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Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

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Quartet-based inference of cell differentiation trees from ChIP-Seq histone modification data.

Nazifa Ahmed Moumi¹, Badhan Das¹, Zarin Tasnim Promi¹

¹Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology, Dhaka, Bangladesh.

|September 27, 2019

Summary

This study introduces novel quartet-based phylogenetic methods to build cell-type trees, enhancing our understanding of developmental biology. These techniques effectively map hierarchical cell differentiation using epigenetic mark data.

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Area of Science:

Developmental Biology
Evolutionary Biology
Genomics
Bioinformatics

Background:

Cell differentiation is crucial for understanding development and evolution.
Transcriptomic and epigenetic data reveal hierarchical relationships among cell types.
Phylogenetic methods have been used with histone modification data to infer cell-type relationships.

Purpose of the Study:

To demonstrate the suitability of quartet-based phylogenetic techniques for constructing cell-type trees.
To propose novel pipelines for inferring cell phylogeny.
To introduce a metric for evaluating the accuracy of cell-type trees.

Main Methods:

Application of two quartet-based phylogenetic pipelines for cell phylogeny construction.
Assessment of methods using ChIP-Seq histone modification data (H3K4me3, H3K27me3, H3K36me3, H3K27ac).
Development of a robust metric for evaluating inferred cell-type trees.

Main Results:

Validated the applicability of quartet-based methods for cell-type tree construction.
Demonstrated successful inference of hierarchical differentiation processes across various cell types.
Showcased the utility of histone mark data in phylogenetic analyses of cell types.

Conclusions:

Quartet-based phylogenetic methods offer a powerful approach for reconstructing cell-type relationships.
The proposed pipelines and evaluation metric advance the study of cellular hierarchies.
This work provides new tools for analyzing epigenetic data in developmental and evolutionary contexts.