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Sample GSM4447727 Query DataSets for GSM4447727
Status Public on Jul 31, 2021
Title 4135447178_D_severe asthma non-smoker
Sample type RNA
 
Source name induced sputum
Organism Homo sapiens
Characteristics tissue: sputum
disease status: severe asthma
age: 63
gender: male
atopy: atopic
smoking history: non-smoker
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_D
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_D

Data table
ID_REF VALUE Detection-4135447178_D
ILMN_1762337 7.059150242 0.36158
ILMN_1736007 6.745415983 0.28814
ILMN_1779670 6.65565876 0.85169
ILMN_1806310 7.310891169 0.99011
ILMN_1671474 9.965530669 0.91384
ILMN_1772582 7.408660903 0.26271
ILMN_1653355 6.473525868 0.37429
ILMN_1717783 7.63379552 0.87429
ILMN_1787689 7.032615415 0.96893
ILMN_1731507 10.31049632 0.36299
ILMN_1814316 6.938369248 0.28672
ILMN_1745607 6.542166212 0.87571
ILMN_1757454 12.06221505 0.97175
ILMN_1735045 8.408971214 0.98305
ILMN_1680754 7.075896211 0.75
ILMN_1659452 6.636223119 0.28814
ILMN_1767388 6.597932237 0.65819
ILMN_1673870 6.597932237 0.21893
ILMN_1675204 6.543796396 0.79661
ILMN_1755321 8.870400861 0.71751

Total number of rows: 22184

Table truncated, full table size 692 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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