|
| Status |
Public on Mar 16, 2015 |
| Title |
TargetSeq-Untreated21 |
| Sample type |
SRA |
| |
|
| Source name |
untreated basal cell cancersÂ
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: basal cell carcinomas (BCCs)
response to smoothened (smo) inhibitors: N/A (Untreated)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
5-8 10um sections were obtained from the FFPE tumor block and DNA was isolated using the Qiagen DNeasy Blood and Tissue kit according to manufacturer’s protocol (Qiagen). The exonic regions of PTCH1 and SMO were amplified using the Access Array platform (Fluidigm).
The samples were amplified in a multiplex format with genomic DNA (100 ng) according to the manufacturer's recommendation (Ambry Genetics). Subsequently, the multiplexed library pools were subjected to deep sequencing using the Illumina MiSeq platform.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
The exonic regions of PTCH1 and SMO were amplified using the Access Array platform (Fluidigm)
|
| Data processing |
Reads were aligned to the human reference genome sequence (hg19) using the BWA aligner. Samtools mpileup was used to call variants. Only bases meeting the minimum base quality score of 20 from reads meeting the minimum mapping quality score of 20 were considered. A minimum allele frequency of 5% at a position with a read depth > 100 was required to make calls.
Identified variants were annotated using SeattleSeq138 to exclude non-pathogenic variants reported in dbSNP138 and to identify variants that had nonsynonymous consequences or affected splice sites.
Genome_build: hg19
Supplementary_files_format_and_content: excel file containing all the variants from all the target resequencing
|
| |
|
| 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 |
GPL15520 |
| Series (2) |
| GSE58376 |
SMO variants explain the majority of drug resistance in basal cell carcinoma [Target Sequencing] |
| GSE58377 |
SMO variants explain the majority of drug resistance in basal cell carcinoma |
|
| Relations |
| BioSample |
SAMN02849570 |
| SRA |
SRX588357 |
