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Temporal chromatin accessibility changes define transcriptional states essential for osteosarcoma metastasis [scATAC-Seq]

ABSTRACT: Temporal profiling of chromatin accessibility during metastasis revealed dynamic changes in chromatin accessibility during osteosarcoma lung colonization. We sought to determine whether these changes were due to epigenomic reprogramming, or shifts in subclonal frequency. To do this we performed scATAC-seq on MG63.3-GFP cells grown in vitro.

ORGANISM(S): Homo sapiens

PROVIDER: GSE215758 | GEO | 2023/09/18

REPOSITORIES: GEO

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Single-cell chromatin accessibility data using scATAC-seq

Project description:Cell-to-cell variation is a universal feature of life that impacts a wide range of biological phenomena, from developmental plasticity to tumor heterogeneity. While recent advances have improved our ability to document cellular phenotypic variation the fundamental mechanisms that generate variability from identical DNA sequences remain elusive. Here we reveal the landscape and principles of cellular DNA regulatory variation by developing a robust method for mapping the accessible genome of individual cells via assay of transposase accessible chromatin sequencing (ATAC-seq). Single-cell ATAC-seq (scATAC-seq) maps from hundreds of single-cells in aggregate closely resemble accessibility profiles from tens of millions of cells and provides insights into cell-to-cell variation. Accessibility variance is systematically associated with specific trans-factors and cis-elements, and we discover combinations of trans-factors associated with either induction or suppression of cell-to-cell variability. We further identify sets of trans-factors associated with cell-type specific accessibility variance across 6 cell types. Targeted perturbations of cell cycle or transcription factor signaling evoke stimulus-specific changes in this observed variability. The pattern of accessibility variation in cis across the genome recapitulates chromosome topological domains de novo, linking single-cell accessibility variation to three-dimensional genome organization. All together, single-cell analysis of DNA accessibility provides new insight into cellular variation of the “regulome.” Profiles of single cell epigenomes, assayed using scATAC-seq, across 8 cell types and 4 targeted cell manipulations. The complete data set contains a total of 1,632 assayed wells.

2015-06-17 | E-GEOD-65360 | biostudies-arrayexpress

Single-cell chromatin accessibility data using scATAC-seq

Project description:Single-cell chromatin accessibility data using scATAC-seq

| PRJNA274006 | ENA

Designing a single cell ATAC-Seq (scATAC-Seq) dataset to benchmark scATAC-Seq analysis methods

Project description:Single cell sequencing technology has been widely used for understanding the heterogeneity of complex tissue and for identifying novel cell types or cell states. Previous efforts of single cell profiling are mostly performed by measuring transcriptomes using single cell RNA sequencing (scRNA-seq). scRNA-seq is relatively well developed and around 500 analysis tools are currently available for performing different tasks. In the past five years, assays for profiling the single cell chromatin accessibility landscape have emerged and provide extra information about gene regulation at the epigenetic level. Due to its simplicity and sensitivity, single cell Assays for Transposase-Accessible Chromatin using sequencing (scATAC-seq) is widely used to obtain chromatin accessibility. This data will be used to comprehensively evaluate scATAC-seq data analysis tools and gaps in analysis workflows together with publicly available bulk ATAC-Seq and scATAC-seq data using optimised universal evaluation metrics.

2024-01-10 | GSE223319 | GEO

Designing a single cell ATAC-Seq (scATAC-Seq) dataset to validate long read RNA-Seq isoforms and benchmark scATAC-Seq analysis methods

2019-12-19 | GSE142285 | GEO

Subtype Heterogeneity and Epigenetic Convergence in Neuroendocrine Prostate Cancer [scATAC-seq]

Project description:We analyzed chromatin accessibility, scATAC-seq and RNA-seq across neuroendocrine carcinomas from distinct anatomic origins including Merkel cell carcinomas, neuroendocrine prostate cancer, small cell lung cancer and gastrointestinal NECs.

2024-03-27 | GSE262623 | GEO

Designing a single cell ATAC-Seq (scATAC-Seq) dataset to validate long read RNA-Seq isoforms and benchmark scATAC-Seq analysis methods II

2023-09-14 | GSE224045 | GEO

d0c374dd-52ba-473d-a7db-7fd4d6343f40 - samples

Project description:Human data for chromatin accessibility (scATAC-Seq) in CD34+ B cell precursors.

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Multi-modal single-cell sequencing of differentiating mESCs using Smart-seq3 and scATAC-seq

Project description:We report dynamics of X-chromosome upregulation (XCU) along X-chromosome inactivation (XCI) in mESCs as they differentiate into EpiSCs. F1 hybrid C57BL6/J × CAST/EiJ male and female mESCs were grown in serum/LIF conditions were differentiated using Fgf2 and Activin A for 1, 2, 4 and 7 days to induce random XCI in female cells. Multi-modal single-cell sequencing was performed using scATAC on nuclei and Smart-seq3 to assay chromatin accessibility and poly-A+ RNA expression, respectively. Allelic resolution is achieved using strain-specific SNPs in the data. We reveal dynamic balancing of X alleles as cells undergo XCI to compensate dosage imbalances between sexes as well as between X and autosomes. Furthermore, we reveal that female naïve mESCs with two active X chromosomes lack XCU on both alleles which has major implications for reprogramming studies. Finally, we estimate allelic transcriptional burst kinetics from the data and find that progressively increased burst frequencies underlies the XCU process.

2022-02-14 | E-MTAB-10714 | biostudies-arrayexpress

Chromatin accessibility profile at the single cell level of splenic LCMV-specific B cells in acute versus chronic LCMV infection [scATAC-seq]

Project description:Chronic viral infection disrupts memory B cell development. We used single cell ATAC sequencing (scATAC-seq) to analyze chromatin accessibility in antigen-specific B cells responding to acute versus chronic LCMV infection.

2024-02-17 | GSE225932 | GEO

Single-cell epigenomics and high-density genetic variation resolve the architecture of the Treg regulatory network [scATAC-seq]

Project description:To systematically examine the transcription factors and cis-regulatory elements that shape diverse Treg regulatory programs, we used single-cell Assay for Transposase-Accessible Chromatin with high-throughput sequencing (scATAC-seq) to generate chromatin accessibility profiles of mouse regulatory and conventional T cells from different organs and genetic backgrounds.

2023-02-01 | GSE216910 | GEO

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