Analysis of synthetic cellular barcodes in the genome and transcriptome with BARtab and bartools

Holze, H; Talarmain, L; Fennell, KA; Lam, EY; Dawson, MA; Vassiliadis, D

Author(s): Holze, H; Talarmain, L; Fennell, KA; Lam, EY; Dawson, MA; Vassiliadis, D;
Details: Publication Year 2024-05-20,Volume 4,Issue #5,Page 100763
Journal Title: Cell Reports Methods
Publication Type: Research article
Abstract: Cellular barcoding is a lineage-tracing methodology that couples heritable synthetic barcodes to high-throughput sequencing, enabling the accurate tracing of cell lineages across a range of biological contexts. Recent studies have extended these methods by incorporating lineage information into single-cell or spatial transcriptomics readouts. Leveraging the rich biological information within these datasets requires dedicated computational tools for dataset pre-processing and analysis. Here, we present BARtab, a portable and scalable Nextflow pipeline, and bartools, an open-source R package, designed to provide an integrated end-to-end cellular barcoding analysis toolkit. BARtab and bartools contain methods to simplify the extraction, quality control, analysis, and visualization of lineage barcodes from population-level, single-cell, and spatial transcriptomics experiments. We showcase the utility of our integrated BARtab and bartools workflow via the analysis of exemplar bulk, single-cell, and spatial transcriptomics experiments containing cellular barcoding information.
Publisher: Cell Press
Keywords: *Transcriptome; *Single-Cell Analysis/methods; Humans; *High-Throughput Nucleotide Sequencing; Software; DNA Barcoding, Taxonomic/methods; Genome/genetics; Cell Lineage/genetics; Gene Expression Profiling/methods; Computational Biology/methods; Animals; CP: Biotechnology; CP: Systems biology; Nextflow pipeline; R package; cellular barcoding; lineage tracing; single cell; spatial transcriptomics
Department(s): Laboratory Research
Publisher's Version: https://doi.org/10.1016/j.crmeth.2024.100763
Open Access at Publisher's Site: https://doi.org/10.1016/j.crmeth.2024.100763
Terms of Use/Rights Notice: Refer to copyright notice on published article.

Creation Date: 2024-07-09 08:01:44

Last Modified: 2024-07-09 08:03:53