Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Spatial reconstruction of immune niches by combining photoactivatable reporter and single-cell RNA-seq

ABSTRACT: Spatial reconstruction of immune niches by combining photoactivatable reporter and single-cell RNA-seq

PROVIDER: PRJNA408125 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Spatial reconstruction of immune niches by combining photoactivatable reporter and single-cell RNA-seq

Project description:Cellular function is strongly dependent on surrounding cells and environmental factors. Current technologies are limited in characterizing the spatial location and unique gene-programs of cells in less structured and dynamic niches. Here we developed a method (NICHE-seq) that combines photoactivatable fluorescent reporters, two-photon microscopy and single-cell RNA-seq to infer the cellular and molecular composition of niches. We applied NICHE-seq to examine the high-order assembly of immune cell networks. NICHE-seq is highly reproducible in spatial tissue reconstruction, enabling identification of rare niche-specific immune subpopulations and unique gene-programs, including natural killer cells within infected B cell follicles and distinct myeloid states in the marginal zone. This study establishes NICHE-seq as a broadly applicable method for elucidating high-order spatial organization of cell types and their molecular pathways.

2017-12-22 | GSE104054 | GEO

Spatial reconstruction of immune niches by combining photoactivatable reporters and scRNA-seq.

Project description: Not available

| S-EPMC7234837 | biostudies-literature

Compound interaction screen on a photoactivatable cellulose membrane (CISCM) identifies drug targets

Project description:Here, we present a compound interaction screen on a photoactivatable cellulose membrane (CISCM) that enables target identification of several drugs in parallel. To this end, we use diazirine-based undirected photoaffinity labeling (PAL) to immobilize compounds on cellulose membranes. Functionalized membranes are then incubated with protein extract and specific targets are identified via quantitative affinity purification and mass spectrometry. CISCM reliably identifies known targets of natural products in less than three hours of analysis time per compound. In summary, we show that combining undirected photoimmobilization of compounds on cellulose with quantitative interaction proteomics provides an efficient means to identify the targets of natural products.

2022-10-25 | PXD033050 | Pride

Photoactivatable senolysis with single-cell resolution reverses aging

Project description:Photoactivatable senolysis with single-cell resolution reverses aging

| PRJNA774276 | ENA

Metabolic labeling of NMT substrates by photoactivatable/clickable myristate probes X3/X8/X10

Project description:Efficiency of labelling by photoactivatable/clickable myristate probes X3/X8/X10 is compared to the positive control probe YnMyr. Additionally, negative controls for each probe were obtained by treatment with NMT ihibitor IMP-366 (DDD85464). The resulting data indicates efficient labeling of NMT substrates by photoactivatable probes that is NMT-dependent.

2023-03-11 | PXD027239 | Pride

Plant niches

Project description:Plant niches rather than soil type or species dominate microbiota structure

| PRJEB27086 | ENA

Dianthus ancestral sequence reconstruction

Project description:Ancestral sequence reconstruction in Dianthus

| PRJEB54098 | ENA

Disseminated melanoma cells transdifferentiate into endothelial cells in intravascular niches at metastatic sites (Li et al. 2020, Cell Reports)

Project description:Here, we combined lineage tracing in a newly developed spontaneous metastatic mouse model of melanoma, advanced imaging and single-cell RNA-sequencing approaches to search for (patho) physiologically-relevant melanoma cellular states. We identified a population of reporter-positive melanoma cells located in intravascular niches of various metastatic organs. These intravascular metastatic cells were dormant, negative for characteristic melanoma markers and acquired endothelial cell markers.

2020-04-15 | GSE148666 | GEO

GNPS Mono-Colonized GF Reporter Mice

Project description:Mono-colonized GF reporter mice fecal metabolomics by LC-MS/MS

2021-08-31 | MSV000088040 | GNPS

Three Distinct Cell Types Express Extracellular Matrix Proteins In Different Niches During Skeletal Muscle Fibrosis

Project description:Tissue extracellular matrix provides structural support and creates unique niches for resident cells . However, the identities of cells responsible for creating specific ECM niches have not been determined. In striated muscle, the identity of these cells becomes important in disease when ECM changes result in fibrosis and subsequent increased tissue stiffness and dysfunction. Here we describe a novel approach to isolate and identify cells that maintain ECM niches in both healthy and fibrotic muscle. Using a collagen I reporter mouse, we show that there are three distinct cell populations that express collagen I in both healthy and fibrotic skeletal muscle. Interestingly, the number of collagen I expressing cells in all three cell populations increase proportionally in fibrotic muscle indicating that all cell types participate in the fibrosis process. Furthermore, it is shown that the ECM gene expression profile is not qualitatively altered in fibrotic muscle. This suggests that muscle fibrosis in this model results from an increased number of collagen I expressing cells and not the initiation of a specific fibrotic gene expression program. Finally, in fibrotic muscle, we show that these collagen I expressing cell populations differentially express distinct ECM proteins – fibroblasts express the fibrillar components of ECM, fibro/adipogenic progenitors cells differentially express basal laminar proteins and skeletal muscle progenitor cells differentially express genes important for the satellite cell niche.

2016-12-04 | GSE89633 | 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