|
| Status |
Public on Jan 01, 2019 |
| Title |
Progressive 40 |
| Sample type |
RNA |
| |
|
| Source name |
Human preinvasive lung squamous cell carcinoma lesions
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Preinvasive lung squamous cell carcinoma lesions
lesion outcome: progression
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Laser-capture micro-dissection (LCM) was used to selectively isolate CIS cells for molecular analysis, reducing the extent of contamination by stromal cells. RNA was extracted using the High Pure FFPE RNA Kit (Roche Applied Science, West Sussex, UK) according to manufacturer’s protocol. Quantification was carried out using the Quant-iT RNA assay kit and the Qubit® 2.0 fluorometer (Life Technologies, Paisley, UK).
|
| Label |
biotin
|
| Label protocol |
Thermofisher/Affymetrix WT Pico Kit Biotin labelling module as per manufacturer's instructions
|
| |
|
| Hybridization protocol |
Thermofisher/Affymetrix Human Clariom D GeneChip as per manufacturer's instructions [Fluidics Station 450]
|
| Scan protocol |
Affymetrix Scanner 3000 7G as per manufacturer's instructions
|
| Data processing |
Processing was performed using R and Bioconductor. Raw data in CEL format were read using the read.celfiles method from the oligo package, and normalised using RMA.
|
| |
|
| Submission date |
Dec 14, 2017 |
| Last update date |
Jan 01, 2019 |
| Contact name |
Vitor H Teixeira |
| E-mail(s) |
v.teixeira@ucl.ac.uk
|
| Organization name |
University College London
|
| Department |
Medicine
|
| Lab |
Lungs for Lungs for Living Research Centre
|
| Street address |
5 University Street
|
| City |
London |
| ZIP/Postal code |
WC1E 6JF |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL23126 |
| Series (2) |
| GSE108082 |
Deciphering the genomic, epigenomic and transcriptomic landscapes of pre-invasive lung cancer lesions to determine prognosis II |
| GSE108124 |
Deciphering the genomic, epigenomic and transcriptomic landscapes of pre-invasive lung cancer lesions to determine prognosis |
|
