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| Status |
Public on Jul 01, 2021 |
| Title |
hiPSC line_36 |
| Sample type |
genomic |
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| Source name |
SC3148-D3
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| Organism |
Homo sapiens |
| Characteristics |
cell type: induced pluripotent stem cell (iPSC) line
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| Treatment protocol |
None
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| Growth protocol |
cells were culture in mTESR medium and passaged every 5 days.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from mononuclear cell preparations of leukemic blasts obtained from peripheral blood or bone marrow at diagnosis using the Qiagen DNA Blood Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, PicoGreen and agarose gel electrophoresis.
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| Label |
cy3, cy5
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| 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.
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| Scan protocol |
The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.
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| Description |
SC3148-D3_68
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| Data processing |
Genotyping was performed using the default parameters in the Birdseed v2 algorithm of Genotyping Console (GTC) 4.2 software (Affymetrix). As a quality control for the genotyping, Contrast QC values were calculated as implemented in the GTC 4.2, and samples used passed the recommended values. Genome annotations applied in data analysis referred to the human reference assembly GRCh37/hg19 as provided by the Affymetrix annotation file
primary data description: Genotype-matrix_42_hPSC_lines.txt contains Genotype Call (SNP call, Forward Strand Base Calls): AA, AT, AC, AG, TT, TC, TG, CC, CG, GG, and NoCall; 'Signal' = Summarized signal
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| Submission date |
Aug 03, 2018 |
| Last update date |
Jul 01, 2021 |
| Contact name |
Shuibing Chen |
| E-mail(s) |
shuibing.chen@gmail.com
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| Phone |
2127465431
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| Organization name |
Weill Cornell Medical College
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| Department |
Surgery
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| Street address |
A 827B, 1300 York Ave
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
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| Platform ID |
GPL6801 |
| Series (2) |
| GSE118086 |
Pharmacogenetics and Drug Discovery for Anthracycline-Induced Cardiotoxicity Enabled by Sinoatrial Node-like Cells Derived from Human Pluripotent Stem Cells [SNP array] |
| GSE118087 |
Pharmacogenetics and Drug Discovery for Anthracycline-Induced Cardiotoxicity Enabled by Sinoatrial Node-like Cells Derived from Human Pluripotent Stem Cells |
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| Supplementary file |
Size |
Download |
File type/resource |
| GSM3318465_SC3148-D3_68.CEL.gz |
28.2 Mb |
(ftp)(http) |
CEL |
| Processed data are available on Series record |
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