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Related Experiment Video

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Single-cell Transcriptomic Analyses of Mouse Pancreatic Endocrine Cells

Single-cell Transcriptomic Analyses of Mouse Pancreatic Endocrine Cells

Published on: September 30, 2018

Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics.

Kelly Street^1,2, Davide Risso³, Russell B Fletcher⁴

¹Division of Biostatistics, School of Public Health, University of California, Berkeley, CA, USA.

|June 20, 2018

Summary

Slingshot, a new method for single-cell transcriptomics, accurately infers cell lineages and pseudotimes. It effectively identifies multiple branching trajectories in complex cell populations, improving upon existing methods.

Keywords:

Lineage inference Pseudotime inference RNA-Seq Single cell

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Area of Science:

Computational Biology
Genomics
Developmental Biology

Background:

Single-cell transcriptomics enables the study of heterogeneous cell communities.
Charting stem cell differentiation requires lineage inference from progenitor to differentiated cells.
Accurate characterization of multiple branching cell lineages remains a computational challenge.

Purpose of the Study:

To introduce Slingshot, a novel computational method for inferring cell lineages and pseudotimes from single-cell gene expression data.
To address the challenge of accurately characterizing multiple branching lineages in complex cellular systems.

Main Methods:

Development of Slingshot, a novel computational method.
Application to previously published single-cell gene expression datasets.
Comparative analysis using simulation studies.

Main Results:

Slingshot successfully identifies biological signals for one to three branching trajectories in existing datasets.
Slingshot demonstrates superior accuracy in inferring pseudotimes compared to other leading methods in simulation studies.

Conclusions:

Slingshot offers a robust and flexible tool for lineage inference from noisy single-cell data.
The method's ability to identify multiple trajectories is crucial for understanding dynamic temporal gene expression.
Accurate cell lineage inference is essential for developmental biology and stem cell research.