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| Status |
Public on Oct 31, 2020 |
| Title |
Phenotypically supervised single cell sequencing parses within-cell-type heterogeneity |
| Organisms |
Homo sapiens; Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
We used a phenotypic cell sorting technique to ask whether phenotypically supervised scRNAseq analysis (pheno-scRNAseq) can provide more insight into heterogeneous cell behaviors than unsupervised scRNAseq. Using a simple 3D in vitro breast cancer (BRCA) model, we conducted pheno-scRNAseq on invasive and non-invasive cells and compared the results to phenotype-agnostic scRNAseq analysis. Pheno-scRNAseq identified unique and more selective differentially expressed genes (DEGs) than unsupervised scRNAseq analysis. Functional studies validated the utility of pheno-scRNAseq in understanding within-cell-type functional heterogeneity and revealed that migration phenotypes were coordinated with specific metabolic, proliferation, stress, and immune phenotypes.
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| Overall design |
Transcriptomic examination of human and mouse breast cancer cells for phenotypic heterogeneity. Phenotypic supervision: Cells were phototagged using photoconversion of Dendra2 that was transduced into MDA-MB-231 cells. Cells were then sorted using fluorescence activated cell sorting. 2 samples were phenotypically supervised, 2 samples were phenotype-agnostic.
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| Web link |
https://doi.org/10.1016/j.isci.2020.101991
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| |
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| Contributor(s) |
Chen K, Ozturk K, Carter H, Fraley SI |
| Citation(s) |
33490901, 34095869 |
| |
| Submission date |
Sep 30, 2020 |
| Last update date |
Jun 15, 2021 |
| Contact name |
Stephanie I Fraley |
| Organization name |
UCSD
|
| Street address |
9500 Gilman Drive MC 0412
|
| City |
San Diego |
| State/province |
CA |
| ZIP/Postal code |
92093 |
| Country |
USA |
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| Platforms (3) |
| GPL20301 |
Illumina HiSeq 4000 (Homo sapiens) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (4)
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| Relations |
| BioProject |
PRJNA666683 |
| SRA |
SRP285944 |
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