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| Status |
Public on Feb 20, 2021 |
| Title |
Perturbation panel profiling of human iPSC-derived cardiac myocytes and primary dermal fibroblasts |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
We report gene expression by RNAtag-seq after treatment with 75 different small molecule perturbations in culture of human iPSC-derived cardiac myocytes and genetically matched primary dermal fibroblasts. Perturbations were chosen from the SelleckChem Bioactive Library, among all molecules targeting any kinases or G-protein coupled receptors, and chosen to have as little overlap in annotated targets as possible. Based on these experiments (and others) we show that transcription factors important for cardiac development and cardiac myocyte identity maintenance were frequently up-regulated (i.e., "responsive") after small molecule perturbations of cultured iPSC-derived cardiac myocytes (i.e., responsive). We also show that the set of highly responsive transcription factors in fibroblasts are enriched for barriers to fibroblast reprogramming to iPSC.
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| Overall design |
RNAtag-seq-based RNA sequencing of 2 human cells types (iPSC-derived cardiac myocytes and primary dermal fibroblasts), each in 75 different small molecule perturbation conditions (each in triplicate) and 1 DMSO vehicle control condition (59 replicates for fibroblasts, 63 replicates for cardiac myocytes), and 4 DMSO vehicle control-treated HeLa samples. 576 total samples, multiplexed by RNAtag-seq in batches of 32 to make a total of 18 paired-end libraries. The 75 perturbation conditions, the same for both cell types, consist of 50 single-drug conditions and 25 two-drug conditions. See Mellis et al. citation for dosing and analysis strategy.
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| Contributor(s) |
Mellis IA, Jain R, Raj A |
| Citation missing |
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| Submission date |
Feb 19, 2021 |
| Last update date |
Feb 21, 2021 |
| Contact name |
Ian A Mellis |
| E-mail(s) |
[email protected]
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| Organization name |
Columbia University
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| Street address |
622 W 168th St
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10032 |
| Country |
USA |
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| Platforms (1) |
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| Samples (18)
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| Relations |
| BioProject |
PRJNA703032 |
| SRA |
SRP307157 |
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