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Sample GSM642757 Query DataSets for GSM642757
Status Public on Jan 31, 2011
Title hiPSC line PB1-2, passage 8
Sample type genomic
 
Source name hiPSC line PB1-2
Organism Homo sapiens
Characteristics cell type: human induced pluripotent stem cell line
cell line/clone: clone PB1-2
cell passage: passage #8
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
 
Submission date Dec 19, 2010
Last update date Jan 31, 2011
Contact name Samer Hussein
E-mail(s) samer.hussein@utoronto.ca
Organization name SLRI-Mount Sinai Hosp.
Street address 25 Orde St.
City Toronto
ZIP/Postal code M5T 3H7
Country Canada
 
Platform ID GPL6801
Series (1)
GSE26173 Affymetrix SNP6.0 data for human induced pluripotent stem cells (hiPSCs), human Fibroblasts, and human embryonic stem cells (hESCs)

Data table header descriptions
ID_REF
VALUE CN STATE
CHROMOSOME
POSITION
LOG2 RATIO
SMOOTH SIGNAL
LOH
ALLELE DIFFERENCE

Data table
ID_REF VALUE CHROMOSOME POSITION LOG2 RATIO SMOOTH SIGNAL LOH ALLELE DIFFERENCE
CN_473963 2.000000 1 51586 -0.669153 1.890045 nan nan
CN_473964 2.000000 1 51659 -0.646060 1.890232 nan nan
CN_473965 2.000000 1 51674 -0.398805 1.890271 nan nan
CN_473981 2.000000 1 52771 0.394052 1.893094 nan nan
CN_473982 2.000000 1 52788 0.325213 1.893138 nan nan
CN_497981 2.000000 1 62627 -0.475447 1.918861 nan nan
CN_502615 2.000000 1 75787 0.224060 1.954279 nan nan
CN_502613 2.000000 1 75849 -0.151024 1.954449 nan nan
CN_502614 2.000000 1 76175 0.259104 1.955339 nan nan
CN_502616 2.000000 1 76192 0.634739 1.955386 nan nan
CN_502843 2.000000 1 88453 0.205916 1.989254 nan nan
CN_466171 2.000000 1 218557 0.072994 2.802161 nan nan
CN_468414 2.000000 1 218926 -0.014543 2.802410 nan nan
CN_468412 2.000000 1 219009 -0.057607 2.802467 nan nan
CN_468413 2.000000 1 219024 0.161290 2.802477 nan nan
CN_470565 2.000000 1 219470 0.736903 2.802779 nan nan
CN_468424 2.000000 1 225521 0.158554 2.806891 nan nan
CN_468425 2.000000 1 225579 0.854648 2.806931 nan nan
CN_460512 2.000000 1 346294 -0.180960 2.727554 nan nan
CN_460513 2.000000 1 346393 0.682704 2.727556 nan nan

Total number of rows: 1813441

Table truncated, full table size 114274 Kbytes.




Supplementary file Size Download File type/resource
GSM642757_B02_PB1-2C.CEL.gz 29.7 Mb (ftp)(http) CEL
GSM642757_B02_PB1-2C.CN5.CNCHP.gz 34.9 Mb (ftp)(http) CNCHP
GSM642757_B02_PB1-2C.CN5.cn_segments.txt.gz 16.8 Kb (ftp)(http) TXT
Processed data included within Sample table
Processed data provided as supplementary file

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