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Status |
Public on Dec 15, 2014 |
Title |
iPSC_WBS1-C2 (GDB-339_C3) aCGH |
Sample type |
genomic |
|
|
Source name |
fibroblast-derived iPSC
|
Organism |
Homo sapiens |
Characteristics |
gender: male genotype: WBS donor: GDB-339 culture: iPSC colonies were grown on feeder-free conditions on plates coated with human-qualified Matrigel (BD Biosciences) diluted 1:40 in DMEM-F12 and in mTeSR-1 (StemCell Technologies) medium. reprogramming method: mRNA reprogramming cell type: fibroblast-derived iPSC
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Genomic DNA was extracted from fibroblasts and feeder-free iPSC lines using the DNeasy Blood and Tissue Kit (Qiagen) according to manufacturer specifications. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and agarose gel electrophoresis.
|
Label |
Biotin
|
Label protocol |
As per manufacturer (Affymetrix)
|
|
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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 7G.
|
Description |
Hybridized to CytoScan HD
|
Data processing |
The array image was acquired using Affymetrix GeneChip® Command Console Software 4.1.2. Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using Chromosome Analysis Suite (ChAS) software. Inferred copy number states were derived from a Hidden Markov Model (HMM) based algorithm implemented in ChAS. CHP files.
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|
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Submission date |
Nov 05, 2014 |
Last update date |
Dec 15, 2014 |
Contact name |
Giuseppe Testa |
E-mail(s) |
giuseppe.testa@ieo.it
|
Organization name |
European Institute of Oncology & University of Milano, Italy
|
Lab |
Neurogenomics Research Centre
|
Street address |
Via Adamello, 16
|
City |
Milano |
ZIP/Postal code |
20139 |
Country |
Italy |
|
|
Platform ID |
GPL16131 |
Series (2) |
GSE63028 |
7q11.23 dosage-dependent dysregulation in the human pluripotent state primes aberrant transcriptional programs in disease-relevant lineages (aCGH) |
GSE63058 |
7q11.23 dosage-dependent dysregulation in the human pluripotent state primes aberrant transcriptional programs in disease-relevant lineages |
|