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Single-cell analysis of accessible chromatin using scATAC-seq and transcriptome analysis using RNA-seq in human mammary epithelial cells

ABSTRACT: Single-cell analysis of accessible chromatin using scATAC-seq and transcriptome analysis using RNA-seq in human mammary epithelial cells

PROVIDER: PRJNA678964 | ENA |

REPOSITORIES: ENA

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Single-cell analysis of accessible chromatin in human mammary epithelial cells using scATAC-seq [scATAC-seq]

Project description:Single-cell analysis of accessible chromatin in human mammary epithelial cells using scATAC-seq [scATAC-seq]

| PRJNA558803 | ENA

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

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

Single-cell chromatin accessibility data using scATAC-seq

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

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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

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

HyDrop: droplet-based scATAC-seq and scRNA-seq using dissolvable hydrogel beads

Project description:HyDrop: droplet-based scATAC-seq and scRNA-seq using dissolvable hydrogel beads

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scATAC-seq of mouse Plasmodium-specific CD4+ T cells

Project description:Plasmodium-specific CD4+ T cells from mice infected with Plasmodium chabaudi chabaudi AS parasites were recovered at Days 0, 4, 7, and 32 to undergo processing and to generate scATAC-seq dataset. At Day 7, CXCR5+ and CXCR6+ cells were recovered separately. At Day 32, mice were administered with either saline or artesunate (intermittent artesunate therapy - IAT). scATAC-seq dataset was analysed to investigate epigenomic landscapes of CD4+ T cells from effector to memory states.

2020-10-14 | E-MTAB-9402 | biostudies-arrayexpress

Single-cell chromatin accessibility data from K562 cells using scATAC-seq

Project description:Profiles of single cell epigenomes, assayed using scATAC-seq, in K562 cells.

2017-05-23 | GSE99172 | GEO

scATAC-seq of early brain organoid development from pluripotency

Project description:To study developmental trajectories in brain organoids, we conducted scRNA-seq and scATAC-seq in parallel on a dense timecourse of early development.

2022-08-18 | E-MTAB-11998 | biostudies-arrayexpress

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