Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Fast and flexible profiling of chromatin accessibility and total RNA expression in single nucleus using Microwell-seq3 [MW3_WT]

ABSTRACT: Fast and flexible profiling of chromatin accessibility and total RNA expression in single nucleus using Microwell-seq3 [MW3_WT]

PROVIDER: PRJNA934473 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR23435000_1.fastq.gz	Fastqsanger.gz
	SRR23435000_2.fastq.gz	Fastqsanger.gz
	SRR23435001_1.fastq.gz	Fastqsanger.gz
	SRR23435001_2.fastq.gz	Fastqsanger.gz
	SRR23435002_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 164

Similar Datasets

Fast and flexible profiling of chromatin accessibility and total RNA expression in single nucleus using Microwell-seq3 [MW3_WT]

Project description:Chromatin accessibility and transcriptome profiling are the most critical tools in single-cell technologies. Here, we present Microwell-seq3, a high-throughput and easy-to-handle platform for high-sensitive single-nucleus chromatin accessibility or full-length gene expression profiling. The method combined pre-indexing and a dual-pass “chip-in-tube” strategy for nuclei loading and DNA amplification. Therefore, Microwell-seq3 does not require specialized equipment and is suitable for any molecular biology lab with simple consumables and thermal cycler. We applied Microwell-seq3 to profile the chromatin accessibility in more than 200,000 single nuclei and the full-length transcriptome in about 50,000 nuclei from multiple adult mouse tissues. Joint analysis of cell-type specific regulatory elements and total RNA uncovered cell type heterogeneity and differentially expressed genes in brain compared with previous polyadenylated transcripts capturing methods. Gene regulatory networks based on full-length transcriptome and chromatin accessibility provided improved cell-cell communications in neurons and glia. Finally, we applied Microwell-seq3 to comprehensively characterize malignant cells in spontaneous tumors from aging mouse.

2024-01-03 | GSE225133 | GEO

Fast and flexible profiling of chromatin accessibility and total RNA expression in single nucleus using Microwell-seq3 [MW3_Tumor]

2024-01-03 | GSE225132 | GEO

Fast and flexible profiling of chromatin accessibility and total RNA expression in single nucleus using Microwell-seq3

Project description:Fast and flexible profiling of chromatin accessibility and total RNA expression in single nucleus using Microwell-seq3

| PRJNA934073 | ENA

Fast and flexible profiling of chromatin accessibility and total RNA expression in single nucleus using Microwell-seq3 [MW3_Tumor]

Project description:Fast and flexible profiling of chromatin accessibility and total RNA expression in single nucleus using Microwell-seq3 [MW3_Tumor]

| PRJNA934469 | ENA

Fast and flexible profiling of chromatin accessibility and total RNA expression in single nuclei using Microwell-seq3.

Project description:Single cell chromatin accessibility profiling and transcriptome sequencing are the most widely used technologies for single-cell genomics. Here, we present Microwell-seq3, a high-throughput and facile platform for high-sensitivity single-nucleus chromatin accessibility or full-length transcriptome profiling. The method combines a preindexing strategy and a penetrable chip-in-a-tube for single nucleus loading and DNA amplification and therefore does not require specialized equipment. We used Microwell-seq3 to profile chromatin accessibility in more than 200,000 single nuclei and the full-length transcriptome in ~50,000 nuclei from multiple adult mouse tissues. Compared with the existing polyadenylated transcript capture methods, integrative analysis of cell type-specific regulatory elements and total RNA expression uncovered comprehensive cell type heterogeneity in the brain. Gene regulatory networks based on chromatin accessibility profiling provided an improved cell type communication model. Finally, we demonstrated that Microwell-seq3 can identify malignant cells and their specific regulons in spontaneous lung tumors of aged mice. We envision a broad application of Microwell-seq3 in many areas of research.

| S-EPMC10966074 | biostudies-literature

Fast and flexible profiling of chromatin accessibility and total RNA expression in single nucleus using Microwell-seq3

Project description:This SuperSeries is composed of the SubSeries listed below.

2024-01-03 | GSE225134 | GEO

Ultraplex: An ultra-fast, flexible, all-in-one fastq demultiplexer

Project description:Ultraplex: An ultra-fast, flexible, all-in-one fastq demultiplexer

| PRJEB44738 | ENA

FLARE: A fast and flexible peak-calling pipeline for identifying RNA editing foci

Project description:FLARE: A fast and flexible peak-calling pipeline for identifying RNA editing foci

| PRJNA889435 | ENA

Mapping Mouse Cell Atlas by Microwell-seq

Project description:We developed Microwell-seq, a high-throughput and low-cost scRNA-seq platform using simple, inexpensive devices. Using Microwell-seq, we constructed a basic scheme for the Mouse Cell Atlas. We reveal single cell hierarchy for many tissues that have not been well previously characterized. Our study demonstrates the wide applicability of the Microwell-seq technology and the Mouse Cell Atlas resource.

2018-02-14 | GSE108097 | GEO

High-throughput Microwell-seq 2.0 reveals massively multiplexed chemical perturbation

Project description:Combining in-cell RT and Microwell-seq 1.0, we established Microwell-seq 2.0 for cost-effective HTS with scRNA-seq-based phenotyping. To assess the fidelity of the Microwell-seq 2.0, we performed a species-mixing experiment with cultured human (293T) and mouse (3T3) cells. Moreover, we assessed the platform on tissue cells with more heterogeneous cell types. By harnessing the power of Microwell-seq 2.0, we analyzed massively multiplexed chemical perturbation of human embryonic stem cells (hESCs) at the single-cell resolution.

2021-11-09 | GSE175413 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data