|
| Status |
Public on Mar 07, 2014 |
| Title |
Moderate dysplasia 4 |
| Sample type |
genomic |
| |
|
| Source name |
preinvasive lesion
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: moderate dysplasia
bronchial location: Right Lower Lung
tissue: Bronchial brushing
representation: MD-4
patient: Patient 7
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Biopsies were homogenized in TRIzol reagent and after chloroform addition, the interface layer was saved. Protein was precipitated from the interface using sodium citrate, followed by ethanol precipitation of the supernatant. The DNA pellet was dissolved in low-EDTA TE buffer. For brushings, after overnight digestion with Proteinase-K, DNA was isolated from protein using sodium chloride (salting out), precipitated by ethanol, and dissolved in TE buffer. For reference blood samples, the column-based extraction protocol was conducted using QuickGene-601. Extracted DNA was quantified, verified to be of high molecular weight. For cell line pair, genomic DNA was purchased from cell bank (ATCC).
|
| Label |
C-Bio and A-DNP
|
| Label protocol |
standard Illumina protocols for Human 660w-Quad chip and HumanOmni2.5-Quad chips
|
| |
|
| Hybridization protocol |
standard Illumina protocols for Human 660w-Quad chip and HumanOmni2.5-Quad chips
|
| Scan protocol |
standard Illumina protocols for Human 660w-Quad chip and HumanOmni2.5-Quad chips using iScan
|
| Description |
Genomic DNA extracted from blood was genotyped using HumanOmni2.5-Quad chip (Illumina), and used as a reference of PI-12 RML
|
| Data processing |
Genotyped data, Log R ratio (LRR) and B allele frequency (BAF) were generated using GenomeStudio (Illumina). All samples (bronchial biopsies/brushings) examined were analyzed as pairs with mathched reference blood samples.
|
| |
|
| Submission date |
Jun 25, 2013 |
| Last update date |
Mar 07, 2014 |
| Contact name |
Ichiro Nakachi |
| E-mail(s) |
ichiro.nakachi@ucdenver.edu
|
| Phone |
303-724-6053
|
| Organization name |
University of Colorado Denver
|
| Department |
Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine
|
| Lab |
Mark Geraci's Lab
|
| Street address |
12700 East 19th Avenue, RC2 9th floor
|
| City |
Aurora |
| State/province |
CO |
| ZIP/Postal code |
80045 |
| Country |
USA |
| |
|
| Platform ID |
GPL16110 |
| Series (1) |
| GSE43168 |
Application of SNP microarrays to the genome-wide analysis of chromosomal instability in premalignant airway lesions |
|
