|
| Status |
Public on Jul 31, 2021 |
| Title |
4310479156_C_severe asthma smoker/ex-smoker |
| Sample type |
RNA |
| |
|
| Source name |
induced sputum
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: sputum
disease status: severe asthma
age: 63
gender: female
atopy: atopic
smoking history: former smoker
packyear: 18
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 |
4310479156_C
|
| 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) |
[email protected]
|
| 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 |
|
