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Sample GSM989158 Query DataSets for GSM989158
Status Public on Sep 20, 2013
Title Subject LST021, biological rep1
Sample type RNA
 
Source name Pre
Organism Homo sapiens
Characteristics response: ER
site: Laval
allergen: Cat Pelt
Sex: M
ethnicity: Caucasian
age: 31
mch pc20 (mg/ml) at pre-challenge: 11.75
mch pc20 (mg/ml) at post-challenge: 16
% fall in fev1 (early): -24.2
% fall in fev1 (late): -7.5
erythrocytes (x10^12/l): 4.74
hemoglobin (g/l): 155
hematocrit (l/l): 0.444
mean cell volume (fl): 93.7
mean cell hb (pg): 32.7
mean cell hb conc. (g/l): 349
red cell distr. width (%): 12.1
platelets (x10^9/l): 137
leukocytes (x10^9/l): 5
neutrophils (x10^9/l): 3.4
lymphocytes (x10^9/l): 1.1
monocytes (x10^9/l): 0.4
eosinophils (x10^9/l): 0.1
basophils (x10^9/l): 0
relative.neutrophils: 0.681
relative.lymphocytes: 0.212
relative.monocytes: 0.081
relative.eosinophils: 0.024
relative.basophils: 0.002
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 1.820183376
7892502 4.420509784
7892503 5.421789566
7892504 8.676944423
7892505 2.412938499
7892506 4.312933604
7892507 5.302264905
7892508 5.228119015
7892509 8.589685135
7892510 4.831243919
7892511 3.558137716
7892512 7.282878629
7892513 3.592140819
7892514 6.371646639
7892515 9.201988312
7892516 4.911903448
7892517 6.279300661
7892518 2.405612823
7892519 4.87559857
7892520 9.053579233

Total number of rows: 32321

Table truncated, full table size 627 Kbytes.




Supplementary file Size Download File type/resource
GSM989158_LST.021.Pre-ER-PAXgene_RNA_HuGene-1_0-st-v1_.CEL.gz 3.7 Mb (ftp)(http) CEL
Processed data included within Sample table

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