Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Simultaneous profiling of transcriptome and chromatin accessibility in single nucleus

ABSTRACT: Simultaneous profiling of transcriptome and chromatin accessibility in single nucleus

PROVIDER: PRJNA520914 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR8528320_1.fastq.gz	Fastqsanger.gz
	SRR8528320_2.fastq.gz	Fastqsanger.gz
	SRR8528321.fastq.gz	Fastqsanger.gz
	SRR8528322_1.fastq.gz	Fastqsanger.gz
	SRR8528322_2.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 66

Similar Datasets

Simultaneous profiling of transcriptome and chromatin accessibility in single nucleus

Project description:Here we describe SNARE-seq, a droplet-based method to simultaneously profile gene expression and chromatin accessibility in each of thousands of single nuclei. Employing this method, we profiled 1047 nuclei from human cell line mixture, 5081 and 10309 nuclei from neonatal and adult mouse brain.

2019-02-05 | GSE126074 | GEO

Single-nucleus chromatin accessibility and transcriptomic characterization of Alzheimer’s Disease

Project description:Single-nucleus chromatin accessibility and transcriptomic characterization of Alzheimer’s Disease

| PRJNA729525 | ENA

Pooled CRISPR screens with joint single-nucleus chromatin accessibility and transcriptome profiling

Project description:A high-throughput CRISPR screening platform with joint single nucleus chromatin accessibility, transcriptome, and guide RNA capture (MultiPerturb-seq) using combinatorial indexing combined with droplet microfluidics to scale throughput and integrate all three modalities. We apply MultiPerturb-seq to identify key genes whose loss can trigger differentiation in a rare pediatric cancer, atypical teratoid/rhabdoid tumor (AT/RT), driven by loss of the SWI/SNF chromatin remodeling subunit SMARCB1.

2024-09-22 | GSE277747 | GEO

Flexible and high-throughput simultaneous profiling of gene expression and chromatin accessibility in single cells

Project description:Gene expression and chromatin accessibility are highly interconnected processes. Disentangling one without the other provides an incomplete picture of gene regulation. However, simultaneous measurements of RNA and accessible chromatin are technically challenging, especially when studying complex organs with rare cell-types. Here, we present easySHARE-seq, an elaboration of SHARE-seq, providing simultaneous measurements of ATAC- and RNA-seq within single cells, enabling identification of cell-type specific cis-regulatory elements (CREs). easySHARE-seq retains high scalability, improves RNA-seq data quality while also allowing for flexible study design. Using 19,664 joint profiles from murine liver nuclei, we linked CREs to their target genes and uncovered complex regulation of key genes such as Gata4. We further identify de-novo genes and cis-regulatory elements displaying zonation in Liver sinusoidal epithelial cells (LSECs), a challenging cell type with low mRNA levels, demonstrating the power of multimodal measurements. EasySHARE-seq therefore provides a flexible platform for investigating gene regulation across cell types and scale.

2024-02-28 | GSE256434 | GEO

Simultaneous profiling of gene expression and chromatin accessibility in single cells.

Project description:Profiling multiple omic layers in a single cell enables the discovery and analysis of biological phenomena that are not apparent from analysis of mono-omic data. While methods for multi-omic profiling have been reported, their adoption has been limited due to high cost and complex workflows. Here, we present a simple method for joint profiling of gene expression and chromatin accessibility in tens to hundreds of single cells. We assess the quality of resulting single cell ATAC- and RNA-seq data across three cell types, examine the link between accessibility and expression at the CD3G and FTH1 loci in human primary T cells and monocytes, and compare the accuracy of clustering solutions for mono-omic and combined data. The new method allows biological laboratories to perform simultaneous profiling of gene expression and chromatin accessibility using standard reagents and instrumentation. This technique, in conjunction with other advances in multi-omic profiling, will enable highly-resolved cell state classification and more specific mechanistic hypothesis generation than is possible with mono-omic analysis.

| S-EPMC6919553 | biostudies-literature

Pooled CRISPR screens with joint single-nucleus chromatin accessibility and transcriptome profiling [CUT&RUN]

2024-10-13 | GSE278910 | GEO

NEAT-seq: Simultaneous profiling of intra-nuclear proteins, chromatin accessibility, and gene expression in single cells

Project description:Oligo-conjugated antibodies have allowed for joint measurement of surface protein abundance and the transcriptome in single cells using high-throughput sequencing. Extending these measurements to gene regulatory proteins in the nucleus would provide a powerful means to link changes in abundance of trans-acting TFs to changes in activity of cis-acting elements and expression of genes regulated by these factors and elements. Here, we introduce Nuclear protein Epitope, chromatin Accessibility, and Transcriptome sequencing (NEAT-seq), a technique to simultaneously measure nuclear protein abundance, chromatin accessibility, and the transcriptome in single cells. We apply this technique to profile CD4 memory T cells using a panel of master transcription factors (TFs) that drive distinct helper T cell subsets and regulatory T cells (Tregs) and identify examples of TFs with regulatory activity gated by three distinct mechanisms: transcription, translation, and regulation of chromatin binding. We further identify regulatory elements and target genes associated with each TF, which we use to link a non-coding GWAS SNP within a GATA motif to both strong allele-specific chromatin accessibility in cells expressing high levels of GATA, and a putative target gene.

2022-02-27 | GSE178707 | GEO

Scalable pooled CRISPR screens with single cell chromatin accessibility profiling.

Project description:A scalable, cost-effective method that combines CRISPR perturbations with a single-cell indexing assay for transposase-accessible chromatin (CRISPR-sciATAC). This method links genome-wide chromatin accessibility to genetic perturbations through simultaneous capture of ATAC-seq fragments and CRISPR guide RNAs from single cells using a 96-well plate combinatorial indexing approach.

2020-11-07 | GSE161002 | GEO

Mapping genetic effects on cell type-specific chromatin accessibility using single nucleus ATAC-seq

Project description:Gene regulation is highly cell type-specific and understanding the function of non-coding genetic variants associated with complex traits requires molecular phenotyping at cell type resolution. In this study we performed single nucleus ATAC-seq (snATAC-seq) and genotyping in peripheral blood mononuclear cells from 13 individuals. We mapped chromatin accessibility QTLs (caQTLs) in each immune cell type and sub-type in a subset of 10 samples of European genetic ancestry.

| EGAS00001006184 | EGA

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

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

| PRJNA698982 | ENA