cell type: human induced pluripotent stem cell line cell line/clone: clone PB1-56 cell passage: passage #4 cell origin: cell line is derived from Human neonatal foreskin fibroblast HFF cell, passage #10
Growth protocol
Cell lines were grown according to standard conditions, and as described in associated manuscript
Extracted molecule
genomic DNA
Extraction protocol
Genomic DNA was extracted from hiPSCs, hESCs, and fibroblast cell culture plates using the Qiagen DNA Blood Mini Kit. DNA quality and quantity was assessed using a Thermo Multiscan Spectrum spectrophotometer, and agarose gel electrophoresis.
Label
Biotin
Label protocol
As per manufacturer user guide (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 and stained using GeneChip fluidics station 450, and scanned using the GeneChip Scanner 3000 with Autoloader.
Description
Hybridized to SNP 6.0 array
Data processing
CEL files were generated by Affymetrix GeneChip Command Console Software 1.1(AGCC), and were processed and analyzed using Affymetrix Genotyping Console 3.0.2 and Birdseed v2-algorithm. Samples were normalized against 40 International HapMap samples hybridized in-house, and which are listed in supplementary table of associated manuscript. CHP files: Copy number analysis, probset coordinates, CN state, signal log2 ratio, LOH and allele difference calls. Segment files: Segment analysis, Copy number variation coordinates and size, CN state, cytoband location, start and end probe position, and CNV annotation
