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Sample GSM2705763 Query DataSets for GSM2705763
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

Supplementary file Size Download File type/resource
GSM2705763_NB_TI501_CYTOSCANHD_JS_20130703.CEL.gz 28.5 Mb (ftp)(http) CEL
GSM2705763_NB_TI501_CYTOSCANHD_JS_20130703.cyhd.cychp.gz 80.2 Mb (ftp)(http) CYCHP
Processed data provided as supplementary file

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