Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Comparative analysis of human brain tissue preprocessing methods for single-nucleus chromatin accessibility profiling

ABSTRACT: Comparative analysis of human brain tissue preprocessing methods for single-nucleus chromatin accessibility profiling

PROVIDER: PRJNA698982 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR13613400.fastq.gz	Fastqsanger.gz
	SRR13613401.fastq.gz	Fastqsanger.gz
	SRR13613402.fastq.gz	Fastqsanger.gz
	SRR13613403.fastq.gz	Fastqsanger.gz
	SRR13613398.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 6

Similar Datasets

Comparative analysis of human brain tissue preprocessing methods for single-nucleus chromatin accessibility profiling

Project description:The ability to analyze chromatin accessibility at the single-nucleus level is a critical step towards capturing the highly complex mechanisms that regulate gene expression in the human brain, and to functionally characterize the genetic architecture of neuropsychiatric traits. The assay for transposase accessible chromatin (ATAC-seq) has rapidly established itself as a robust means of studying epigenome regulation in bulk tissues and, more recently, at the single-cell level. To facilitate optimal preparation of frozen archival human brain tissue samples for single-nuclear ATAC-seq (snATAC-seq), we assessed the impact of different sample preparation approaches on the quality of snATAC-seq libraries. We tested six conditions, including different fluorescent activated nuclear sorting (FANS) strategies, from nuclei isolated from a sample of human cortical tissue. Using an unbiased computational approach, we were able to identify major cell populations in all snATAC-seq libraries, including those not subjected to FANS. When FANS was used, we observed that the choice of DNA stain impacts the quality of ATAC-seq libraries. Staining samples with DAPI can lead to insufficient detection of open chromatin regions, whereas 7aad provides improved identification of some nuclear sub-populations. We also observed that use of fluorescent dyes (in particular, DAPI) can lead to under-sampling of excitatory neurons. Our work provides guidelines on the trade-offs associated with different nuclear isolation strategies when preparing samples for snATAC-seq.

2022-01-29 | GSE166016 | GEO

Single-nucleus chromatin accessibility and gene expression co-profiling by ISSAAC-seq

Project description:Multi-modal profiling of different molecular layers from the same single cell enables more comprehensive characterisations of cellular heterogeneity compared to conventional single-modality approaches. A key example is co-detection of chromatin accessibility and gene expression that offers the opportunity to investigate the cell type-resolved gene regulatory mechanisms. Here, we described a sensitive and robust protocol of in situ SHERRY after ATAC-seq (ISSAAC-seq) for the concurrent measurement of chromatin accessibility and gene expression from the same single nucleus. The method begins with dual Tn5 tagging of open chromatin regions and DNA/RNA hybrid after reverse transcription that take place in bulk nuclei. Then various single-nucleus isolation strategies can be used based on the experimental purpose of the user. The protocol is highly modular with flexible throughputs ranging from several hundreds to tens of thousands of nuclei. The generated data are of high quality in both modalities. The entire workflow can be finished within 1 or 2 days, and the procedures works on multiple different platforms.

2025-06-01 | E-MTAB-15131 | biostudies-arrayexpress

Chromatin accessibility in mouse hypothalamic arcuate nucleus in puberty onset

Project description:To better understand the epigenetic mechanism underlying pubertal onset, the hypothalamic genome-wide chromatin accessibility patterns in mouse arcuate nucleus at early and late pubertal stages were explored. Female mice have been widely used in multiple studies on pubertal development as they present the similar molecular behaviors in HPG axis and stable cycles of menstrual calendar like human. Hypothalamic ARC underwent a huge epigenetic and genetic reprogramming to adapt to the response and feedback on sexual hormones during the stages of early pubertal (2-5-week of age) and late puberty (5-8-week of age) . We harvested 4- and 8-week hypothalamic ARC and employed ATAC-seq on a genome-wide scale. Combined with previous RRBS, RRHP and RNA-seq, the connections between DNA (hydroxyl)methylation in retroelements and gene expression were studied, emphasizing the importance of epigenetic alterations in regulating transcription in puberty onset.

2021-04-02 | E-MTAB-10263 | biostudies-arrayexpress

Single-nucleus chromatin accessibility landscape in mouse preimplantation embryos

Project description:Single-nucleus chromatin accessibility landscape in mouse preimplantation embryos

| PRJNA1187588 | ENA

A comparative atlas of single-cell chromatin accessibility in the human brain

Project description:A comparative atlas of single-cell chromatin accessibility in the human brainRecent advances in single-cell transcriptomics have illuminated the diverse neuronal and glial cell types within the human brain. However, the regulatory programs governing cell identity and function remain unclear. Using a single-nucleus assay for transposase-accessible chromatin using sequencing (ATAC-seq), we explored open chromatin landscapes across 1.1 million cells in 42 brain regions from three adults. Integrating this data unveiled 107 distinct cell types and their specific utilization of 544,735 candidate cis-regulatory DNA elements (cCREs) in the human genome. Nearly a third of the cCREs demonstrated conservation and chromatin accessibility in the mouse brain cells. We reveal strong links between specific brain cell types and neuropsychiatric disorders including schizophrenia, bipolar disorder, Alzheimer’s disease (AD), and major depression, and have developed deep learning models to predict the regulatory roles of noncoding risk variants in these disorders.

2023-10-04 | GSE244618 | GEO

Systematic comparative analysis of single cell RNA-sequencing methods

Project description:A multitude of single-cell RNA sequencing methods have been developed in recent years, with dramatic advances in scale and power, and enabling major discoveries and large scale cell mapping efforts. However, these methods have not been systematically and comprehensively benchmarked. Here, we directly compare seven methods for single cell and/or single nucleus profiling from three types of samples – cell lines, peripheral blood mononuclear cells and brain tissue – generating 36 libraries in six separate experiments in a single center. To analyze these datasets, we developed and applied scumi, a flexible computational pipeline that can be used for any scRNA-seq method. We evaluated the methods for both basic performance and for their ability to recover known biological information in the samples. Our study will help guide experiments with the methods in this study as well as serve as a benchmark for future studies and for computational algorithm development.

2019-06-01 | GSE132044 | GEO