Comprehensive Integration of Single-Cell Data.
Cell
; 177(7): 1888-1902.e21, 2019 06 13.
Article
in En
| MEDLINE
| ID: mdl-31178118
ABSTRACT
Single-cell transcriptomics has transformed our ability to characterize cell states, but deep biological understanding requires more than a taxonomic listing of clusters. As new methods arise to measure distinct cellular modalities, a key analytical challenge is to integrate these datasets to better understand cellular identity and function. Here, we develop a strategy to "anchor" diverse datasets together, enabling us to integrate single-cell measurements not only across scRNA-seq technologies, but also across different modalities. After demonstrating improvement over existing methods for integrating scRNA-seq data, we anchor scRNA-seq experiments with scATAC-seq to explore chromatin differences in closely related interneuron subsets and project protein expression measurements onto a bone marrow atlas to characterize lymphocyte populations. Lastly, we harmonize in situ gene expression and scRNA-seq datasets, allowing transcriptome-wide imputation of spatial gene expression patterns. Our work presents a strategy for the assembly of harmonized references and transfer of information across datasets.
Key words
Full text:
1
Collection:
01-internacional
Database:
MEDLINE
Main subject:
Software
/
Sequence Analysis, RNA
/
Gene Expression Profiling
/
Databases, Nucleic Acid
/
Single-Cell Analysis
/
Transcriptome
Limits:
Humans
Language:
En
Journal:
Cell
Year:
2019
Type:
Article
Affiliation country:
United States