Aspartate signalling drives lung metastasis via alternative translation

Nature, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 1, 2025

Language: Английский

---

The effect of background noise and its removal on the analysis of single-cell expression data

Genome biology, Journal Year: 2023, Volume and Issue: 24(1)

Published: June 19, 2023

In droplet-based single-cell and single-nucleus RNA-seq experiments, not all reads associated with one cell barcode originate from the encapsulated cell. Such background noise is attributed to spillage cell-free ambient RNA or swapping events.

Language: Английский

---

Comparative Analysis of Single-Cell RNA Sequencing Methods with and without Sample Multiplexing

International Journal of Molecular Sciences, Journal Year: 2024, Volume and Issue: 25(7), P. 3828 - 3828

Published: March 29, 2024

Single-cell RNA sequencing (scRNA-seq) has emerged as a powerful technique for investigating biological heterogeneity at the single-cell level in human systems and model organisms. Recent advances scRNA-seq have enabled pooling of cells from multiple samples into single libraries, thereby increasing sample throughput while reducing technical batch effects, library preparation time, overall cost. However, comparative analysis methods with without multiplexing is lacking. In this study, we benchmarked two representative platforms: Parse Biosciences (Parse; multiplexing) 10x Genomics (10x; multiplexing). By using peripheral blood mononuclear (PBMCs) obtained healthy individuals, demonstrate that demultiplexed data showed similar cell type frequencies compared to where were not multiplexed. Despite relatively lower capture affecting preparation, can detect rare types (e.g., plasmablasts dendritic cells) which likely due its higher sensitivity gene detection. Moreover, transcript quantification between platforms revealed platform-specific distributions length GC content. These results offer guidance researchers designing high-throughput studies.

Language: Английский

---

Private information leakage from single-cell count matrices

Cell, Journal Year: 2024, Volume and Issue: 187(23), P. 6537 - 6549.e10

Published: Oct. 2, 2024

Language: Английский

---

Molecular connectomics reveals a glucagon-like peptide 1-sensitive neural circuit for satiety

Nature Metabolism, Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 3, 2024

Language: Английский

---

Revealing the Prevalence of Suboptimal Cells and Organs in Reference Cell Atlases: An Imperative for Enhanced Quality Control

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

Published: April 22, 2024

Abstract The advent of droplet-based single-cell RNA-sequencing (scRNA-seq) has dramatically increased data throughput, enabling the release a diverse array tissue cell atlases to public. However, we will show that prominent initiatives such as Human Cell Atlas, Tabula Muris, and Sapiens contain significant amount contamination products (frequently affecting whole organ) in their portals due suboptimal quality filtering. Our work addresses critical gap by advocating for more stringent filtering, highlighting imperative shift from existing standards, which currently lean towards greater permissiveness. We importance incorporating intronic fraction control -or MALAT1 expression otherwise- showcasing its informative nature potential elevate atlas reliability. In summary, here, unveil hidden landscape every highlight rigorous assessment enhance applicability downstream analyses.

Language: Английский

---

Revisiting Cardiac Biology in the Era of Single Cell and Spatial Omics

Circulation Research, Journal Year: 2024, Volume and Issue: 134(12), P. 1681 - 1702

Published: June 6, 2024

Throughout our lifetime, each beat of the heart requires coordinated action multiple cardiac cell types. Understanding biology, its intricate microenvironments, and mechanisms that govern their function in health disease are crucial to designing novel therapeutical behavioral interventions. Recent advances single-cell spatial omics technologies have significantly propelled this understanding, offering insights into cellular diversity complex interactions tissue. This review provides a comprehensive overview landscape heart, bridging gap between suspension-based emerging situ approaches, focusing on experimental computational challenges, comparative analyses mouse human systems, rising contextualization cells within niches. As we explore at unprecedented resolution, integrating from both studies will pave way for diagnostic tools therapeutic interventions, ultimately improving outcomes patients with cardiovascular diseases.

Language: Английский

---

Differences in molecular sampling and data processing explain variation among single-cell and single-nucleus RNA-seq experiments

Genome Research, Journal Year: 2024, Volume and Issue: 34(2), P. 179 - 188

Published: Feb. 1, 2024

A mechanistic understanding of the biological and technical factors that impact transcript measurements is essential to designing analyzing single-cell single-nucleus RNA sequencing experiments. Nuclei contain same pre-mRNA population as cells, but they a small subset mRNAs. Nonetheless, early studies argued analysis yielded results comparable cellular samples if were included. However, typical workflows do not distinguish between mRNA when estimating gene expression, variation in their relative abundances across cell types has received limited attention. These gaps are especially important given incorporating become commonplace for both assays, despite known length bias capture. Here, we reanalyze public data sets from mouse human describe mechanisms contrasting effects sampling on expression marker selection RNA-seq. We show levels vary considerably among types, which mediates degree limits generalizability recently published normalization method intended correct this bias. As an alternative, repurpose existing post hoc length–based correction conventional RNA-seq set enrichment analysis. Finally, inclusion bioinformatic processing can impart larger effect than assay choice itself, pivotal effective reuse data. analyses advance our sources experiments provide useful guidance future studies.

Language: Английский

---

Reanalysis of single-cell RNA sequencing data does not support herpes simplex virus 1 latency in non-neuronal ganglionic cells in mice

Journal of Virology, Journal Year: 2024, Volume and Issue: 98(4)

Published: March 6, 2024

ABSTRACT Most individuals are latently infected with herpes simplex virus type 1 (HSV-1), and it is well-established that HSV-1 establishes latency in sensory neurons of peripheral ganglia. However, was recently proposed latent also present immune cells recovered from the ganglia experimentally mice. Here, we reanalyzed single-cell RNA sequencing (scRNA-Seq) data formed basis for conclusion. Unexpectedly, off-target priming 3’ scRNA-Seq experiments enabled detection non-polyadenylated latency-associated transcript ( LAT ) intronic RNAs. reads were near-exclusively detected mixed populations undergoing cell death. Specific loss neuronal transcripts during quality control filtering indicated widespread destruction neurons, supporting presence contaminating cell-free other following tissue processing. In conclusion, reported non-neuronal best explained using compromised datasets. IMPORTANCE people (HSV-1) their life. Once infected, generally remains a (silent) state, hiding within Periodic reactivation (reawakening) may cause fresh diseases such as cold sores. A recent study can establish mice, challenging existing dogma. We identified several flaws methodologies analyses performed invalidate published conclusions. Specifically, showed used resulted which contaminants confound analysis. thus conclude there little to no evidence cells.

Language: Английский

---

Immunomodulation by endothelial cells: prospects for cancer therapy

Trends in cancer, Journal Year: 2024, Volume and Issue: 10(11), P. 1072 - 1091

Published: Sept. 16, 2024

Language: Английский

---