Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Cell type prioritization in single-cell data

ABSTRACT: Cell type prioritization in single-cell data

PROVIDER: PRJNA596378 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR10729600.fastq.gz	Fastqsanger.gz
	SRR10729601.fastq.gz	Fastqsanger.gz
	SRR10729602.fastq.gz	Fastqsanger.gz
	SRR10729603.fastq.gz	Fastqsanger.gz
	SRR10729604.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 48

Similar Datasets

Cell type prioritization in single-cell data

Project description:We present a machine-learning method to prioritize the cell types most responsive to biological perturbations within high-dimensional single-cell data. We validate our method, Augur (https://github.com/neurorestore/Augur), on a compendium of single-cell RNA-seq, chromatin accessibility, and imaging transcriptomics datasets. We apply Augur to expose the neural circuits that enable walking after paralysis in response to spinal cord neurostimulation.

2020-06-05 | GSE142245 | GEO

Machine learning sequence prioritization for cell type-specific enhancer design

Project description:Machine learning sequence prioritization for cell type-specific enhancer design

| PRJNA720048 | ENA

Cell type prioritization in single-cell data.

Project description:We present Augur, a method to prioritize the cell types most responsive to biological perturbations in single-cell data. Augur employs a machine-learning framework to quantify the separability of perturbed and unperturbed cells within a high-dimensional space. We validate our method on single-cell RNA sequencing, chromatin accessibility and imaging transcriptomics datasets, and show that Augur outperforms existing methods based on differential gene expression. Augur identified the neural circuits restoring locomotion in mice following spinal cord neurostimulation.

| S-EPMC7610525 | biostudies-literature

Expression data from wild-type single muscle fibers

Project description:Expression data from wild-type single muscle fibers

| PRJNA557650 | ENA

Comprehensive integration of single-cell data

Project description:Comprehensive integration of single-cell data

| PRJNA528319 | ENA

Modulation of Influenza A virus NS1 expression reveals prioritization of host response antagonism at single-cell resolution

Project description:Influenza A virus (IAV) is an important human respiratory pathogen that causes significant seasonal epidemics and potential devastating pandemics. As part of its life cycle, IAV encodes the multifunctional protein NS1, that, among many roles, prevents immune detection and limits interferon (IFN) production. As different host immune pathways exert different selective pressures against IAV as replication progresses, we expect a prioritization in the host immune antagonism by NS1. In this work, we profiled bulk transcriptomic differences in a primary bronchial epithelial cell model facing IAV infections at distinct NS1 levels. We further demonstrated that the intracellular NS1 levels in-part shapes the host response heterogeneity at single cell level. We found that modulation of NS1 levels reveal a ranking in its inhibitory roles: modest NS1 expression is sufficient to inhibit immune detection, and thus the expression of pro-inflammatory cytokines (including IFNs), but higher levels are required to inhibit IFN signaling and ISG expression. Lastly, inhibition of chaperones related to the unfolded protein response requires the highest amount of NS1, often associated with later stages of viral replication. This work demystifies some of the multiple functions ascribed to IAV NS1, highlighting the prioritization of NS1 in antagonizing the different pathways involved in the host response to IAV infection.

2023-09-25 | GSE243730 | GEO

Cell type purification by single-cell transcriptome-trained sorting

Project description:Cell type purification by single-cell transcriptome-trained sorting

| PRJNA446034 | ENA

Single-cell ftATACseq data of mouse thymocytes

Project description:Single-cell ftATACseq data of mouse thymocytes

| PRJNA628737 | ENA

Single cell RNAseq data of CD1 microglia

Project description:Single cell RNAseq data of CD1 microglia

| PRJNA494396 | ENA

HuBMAP Single-Cell Data from Human Tissues

Project description:HuBMAP Single-Cell Data from Human Tissues