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Sample GSM1538311 Query DataSets for GSM1538311
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)
 
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.
 
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

Data table header descriptions
ID_REF
VALUE LOG2 RATIO
WEIGHTED LOG2 RATIO
SMOOTH SIGNAL

Data table
ID_REF VALUE WEIGHTED LOG2 RATIO SMOOTH SIGNAL
C-7SARK 0.496633 0.217196 2.034428
C-4WYLN -0.225446 0.053818 2.035756
C-3BFNY 0.208620 0.096180 2.035980
C-7ONNE -0.177918 -0.065305 2.036762
C-6HYCN 0.031081 -0.028697 2.036864
C-7SCGC -0.017509 -0.186491 2.037199
C-7RZQQ -0.291596 -0.141751 2.037965
C-7RZWZ -0.373152 -0.294240 2.037605
C-7SEBI 0.106080 0.220343 2.036916
C-7RZIL 0.070195 0.074531 2.038254
C-4NQTX 0.100238 0.122488 2.039702
C-7SDKW 0.125293 -0.015557 2.039535
S-3WRNV nan nan nan
C-7RXVK -0.053866 0.077449 2.039960
C-4LHKS -0.133797 -0.052041 2.040115
C-7RWHE 0.007988 -0.001449 2.040292
C-7SBEJ 0.081759 -0.121876 2.040458
C-7RYJO 0.047651 -0.202605 2.040217
C-7SEGS -0.400489 -0.313723 2.040761
C-4LLXK -0.378634 -0.259619 2.040943

Total number of rows: 2749693

Table truncated, full table size 96034 Kbytes.




Supplementary file Size Download File type/resource
GSM1538311_GDB-339_C3_CytoScanHD_Array_.CEL.gz 29.3 Mb (ftp)(http) CEL
GSM1538311_GDB-339_C3_CytoScanHD_Array_.cyhd.cychp.gz 80.2 Mb (ftp)(http) CYCHP
Processed data included within Sample table
Processed data provided as supplementary file

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