Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

CleanBar: a versatile demultiplexing tool for split-and-pool barcoding in single-cell omics

ABSTRACT:

SUBMITTER:

PROVIDER: S-EPMC12376035 | biostudies-literature | 2025 Jan

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Microbial single-cell RNA sequencing by split-pool barcoding.

Project description: Not available

| S-EPMC8269303 | biostudies-literature

Microbial single-cell RNA sequencing by split-pool barcoding

Project description:We introduce microSPLiT, a low cost and high-throughput single-cell RNA-sequencing method for gram-negative and gram-positive bacteria. We applied microSPLiT to >25,000 Bacillus subtilis cells sampled at different growth stages, creating a detailed atlas of changes in metabolism and lifestyle. We not only retrieve detailed gene expression profiles associated with known, but rare, states such as competence and PBSX prophage induction, but also identify novel and unexpected gene expression states including a heterogeneous activation of a niche metabolic pathway (myo-inositol catabolism) in a subpopulation of cells.

2020-07-03 | GSE151940 | GEO

Single-cell profiling of the developing mouse brain and spinal cord with split-pool barcoding.

Project description: Not available

| S-EPMC7643870 | biostudies-literature

Microbial single-cell RNA sequencing by split-pool barcoding

Project description:Microbial single-cell RNA sequencing by split-pool barcoding

| PRJNA637771 | ENA

A fast, scalable and versatile tool for analysis of single-cell omics data.

Project description: Not available

| S-EPMC10864184 | biostudies-literature

Split-pool combinatorial barcoding sequencing of murine immune cells

Project description:Single-cell RNA sequencing experiments commonly use 10x Genomics kits due to their high-throughput capacity and standardized protocols. Recently, Parse Biosciences introduced an alternative technology that uses multiple in-situ barcoding rounds within standard 96-well plates. The Parse technology allows the analysis of more cells from multiple samples in a single run without using additional reagents or specialized microfluidics equipment. To assess the efficacy of both platforms, we carried out a benchmark study using biological and technical replicates of young murine thymus as a complex immune tissue. To optimally utilize the capacity of Parse high-throughput kits, we also performed sequencing of murine splenocytes from a chronic stress model and control animals.

2024-10-23 | GSE253406 | GEO

Single cell profiling of the developing mouse brain and spinal cord with split-pool barcoding

Project description:To facilitate scalable profiling of single cells, we developed Split Pool Ligation-based Transcriptome sequencing (SPLiT-seq), a single-cell RNA-seq (scRNA-seq) method that labels the cellular origin of RNA through combinatorial barcoding. SPLiT-seq is compatible with fixed cells or nuclei, allows efficient sample multiplexing and requires no customized equipment. We used SPLiT-seq to analyze 156,049 single-nucleus transcriptomes from postnatal day 2 and 11 mouse brains and spinal cords. Over 100 cell types were identified, with gene expression patterns corresponding to cellular function, regional specificity, and stage of differentiation. Pseudotime analysis revealed transcriptional programs driving four developmental lineages, providing a snapshot of early postnatal development in the murine central nervous system. SPLiT-seq provides a path towards comprehensive single-cell transcriptomic analysis of other similarly complex multicellular systems.

2018-02-21 | GSE110823 | GEO

SNACS: a tool for demultiplexing single-cell DNA sequencing data.

Project description: Not available

| S-EPMC12208073 | biostudies-literature

Spatial-Live: A lightweight and versatile tool for single cell spatial-omics data visualization.

Project description: Not available

| S-EPMC10592799 | biostudies-literature

Split Pool Ligation-based Single-cell Transcriptome sequencing (SPLiT-seq) data processing pipeline comparison.

Project description: Not available

| S-EPMC11010347 | biostudies-literature