NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM989164 Query DataSets for GSM989164
Status Public on Sep 20, 2013
Title Subject LST020, biological rep1
Sample type RNA
 
Source name Pre
Organism Homo sapiens
Characteristics response: DR
site: Laval
allergen: Cat Hair
Sex: M
ethnicity: Caucasian
age: 26
mch pc20 (mg/ml) at pre-challenge: 0.93
mch pc20 (mg/ml) at post-challenge: 1.02
% fall in fev1 (early): -31.5
% fall in fev1 (late): -15.6
erythrocytes (x10^12/l): 4.84
hemoglobin (g/l): 156
hematocrit (l/l): 0.46
mean cell volume (fl): 95
mean cell hb (pg): 32.1
mean cell hb conc. (g/l): 338
red cell distr. width (%): 12.8
platelets (x10^9/l): 182
leukocytes (x10^9/l): 3.5
neutrophils (x10^9/l): 1.5
lymphocytes (x10^9/l): 1.5
monocytes (x10^9/l): 0.2
eosinophils (x10^9/l): 0.2
basophils (x10^9/l): 0
relative.neutrophils: 0.431
relative.lymphocytes: 0.448
relative.monocytes: 0.067
relative.eosinophils: 0.049
relative.basophils: 0.005
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 1.820183093
7892502 4.420510108
7892503 5.421788839
7892504 8.67694531
7892505 2.412938222
7892506 4.312932794
7892507 5.302265194
7892508 5.228116225
7892509 8.589683958
7892510 4.831242596
7892511 3.558137791
7892512 7.282880197
7892513 3.592140681
7892514 6.371647283
7892515 9.201992516
7892516 4.911903386
7892517 6.279300888
7892518 2.4056123
7892519 4.875599576
7892520 9.053579166

Total number of rows: 32321

Table truncated, full table size 627 Kbytes.




Supplementary file Size Download File type/resource
GSM989164_LST.020.Pre-DR-PAXgene_RNA_HuGene-1_0-st-v1_.CEL.gz 3.7 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap