|
| Status |
Public on Jan 11, 2022 |
| Title |
Wilms tumor (array) |
| Sample type |
genomic |
| |
|
| Source name |
Wilms tumor A6130
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Primary Wilms tumor
genotype: de novo germline mutation in CTCF
|
| Treatment protocol |
None
|
| Growth protocol |
Wilms tumor was obtained at surgery from patient.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from pathologist supervised Wilms tumor sample 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.
|
| |
|
| Submission date |
Jan 04, 2022 |
| Last update date |
Jan 12, 2022 |
| Contact name |
Jaime Font de Mora Sain |
| E-mail(s) |
jaime.fontdemora@gmail.com
|
| Phone |
+34961246646
|
| Organization name |
Instituto de Investigación Sanitaria La Fe
|
| Department |
Oncology
|
| Lab |
Laboratory of Cellular and Molecular Biology
|
| Street address |
Avenida Fernando Abril Martorell, 106
|
| City |
Valencia |
| State/province |
Valencia |
| ZIP/Postal code |
46026 |
| Country |
Spain |
| |
|
| Platform ID |
GPL16131 |
| Series (2) |
| GSE193017 |
SNP array data for Wilms Tumor harboring de novo germline mutation in CTCF |
| GSE193235 |
Germline Variant in *Ctcf* Links Mental Retardation to Wilms Tumor Predisposition |
|
