Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Well-paired-seq: a Size-exclusion and Locally Quasi-static Hydrodynamic Microwell Chip for Single-cell RNA-seq

ABSTRACT: Well-paired-seq: a Size-exclusion and Locally Quasi-static Hydrodynamic Microwell Chip for Single-cell RNA-seq

PROVIDER: PRJNA792809 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR17349300_1.fastq.gz	Fastqsanger.gz
	SRR17349300_2.fastq.gz	Fastqsanger.gz
	SRR17349301_1.fastq.gz	Fastqsanger.gz
	SRR17349301_2.fastq.gz	Fastqsanger.gz
	SRR17349302_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 50

Similar Datasets

Well-paired-seq: a Size-exclusion and Locally Quasi-static Hydrodynamic Microwell Chip for Single-cell RNA-seq

Project description:High throughput single-cell RNA sequencing (scRNA-seq) is a powerful technology for revealing new cell types and cellular states. However, the existing droplet or well-based methods are primarily based on the stochastic pairing of single cells and barcoded beads, resulting in a large number of empty microreactors and a low cell/bead utilization efficiency. Here, we present Well-paired-seq, consisting of thousands of size-exclusion and quasi-static hydrodynamic dual wells to address these limitations. The size-exclusion based dual-well structure allowed one cell and one bead to be trapped in the bottom well (cell-capture-well) and the top well (bead-capture-well), respectively, while the quasi-static hydrodynamic principle ensured that the trapped cells were unable to escape from cell-capture-wells, achieving cumulative capture of cells and buffer exchange in the Well-paired-seq chip. By the integration of quasi-static hydrodynamic and size-exclusion principles, the structure of the dual-well ensures one cell and one bead pairing with high density, acheiving high efficiency of cell/bead pairings (~80%) and low cell doublets. The high utilization of microreactors and single cells/beads enable us to achieve an ultra-high throughput (~105 cells ) with low collision rates (6.2%). We demonstrate the technical performance of Well-paired-seq by collecting transcriptome data from around 200,000 cells across 21 samples including various cell lines, peripheral blood mononuclear cells, and drug-treated cells, successfully revealing the heterogeneity of single cells and showing the wide applicability of Well-paired-seq for basic or clinical biomedical research.

2022-01-04 | GSE192708 | GEO

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

NRAS hydrodynamic tail vein injection

Project description:NRAS hydrodynamic tail vein injection

| PRJNA892576 | ENA

Mapping Mouse Cell Atlas by Microwell-seq

Project description:Mapping Mouse Cell Atlas by Microwell-seq

| PRJNA422441 | ENA

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

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 | GSE225132 | GEO

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

2024-01-03 | GSE225133 | GEO

Transcriptomic quasi-aposymbiotic Blattella germanica

Project description:Transcriptomic analysis of fat body from quasi-aposymbiotic Blattella germanica

| PRJEB67739 | ENA

An automatec microwell platform for large-scale single cell RNA-seq.

Project description:We report an automated microwell array platform for single cell RNA-seq with significantly improved performance over previous implementations. We demonstrate cell capture efficiencies of >50%, compatibility with commercially available barcoded mRNA capture beads, and parallel expression profiling from thousands of individual cells. We apply our system to comprehensively assess heterogeneity in gene expression of patient-derived glioma neurospheres and uncover subpopulations similar to those observed in human glioma tissue.

2016-08-13 | GSE85575 | GEO

RNA-seq of plko-scramble or shBicd2 plasmid hydrodynamic-injected mice livers under ConA-induced acute autoimmune hepatitis

Project description:To explore the effect of Bicd2 in ConA-induced acute autoimmune hepatitis, we conducted RNA transcriptome profiling of plko-scramble or shBicd2 plasmid hydrodynamic-injected mice livers in response to ConA injection.

2023-10-31 | GSE245352 | 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