ATAC
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Related Articles from SNS
Chromap Suite: an open-source single-binary platform for agentic multiomic RNA + ATAC profiling
Single-cell multiomic profiling of RNA expression and chromatin accessibility is now a standard tool for resolving regulatory state in single cells, but existing analysis toolchains have lagged. Cell Ranger ARC, the proprietary multiomic pipeline, uses a custom broad peak caller rather than the MACS3 narrow peaks that the ATAC field has consolidated on, and its restrictive end-user licence forbids redistribution of analysis pipelines that include it. A fully open-source,...
Multi-omics analysis reveals chromatin and transcriptomic remodeling in hippocampal CA1 following adolescent social isolation
Social isolation (SI) during adolescence is associated with long-term vulnerability to psychiatric disorders; however, its effect on the hippocampal epigenome and transcriptome remains unclear. Here, we performed integrative ATAC-seq and RNA-seq of the hippocampal CA1 region using an adolescent mouse SI model, combined with single-cell RNA-seq reference mapping and cell type deconvolution. ATAC-seq identified SI-associated alterations in chromatin accessibility, including an increase in...
Learning quality scores for chromatin accessibility bigWig tracks using Machine Learning
High-throughput chromatin accessibility assays such as bulk and single-cell ATAC-seq have generated large collections of processed signal tracks in bigWig format, which are widely used for visualisation, data integration, and Machine Learning (ML)-based analyses. Despite their central role, systematic quality control (QC) frameworks operating directly at the level of bigWig signal tracks remain underdeveloped. This gap limits the ability to assess data reliability and hampers robust...
Single-cell multimodal profiling of pan-cancer cell lines uncovers gene regulatory principles underlying intrinsic cell states and environmental features
Cancer arises from extensive genetic and epigenetic alterations that reshape chromatin, transcriptional regulation, and malignant cell states. To systematically chart cancer-intrinsic regulatory programs, we constructed a pan-cancer single-cell transcriptomic and epigenomic atlas encompassing 60 human cell lines representing 16 tissue origins and 20 cancer types, comprising 240,957 single-nucleus RNA-seq and 223,347 single-nucleus ATAC-seq profiles. Integrative analyses revealed extensive...
Metadata Collector: An Open-Source Platform for Standardized Metadata Management in Multi Centre Sequencing Projects
Background: Next-generation sequencing (NGS) projects generate increasingly complex metadata that are critical for reproducibility, interoperability, and compliance with FAIR principles. Nevertheless, metadata curation in multi-institutional settings often still relies on spreadsheets, manual data entry and curation, as well as non-standardized terminology. These practices frequently result in incomplete or inconsistent annotations, hinder metadata sharing, and delay submission to public...
Characterization of Human Ectocentromeric Sites.
Centromeres are composed of DNA repeats within chromosomes primary constriction. CENP-B is the only centromeric protein known to bind a specific motif, the CENP-B box, promoting kinetochore stability. We recently uncovered degenerate CENP-B binding motifs outside centromeres, whose position and orientation defines chromosome specific banding patterns.
Epigenetic Profiling of Human Insulinomas Reveals AP-1 Family as Critical Regulators of Beta Cell Maturation
Insulinomas are rare and benign human pancreatic adenomas that overproduce insulin and display increased beta cell mass. We and others have shown that transcriptomic and genomic profiling on insulinomas provides a data mine for identifying targets that can be manipulated to induce human beta cell regeneration. Majority of causative genetic variants in insulinomas involve epigenetic regulatory genes.