Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: Nuclei multiplexing with barcoded antibodies for single-nucleus genomics

PROVIDER: PRJNA526262 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR8703773_1.fastq.gz	Fastqsanger.gz
	SRR8703773_2.fastq.gz	Fastqsanger.gz
	SRR8703774_1.fastq.gz	Fastqsanger.gz
	SRR8703774_2.fastq.gz	Fastqsanger.gz
	SRR9132175_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 10

Similar Datasets

Low-input Nucleus Isolation and Multiplexing with Barcoded Antibodies of Mouse Sympathetic Ganglia for Single-nucleus RNA Sequencing

Project description:Low-input Nucleus Isolation and Multiplexing with Barcoded Antibodies of Mouse Sympathetic Ganglia for Single-nucleus RNA Sequencing

| PRJNA971549 | ENA

Single nucleus ATAC-seq datasets for "Temporally Specific Gene Expression and Chromatin Remodeling Programs Regulate a Conserved Pdyn Enhancer"

Project description:This dataset contains single nucleus Assay for Transposase-Accessible Chromatin (ATAC) sequencing results from rat nucleus accumbens tissue. Rats received repeated cocaine injections (20mg/kg, intraperitoneal injection), or saline injections as a control. Single-nucleus ATAC-seq was carried out with FACS-sorted nuclei using the 10X Genomics Chromium single cell sequencing platform using the Chromium Next GEM Single Cell ATAC Kit v2.

2023-08-07 | GSE233754 | GEO

Progressively overloaded single-cell RNA-seq with cell hashing

Project description:Barcode-based multiplexing methods can be used to increase throughput and reduce batch effects in large single-cell genomics studies. To evaluate methods for demultiplexing barcode-multiplexed data, we generated a dataset by labeling samples separately with barcode-tagged antibodies, mixing those samples, and progressively overloading a droplet-based scRNA-seq system.

2021-12-01 | GSE181862 | GEO

An optimized approach for multiplexing single-cell ATAC-seq using oligonucleotide conjugated antibodies

Project description:An optimized approach for multiplexing single-cell ATAC-seq using oligonucleotide conjugated antibodies

2023-04-28 | GSE227522 | GEO

The Tabulae Paralytica: Multimodal single-cell and spatial atlases of spinal cord injury

Project description:This submission is a dataset of two modalities, single-nucleus transcriptomics and single-nuclei spatial transcriptomics in the spinal cords of mice. The single-nuclei transcriptomics data is harvested and profiled using 10x Genomics Chromium Single Cell Kit Version. The single-nuclei spatial transcriptomics data is harvested and profiled using Visium Spatial Gene Expression.

2024-01-30 | GSE234774 | GEO

Single-cell RNA-sequencing analysis for the molecular taxonomy of primate amygdala

Project description:We thus isolated amygdala from rhesus macaques and performed single-cell RNA-sequencing analysis. The scRNA-Seq libraries were generated using the 10X Genomics Chromium Controller Instrument and Chromium Single Cell 3’ V2 Reagent Kits (10X Genomics, Pleasanton, USA). Briefly, cells nuclei were concentrated to 1000 nuclei/μL and approximately 15000 nuclei were loaded into each channel to generate single-cell Gel Bead-In-Emulsions (GEMs), which results into expected mRNA barcoding of 9000 single nucleus for each sample.

2020-11-19 | GSE145765 | GEO

CASB: A concanavalin A-based sample barcoding strategy for single-cell sequencing [snATAC-seq]

Project description:We reported a Concanavalin A-based Barcoding Strategy (CASB) for single-cell and single-nucleus sample multiplexing, which could be followed by different single-cell sequencing techniques. The method involves minimal sample processing, thereby preserving intact transcriptomic or epigenomic patterns. Besides sample multiplexing, the CASB could further improve data quality through doublet identification.

2021-03-09 | GSE165048 | GEO

CASB: A concanavalin A-based sample barcoding strategy for single-cell sequencing [snATAC]

2021-03-09 | GSE153115 | GEO

Metastable Intermediates Identified in Epithelial to Mesenchymal Transition are Regulated by G-quadruplex DNA Structures

Project description:Cancer is a heterogenous disease, with multiple cellular subpopulations present within a single tumour mass that differ genetically and morphologically, and thus respond differently to chemotherapeutics. Epithelial-to-Mesenchymal transition (EMT) has been shown to play a role in tumour heterogeneity. Single-cell sequencing is critical to identify cell-type-specific transcriptomic differences with multiplexing methods increasing experimental scope with reduced cost. Cell hashing with barcoded antibodies is commonly used to multiplex samples but is limited to samples expressing target antigens. Antigen-independent methods of barcoding cells, such as barcoded lipid-anchors, have gained traction but present substantial populations that cannot be unambiguously demultiplexed. Herein we report a multiplexed single-cell transfection-enabled cell hashing sequencing (scTECH-seq) platform, which uses antigen-independent endocytic uptake to barcode cells, resulting in efficient, uniform barcoding with high cell recovery. We apply this methodology to identify distinct metastable cell states in human mammary cells undergoing EMT and show that stabilisation of G-quadruplex DNA has the potential to inhibit EMT.

2024-07-01 | GSE225155 | GEO

Comparison of different hashing methods on human PBMCs and primary mice tissues

Project description:the aim 1 was to evaluate hashing (sample multiplexing) accuracy of TotalSeq-B antibodies and CellPlex (a multiplexing solution from 10x Genomics) on 2 pools of PBMCs from 3 different donors. Thus the genetic difference between donors was used as a ground truth for sample demultiplexing based on antibody or lipid hashing hashing. the aim 2 was to evaluate TotalSeq antibody and lipid hashing on different mice primary tissues using different hashing protocols.

2022-02-12 | E-MTAB-11401 | biostudies-arrayexpress

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