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Sample GSM4447730 Query DataSets for GSM4447730
Status Public on Jul 31, 2021
Title 4135447178_H_mild/moderate asthma
Sample type RNA
 
Source name induced sputum
Organism Homo sapiens
Characteristics tissue: sputum
disease status: mild/moderate asthma
age: 76
gender: male
atopy: atopic
smoking history: former smoker
packyear: 1.7
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 4135447178_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-4135447178_H

Data table
ID_REF VALUE Detection-4135447178_H
ILMN_1762337 7.38073512 0.31356
ILMN_1736007 6.696476394 0.84887
ILMN_1779670 6.863522581 0.92655
ILMN_1806310 7.767301884 0.99576
ILMN_1671474 10.63486075 0.46751
ILMN_1772582 8.063871023 0.91949
ILMN_1653355 6.569579519 0.60876
ILMN_1717783 6.978831932 0.91808
ILMN_1787689 6.611859172 0.83616
ILMN_1731507 9.6443534 0.15254
ILMN_1814316 7.029878675 0.65678
ILMN_1745607 6.599487745 0.24435
ILMN_1757454 11.56083212 0.65254
ILMN_1735045 8.334159529 0.94915
ILMN_1680754 6.556757917 0.07486
ILMN_1659452 6.614932048 0.75847
ILMN_1767388 6.634714874 0.44492
ILMN_1673870 6.668931262 0.34181
ILMN_1675204 6.527392923 0.82486
ILMN_1755321 9.026373777 0.75847

Total number of rows: 22184

Table truncated, full table size 695 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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