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| Status |
Public on May 29, 2021 |
| Title |
Drug Combination Signatures for Prediction and Mitigation of Toxicity [single cell] |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Single cell transcriptomic signatures of cardiomyocytes differentiated from hiPSC lines generated from clinically well-characterized, diverse healthy human individuals. We provide single cell mRNAseq data of cardiomyocytes differentiated from 4 hiPSC lines.
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| Overall design |
The overall goal of the drug signatures for prediction and mitigation of toxicity study is to use genomic and proteomic high-throughput measurements as the basis for computational analysis that integrates network analyses with structural constraints and dynamical models in multiple cell types to identify signatures that predict toxicity induced by 55 FDA-approved chemotherapeutic drugs and potential mitigation of this toxicity. For this purpose, we have generated human induced pluripotent cell (hiPSC) lines from established fibroblast lines of forty clinically healthy racially diverse male and female study participants who ranged in age from 22 and 61 years. One clone from each of the forty hiPSC line was fully characterized for normal karyotype, short-tandem repeat matching to the original fibroblast line (authentication), pluripotency by select pluripotent marker expression via immunocytochemistry and by mRNAseq-based PluriTest analysis, and whole-genome sequencing. In order to establish singel cell transcriptomic signatures specific to clinically well-characterized healthy individuals, cardiomyocytes were differentiated from four hiPSC lines derived from 2 male and 2 female, age matched (23 and 33 yrs old, and 24 and 36 yrs old, respectively) persons using an established protocol, purified to 95% purity (SIRPA+CD90-) using a metabolic switch protocol, reseeded and treated for 24 hrs with DMSO (14.1mM) before single cell mRNAseq was performed using the 10x Genomics platform.
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| Citation(s) |
34739849, 39261481 |
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| Submission date |
May 28, 2021 |
| Last update date |
Oct 09, 2024 |
| Contact name |
Ravi Iyengar |
| Organization name |
Icahn School of Medicine at Mount Sinai
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| Department |
Pharmacological Sciences
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| Street address |
1425 Madison Avenue, Room 12-70C
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10029 |
| Country |
USA |
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| Platforms (1) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (4)
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| Relations |
| BioProject |
PRJNA733493 |
| SRA |
SRP321795 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE175761_Genenrate-iPSC-CM-scRNA-Ensembl-Gene-Counts-Table.GEO.R.gz |
907 b |
(ftp)(http) |
R |
| GSE175761_RAW.tar |
339.9 Mb |
(http)(custom) |
TAR (of TAR, TSV) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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