|
| Status |
Public on Mar 16, 2015 |
| Title |
DNASeq-BCC10-control |
| Sample type |
SRA |
| |
|
| Source name |
matched adjacent normal skin
|
| Organism |
Homo sapiens |
| Characteristics |
tissue/cell type: normal skin
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Fresh tissue samples of resistant BCCs and adjacent normal skin were obtained and stored in RNALater at -20 ̊C (Ambion). DNA was isolated using the DNeasy Blood & Tissue kit according to manufacturer’s protocols (Qiagen).
Capture libraries were constructed from 2 μg of DNA from BCC and normal skin using the Agilent SureSelect XT Human All Exon V4 kit according to manufacturer’s specifications. Enriched exome libraries were multiplexed and sequenced on the Illumina HiSeq 2500 platform.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Sequencing reads were aligned to the human reference genome sequence (hg19) using Burrows-Wheeler Aligner (BWA). SAM to BAM conversion and marking of PCR duplicates were performed using Picard tools (version 1.86), followed by local realignment around indels and base quality score recalibration using the Genome Analysis Toolkit (GATK) (v2.3.9). Somatic SNVs and indels were called using GATK.
Genome_build: hg19
|
| |
|
| Submission date |
Jun 10, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Jiang Li |
| E-mail(s) |
jiangli@stanford.edu
|
| Phone |
6507258839
|
| Organization name |
Stanford University
|
| Department |
Dermatology
|
| Lab |
Tony Oro
|
| Street address |
269 Campus Drive, Stanford University
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE58374 |
SMO variants explain the majority of drug resistance in basal cell carcinoma [exome-seq] |
| GSE58377 |
SMO variants explain the majority of drug resistance in basal cell carcinoma |
|
| Relations |
| BioSample |
SAMN02849593 |
| SRA |
SRX588219 |
