Improving Doublet Cell Removal Efficiency through Multiple Algorithm Runs

Computational and Structural Biotechnology Journal, Journal Year: 2025, Volume and Issue: 27, P. 451 - 460

Published: Jan. 1, 2025

Language: Английский

---

Mitigating ambient RNA and doublets effects on single cell transcriptomics analysis in cancer research

Cancer Letters, Journal Year: 2025, Volume and Issue: unknown, P. 217693 - 217693

Published: April 1, 2025

Language: Английский

---

Genetically Encoded Fluorescence Barcodes Allow for Single-Cell Analysis via Spectral Flow Cytometry

ACS Synthetic Biology, Journal Year: 2025, Volume and Issue: unknown

Published: May 6, 2025

Genetically encoded, single-cell barcodes are broadly useful for experimental tasks such as lineage tracing or genetic screens. For applications, a barcode library would ideally have high diversity (many unique barcodes), nondestructive identification (repeated measurements in the same cells population), and fast, inexpensive readout conditions). Current nucleic acid barcoding methods generate but require destructive slow/expensive readout, current fluorescence nondestructive, to lack diversity. We recently proposed theory how fluorescent protein combinations may high-diversity with identification. Here, we present an initial proof-of-concept by generating of ∼150 from two-way 18 proteins, 61 which tested experimentally. use pooled cloning strategy that is validated contain every possible combination proteins. Experimental results using single mammalian spectral flow cytometry demonstrate excellent classification performance individual exception mTFP1, most evaluated barcodes, many true positive rates >99%. The compatible screening hundreds genes (or gene pairs) clones. This work lays foundation greater libraries (potentially ∼105 more) generated spectrally resolvable tandem probes.

Language: Английский

---

Prevalence of and gene regulatory constraints on transcriptional adaptation in single cells

Genome biology, Journal Year: 2024, Volume and Issue: 25(1)

Published: Aug. 12, 2024

Cells and tissues have a remarkable ability to adapt genetic perturbations via variety of molecular mechanisms. Nonsense-induced transcriptional compensation, form adaptation, has recently emerged as one such mechanism, in which nonsense mutations gene trigger upregulation related genes, possibly conferring robustness at cellular organismal levels. However, beyond handful developmental contexts curated sets no comprehensive genome-wide investigation this behavior been undertaken for mammalian cell types conditions. How the regulatory-level effects inherently stochastic compensatory networks contribute phenotypic penetrance single cells remains unclear. We analyze existing bulk single-cell transcriptomic datasets uncover prevalence adaptation systems across diverse types. perform regulon expression analyses transcription factor target both pooled perturbation datasets. Our results reveal greater regulons factors exhibiting compared those that do not. Stochastic mathematical modeling minimal qualitatively recapitulates several aspects including paralog mutation. Combined with machine learning analysis network features interest, our framework offers potential explanations regulatory steps are most important adaptation. integrative approach identifies putative hits—genes demonstrating possible adaptation—to follow-up on experimentally provides formal quantitative test refine models

Language: Английский

---

More cells, more doublets in highly multiplexed single-cell data

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 4, 2024

Abstract Sample barcoding allows deconvolution of multiplets in multiplexed droplet-based single-cell RNA-sequencing experiments. However, this is only possible when each cell comes from a different sample. As the number cells droplet increases, probability two or more coming same sample increases rapidly. We show that these unresolvable greater than previously estimated for 10X Flex scRNA-seq protocol, and provide formula estimating fraction data set given measured average occupancy unique samples pool. also existing doublet detection tools should be applied to identify multiplets, demonstrate filtering out barcodes identified by improves downstream analysis.

Language: Английский

---

Mapping cell-cell fusion at single-cell resolution

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 14, 2024

Cell-cell fusion is a tightly controlled process in the human body known to be involved fertilization, placental development, muscle growth, bone remodeling, and viral response. Fusion between cancer cells results first whole-genome doubled state, which may followed by generation of aneuploidies; these genomic alterations are drivers tumor evolution. The role cell-cell progression treatment response has been understudied due limited experimental systems for tracking analyzing individual events. To meet this need, we developed molecular toolkit map origins outcomes cell events within population. This platform, ClonMapper Duo ('CMDuo'), identifies that have undergone through combination reporter expression engineered fluorescence-associated index sequences paired randomly generated nucleotide barcodes. scRNA-seq indexed barcodes enables mapping each set parental progeny throughout In triple-negative breast CMDuo uncovered subclonal transcriptomic hybridization unveiled distinct cell-states arise direct consequence homotypic fusion. platform high-throughput single data study disease therapeutic

Language: Английский

---