphocytes: 0.361
relative.monocytes: 0.037
relative.eosinophils: 0.039
relative.basophils: 0.004
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 1.820184428
7892502 4.420509702
7892503 5.421789048
7892504 8.676945159
7892505 2.41293848
7892506 4.312933682
7892507 5.302265062
7892508 5.228119317
7892509 8.589685445
7892510 4.831244164
7892511 3.558137961
7892512 7.282879399
7892513 3.592141544
7892514 6.371646925
7892515 9.201991118
7892516 4.911905015
7892517 6.27930158
7892518 2.405612695
7892519 4.875600056
7892520 9.053579369

Total number of rows: 32321

Table truncated, full table size 627 Kbytes.




Supplementary file Size Download File type/resource
GSM989175_LST.013.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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