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| Status |
Public on Feb 06, 2019 |
| Title |
Single-cell RNA-sequencing of CD14+ monocyte differentiation with M-CSF stimulus |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
We obtained single-cell RNA-sequencing (scRNA-seq) profiles of CD14+ monocytes isolated from human peripheral blood at 0, 3 and 6 days after M-CSF stimulation (to differentiate the cells into macrophages) across multiple donors.
Integration of single-cell RNA sequencing (scRNA-seq) data from multiple experiments, laboratories, and technologies can uncover biological insights, but current methods for scRNA-seq data integration are limited by a requirement for datasets to derive from functionally similar cells. We use a novel algorithm, Scanorama, to identify and merge the shared cell types among all pairs of datasets and to accurately integrate heterogeneous scRNA-seq datasets. Scanorama is sensitive to subtle temporal changes within the same cell lineage, successfully integrating functionally similar cells across time series data of CD14+ monocytes at different stages of differentiation into macrophages. Scanorama is not only able to differentiate between completely disparate cell types but is also sensitive to subtler transcriptional changes within a cell type due to processes like stimulation.
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| |
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| Overall design |
scRNA-seq of human CD14+ monocytes at 0, 3, and 6 days after M-CSF stimulation in multiple donors
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| |
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| Contributor(s) |
Hie B, Bryson B, Berger B |
| Citation(s) |
31061482 |
| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| R01 GM081871 |
Structure based Prediction of the interactome |
MASSACHUSETTS INSTITUTE OF TECHNOLOGY |
Bonnie Berger |
|
| Submission date |
Feb 05, 2019 |
| Last update date |
May 08, 2019 |
| Contact name |
Brian Hie |
| E-mail(s) |
brianhie@mit.edu
|
| Organization name |
MIT
|
| Street address |
77 Massachusetts Ave
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02139 |
| Country |
USA |
| |
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| Platforms (1) |
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| Samples (8)
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| Relations |
| BioProject |
PRJNA520990 |
| SRA |
SRP183682 |
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