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Sample GSM989172 Query DataSets for GSM989172
Status Public on Sep 20, 2013
Title Subject LST021, biological rep2
Sample type RNA
 
Source name Post
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): 4.76
hemoglobin (g/l): 156
hematocrit (l/l): 0.454
mean cell volume (fl): 95.5
mean cell hb (pg): 32.8
mean cell hb conc. (g/l): 344
red cell distr. width (%): 12.5
platelets (x10^9/l): 138
leukocytes (x10^9/l): 5.6
neutrophils (x10^9/l): 3.9
lymphocytes (x10^9/l): 1.1
monocytes (x10^9/l): 0.5
eosinophils (x10^9/l): 0.1
basophils (x10^9/l): 0
relative.neutrophils: 0.695
relative.lymphocytes: 0.197
relative.monocytes: 0.084
relative.eosinophils: 0.02
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 1.820184342
7892502 4.420509771
7892503 5.421789376
7892504 8.676945816
7892505 2.412938522
7892506 4.312934042
7892507 5.302264916
7892508 5.228119271
7892509 8.589684403
7892510 4.831243329
7892511 3.558137649
7892512 7.282880316
7892513 3.592137532
7892514 6.37164558
7892515 9.201992558
7892516 4.911901406
7892517 6.279299587
7892518 2.405614295
7892519 4.875600253
7892520 9.053578861

Total number of rows: 32321

Table truncated, full table size 627 Kbytes.




Supplementary file Size Download File type/resource
GSM989172_LST.021.Pst-ER-PAXgene_RNA_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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