|
| Status |
Public on Jul 28, 2017 |
| Title |
Neuroblastoma tumor TI_501 (seq) |
| Sample type |
SRA |
| |
|
| Source name |
Neuroblastoma tumor TI_501
|
| Organism |
Homo sapiens |
| Characteristics |
tumor: Primary neroblastoma
|
| Treatment protocol |
None
|
| Growth protocol |
Cell lines were grown according to standard conditions.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from cell lines and tumors using standard proteinase K and phenol-chloroform extraction protocol. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, PicoGreen and agarose gel electrophoresis.
Amplicon library was prepared using GeneRead DNAseq Targeted HC Panel V2 (NGHS-501X-12, Qiagen) according to manufacturer instructions. DNA high-throughput sequencing was performed on Ion Proton instrument using Ion PI HiQ Sequencing Kit on the Ion PI sequencing chip (ThermoFisher Scientific)
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Ion Torrent Proton |
| |
|
| Description |
Human Comprehensive Cancer GeneRead DNAseq Targeted Panel (Qiagen)
|
| Data processing |
Quality check by Fasq toolkit v0.11.4
Trimming and quality filtering by cutadapt v1.13
Alignment againts reference genome with BWA 0.7.15-r1140
TSV files were generated by uploading VCF files into Ion Reporter v5.0
Genome_build: hg19
Supplementary_files_format_and_content: In the TSV file, Locus and Genotype columns were initially used to identified potential rare variants that were further screened with Allele coverage and minor allele frequency (MAF) columns. In the Ref+/Ref-/Var+/Var- column we considered only variants with balanced numbers of forward and reverse reads. Variant calls with MAF > 1% (1000 Genomes Project, http://www.internationalgenome.org) were excluded from further analyses.
|
| |
|
| Submission date |
Jul 28, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Jaime Font de Mora |
| E-mail(s) |
fontdemora@iislafe.es
|
| Organization name |
Instituto de Investigación Sanitaria La Fe
|
| Lab |
Cellular an Molecular Bioogy Laboratory
|
| Street address |
Avenida Fernando Abril Martorell, 106; Torre A, 5-07
|
| City |
Valencia |
| ZIP/Postal code |
46026 |
| Country |
Spain |
| |
|
| Platform ID |
GPL17303 |
| Series (2) |
| GSE101989 |
Deletion of 11q in neuroblastomas drives sensitivity to PARP inhibition [SEQ] |
| GSE101990 |
Deletion of 11q in neuroblastomas drives sensitivity to PARP inhibition |
|
| Relations |
| BioSample |
SAMN07421201 |
| SRA |
SRX3045028 |
