Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Mapping Mouse Cell Atlas by Microwell-seq

ABSTRACT: 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.

OTHER RELATED OMICS DATASETS IN: PRJNA422441

ORGANISM(S): Mus musculus Homo sapiens

PROVIDER: GSE108097 | GEO | 2018/02/14

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

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

Mapping Mouse Cell Atlas by Microwell-seq

Project description:Mapping Mouse Cell Atlas by Microwell-seq

| PRJNA422441 | 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

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

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

Project description:High-throughput Microwell-seq 2.0 reveals massively multiplexed chemical perturbation

| PRJNA732361 | ENA

SCRB-seq comparison with TruSeq on bulk RNA-seq human LCL (DMSO) and BAY treated LCL (BAY)

Project description:Here, we validate a novel protocol, Bulk RNA Barcoding and sequencing (BRB-seq), that combines the multiplexing-driven cost-effectiveness of a single-cell RNA-seq protocol with the efficiency of a bulk RNA-seq procedure. For this we first gauge the applicability of the SCRB-seq protocol on bulk DMSO and BAY treated human LCL, and compare its effectiveness as compared to TruSeq.

2018-07-07 | E-MTAB-6984 | biostudies-arrayexpress

Comparative Transcriptomic Analysis of Hematopoietic System Across Species by Microwell-Seq

Project description:Comparative Transcriptomic Analysis of Hematopoietic System Across Species by Microwell-Seq

| PRJNA357074 | ENA

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

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

| PRJNA338815 | ENA

Construction the larval and adult zebrafish cell atlas at single cell resolution

Project description:Single-cell mRNA sequencing (scRNA-seq) technologies are reshaping the current cell-type classification system. In previous studies, we built the mouse cell atlas (MCA) and human cell landscape (HCL) to catalog all cell types by collecting scRNA-seq data. However, systematically study for zebrafish (Danio rerio) and fruit fly (Drosophila melanogaster) are still lacking. Here, we construct the zebrafish and Drosophila cell atlas with Microwell-seq protocols, which provides valuable resources for characterization of diverse cell populations of zebrafish and Drosophila, and studying difference between vertebrates and Invertebrates at single cell level.

2022-07-08 | GSE178150 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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