NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM4447736 Query DataSets for GSM4447736
Status Public on Jul 31, 2021
Title 4135447179_H_severe asthma non-smoker
Sample type RNA
 
Source name induced sputum
Organism Homo sapiens
Characteristics tissue: sputum
disease status: severe asthma
age: 53
gender: male
atopy: atopic
smoking history: former smoker
packyear: 4.8
daily oral corticosteroid: no
Treatment protocol Samples were lysed (RNeasy Lysis Buffer, Qiagen, Hilden, Germany) and homogenised (TissueLyser II, Qiagen, Hilden, Germany) prior to RNA extraction.
Growth protocol Induced sputum were placed in RNA-later (Qiagen, Hilden, Germany) for storage at -20 °C prior to RNA extraction. 
Extracted molecule total RNA
Extraction protocol RNA extraction was perfomed using (RNeasy Mini Kit and RNAse-free DNAse, Qiagen, Hilden, Germany). RNA was quantified (Quant-iT RiboGreen RNA Quantitation Assay Kit, Life Technologies Corporation, USA)
Label biotin
Label protocol biotin
 
Hybridization protocol 750 ng of cRNA was hybridized to Illumina HumanRef‐8 V2 Beadchips
Scan protocol BeadChips were scanned using the Illumina Bead Station and data was captured using BeadScan 3.5.11 (Illumina, San Diego, USA).
Description 4135447179_H
Data processing Array raw data were processed using GenomeStudio software, Illumina and analysed using R Bioconductor lumi and limma packages. Sample and gene profiling results were included in the analysis if the sample was successfully amplified (sufficient cRNA generated) and hybridized (95th percentile of fluorescence score>500) and data passed quality control in R during analysis. Data was log2‐transformed and quantile‐normalised.
 
Submission date Apr 01, 2020
Last update date Jul 31, 2021
Contact name Stephany Sanchez
E-mail(s) steph.chelonia@gmail.com
Organization name University of Newcastle
Department Respiratory and Sleep Medicine
Lab Respiratory
Street address Lot 1 Kookaburra Circuit
City New Lambton Heights
State/province NSW
ZIP/Postal code 2305
Country Australia
 
Platform ID GPL6104
Series (2)
GSE147880 Comparative transcriptomic profiles in U-BIOPRED and Australian Newcastle severe asthma cohorts [sputum]
GSE147881 Comparative transcriptomic profiles in U-BIOPRED and Australian Newcastle severe asthma cohorts

Data table header descriptions
ID_REF
VALUE R Bioconductor computarized normalised signal intensity
Detection-4135447179_H

Data table
ID_REF VALUE Detection-4135447179_H
ILMN_1762337 7.678956154 0.36299
ILMN_1736007 6.651201618 0.44633
ILMN_1779670 6.679153389 0.64548
ILMN_1806310 7.136695056 0.61582
ILMN_1671474 8.611398655 0.64124
ILMN_1772582 7.09500295 0.91102
ILMN_1653355 6.556757917 0.4435
ILMN_1717783 8.266307068 0.96469
ILMN_1787689 7.256505678 0.96469
ILMN_1731507 11.1936668 0.0113
ILMN_1814316 7.658193078 0.68785
ILMN_1745607 6.583840378 0.94209
ILMN_1757454 11.00217945 0.98588
ILMN_1735045 9.016381351 0.99859
ILMN_1680754 7.642121417 0.9774
ILMN_1659452 6.608778346 0.43362
ILMN_1767388 6.567984365 0.9887
ILMN_1673870 6.545424345 0.19774
ILMN_1675204 6.519105372 0.95057
ILMN_1755321 7.813760484 0.97034

Total number of rows: 22184

Table truncated, full table size 682 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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