|
Status |
Public on Jul 18, 2017 |
Title |
Neuroblastoma tumor TI_501 |
Sample type |
genomic |
|
|
Source name |
Neuroblastoma tumor TI_501
|
Organism |
Homo sapiens |
Characteristics |
tissue: 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.
|
Label |
Biotin
|
Label protocol |
As per manufacturer (Affymetrix)
|
|
|
Hybridization protocol |
DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.
|
Scan protocol |
The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.
|
Description |
Hybridized to CytoScan HD
|
Data processing |
The array image was acquired using Affymetrix GeneChip® Operating Software (GCOS version 1.4). Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using GTYPE 4.1 and Affymetrix Copy Number Analysis Tool (CNAT 4.0.1) softwares. Genomic Smoothing analysis was performed by using the smoothing window of 0 Mb, and inferred copy number states were derived from a Hidden Markov Model (HMM) based algorithm implemented in CNAT 4.0.1. Circular Binary Segmentation (Ohlsen et al., 2004) was applied using DNAcopy package for R Bioconductor on raw data. Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal
|
|
|
Submission date |
Jul 17, 2017 |
Last update date |
Jan 23, 2018 |
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 |
GPL16131 |
Series (2) |
GSE101533 |
Deletion of 11q in neuroblastomas drives sensitivity to PARP inhibition [SNP array] |
GSE101990 |
Deletion of 11q in neuroblastomas drives sensitivity to PARP inhibition |
|