|
| Status |
Public on Oct 23, 2019 |
| Title |
Lung adenocarcinoma 3003_T |
| Sample type |
genomic |
| |
|
| Source name |
Lung adenocarcinoma
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Lung adenocarcinoma
patient: 3003
sample: 3003_T
tissue: Tumor
age (years): 61
Sex: Female
race: Caucasian
smoking history: Current
pack-years: 40
Stage: IIA
egfr mutation: WT
kras mutation: MUT
|
| Growth protocol |
Fresh frozen tissue
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted using standard phenol:chloroform procedures
|
| Label |
biotin
|
| Label protocol |
DNA was labeled according to manufacturer's instructions
|
| |
|
| Hybridization protocol |
DNA was hybridized according to manufacturer's instructions
|
| Scan protocol |
Arrays were scanned according to manufacturer's instructions
|
| Description |
Fresh frozen lung adenocarcinoma sample
|
| Data processing |
Probe intensity files were processed in Partek Genomics Suite (Partek Incorporated, Missouri, USA). Probe sequencing, GC content, fragment length, and background adjustments were applied to correct for biases in signal intensities. DNA copy number profiles were generated in the Copy Number, Paired Analysis Workflow using patient-matched non-malignant lung as a baseline for each lung tumour sample. Segmentation was applied using stringent significance thresholds to identify regions of copy number gain and loss (signal to noise >0.3, minimum of 50 markers per segment, p-value < 10-7). Segments were merged using a 1 Mbp windown. Genomic mapping was based on the hg18 genomic build.
|
| |
|
| Submission date |
Oct 23, 2019 |
| Last update date |
Oct 23, 2019 |
| Contact name |
Katey SS Enfield |
| E-mail(s) |
kenfield@bccrc.ca, katey.enfield@crick.ac.uk
|
| Phone |
6046758111
|
| Organization name |
BC Cancer Research Centre
|
| Street address |
675 West 10th Ave
|
| City |
Vancouver |
| State/province |
BC |
| ZIP/Postal code |
V5Z 1L3 |
| Country |
Canada |
| |
|
| Platform ID |
GPL6801 |
| Series (2) |
| GSE137481 |
Epithelial Tumour Suppressor ELF3 is a Lineage-Specific Amplified Oncogene in Lung Adenocarcinoma |
| GSE139294 |
DNA copy number profiling of lung adenocarcinomas and patient-matched non-malignant lung |
|
