Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Single cell RNA-seq on FACS purfied murine paneth cells

ABSTRACT: The small intestinal crypts harbour secretory Paneth cells (PCs) which express bactericidal peptides that are crucial for maintaining intestinal homeostasis. Considering the diverse environmental conditions throughout the course of the small intestine, multiple subtypes of PCs are expected to exist. We applied single cell RNA-sequencing of PCs combined with deep bulk RNA-sequencing on PC populations of different small intestinal locations and discovered several expression-based PC clusters. Some of these are discrete and resemble tuft cell-like PCs, goblet cell (GC)-like PCs, PCs expressing stem cell markers, and atypical PCs. Other clusters are less discrete but appear to be derived from different locations along the intestinal tract and have environment-dictated functions such as food digestion and antimicrobial peptide production

ORGANISM(S): Mus musculus

PROVIDER: GSE273983 | GEO | 2024/09/18

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

RNA-seq on FACS sorted paneth cells from the murine duodenum, jejunum and ileum

Project description:The small intestinal crypts harbour secretory Paneth cells (PCs), which express bactericidal peptides that are crucial for maintaining intestinal homeostasis. Considering the diverse environmental conditions throughout the course of the small intestine, multiple subtypes of PCs are expected to exist. We applied single cells RNA-sequencing of PCs combined with deep bulk RNA-sequencing on PC populations of different locations (duodenum, jejunum, ileum) and discovered several expression-based clusters. Some of these are discrete and resemble tuft cell-like PCs, goblet cell-like PCs, PCs expressing stem cell markers, and senescent PCs. Other clusters are less discrete, but based on bulk RNA-seq appear to be derived from different locations along the small intestinal tract. Furthermore, a comprehensive spatial analysis was conducted using the Resolve bioscience technique, identifying different PCs clusters along the small intestine, but not along the crypts themselves.

2024-03-07 | GSE255507 | GEO

Single-cell RNA-seq reveals distinct maturation stages of the Paneth cell lineage

Project description:Paneth cells (PCs) are long-lived secretory cells that reside at the bottoms of small intestinal crypts. Besides serving as niche cells for the neighboring Lgr5-positive stem cells, PCs secrete granules containing a broad spectrum of antimicrobial proteins, including lysozymes and defensins1. Here, we have used single-cell RNA sequencing to explore PC differentiation. We found a maturation gradient from early secretory progenitors to mature PCs, capturing the full maturation path of PCs. Moreover, differential expression of a subset of defensin genes in lysozyme-high PCs, e.g. Defa20, reveals at least two distinct stages of maturation.

2016-06-23 | GSE76408 | GEO

Single-cell RNA-seq reveals distinct maturation stages of the Paneth cell lineage

2016-06-23 | E-GEOD-76408 | biostudies-arrayexpress

Chemically Induced Paneth Cells Provide Superior In Vivo Mimic to Organoid-derived Analog

Project description:Paneth cells (PCs) are post-mitotic secretory cells of the small intestine that produce antimicrobials, growth factors, and cytokines. Multiple diseases have been linked to alterations in PC function. Past studies of PCs have relied on in vivo models, and limited in vitro models, including organoids. While useful, whether the in vitro models recapitulate in vivo biology is an important, yet unanswered question. Here, we present a bona fide in vitro PC-enriched population derived via chemically-induced (CI) differentiation of primary murine adult stem cells. We define the identity of PCs in our system and compare to PCs of established organoid systems and those found in vivo. Importantly, we demonstrate stimulant-induced and microbe-responsive antimicrobial function of our CI-PCs – hallmark functions of PCs in vivo. Thus, we define and produce the most physiologically-relevant in vitro PC population to date, providing a superior tool to study cellular development, host-microbe interactions, and inflammatory disease.

2018-04-02 | GSE100274 | GEO

Transcriptome analysis of human colonic IgA+ plasma cell subsets and naïve B cells

Project description:Immunoglobulin A (IgA) is the most abundant antibody in the intestinal tract. Recent studies show that discrete subsets of gut human plasma cells (PCs) release IgA, which contributes to the maintenance of gut homeostasis. To better characterize the properties of these PC subsets, we performed global transcriptome analysis in naïve B cells as well as immature CD19+IgA+CD138- PCs, mature CD19+IgA+CD138+ PCs and late CD19-IgA+CD138+ PCs after their purification from human colon samples.

2020-03-29 | GSE141005 | GEO

Diet-induced changes in tuft cell dynamics couple with type 2 immune response modulation and energy metabolism

Project description:Purpose: To examine the temporal changes in intestinal tuft cell number and activity in response to intake of a high fat diet and investigate the relation to whole-body energy metabolism and the immune phenotype of the small intestine and epididymal white adipose tissue (eWAT). Methods: C57BL/6J mice were fed either a low fat reference diet (RFD, 10 % kcal fat) or a high fat diet (HFD, 60% kcal fat) for 9 or 22 weeks, followed by characterization of whole-body metabolic parameters, transcription profiles of sorted intestinal tuft cells, and immune phenotypes of tissues. Results: HFD feeding was associated with reductions in the overall number of small intestinal epithelial cells and tuft cells and reduced expression of the intestinal type 2 tuft cell markers Il25 and Tslp. Amongst >1,700 diet-regulated genes in tuft cells identified by RNA-seq, we observed an early association between body mass expansion and increased expression of Serpini1, which encodes the serine protease inhibitor neuroserpin. By contrast, tuft cell expression of genes encoding the GABA-receptors linked to reduced body mass gain. Although we observed a HFD-induced change in the eWAT inflammatory profile, the small intestinal lamina propria displayed a consistent non-inflammatory phenotype, and small intestinal tuft cell-derived transcripts were found to correlate with whole body metabolic features independently of intestinal immune cell involvement. Conclusion: Our These findings point to a role for small intestinal tuft cells in systems-wide metabolic regulation.

2019-11-26 | GSE141002 | GEO

Tissue specific gene expression of epithelial tuft cells from small intestine and gallbladder in mouse

Project description:Rare chemosensory epithelial cells called tuft cells have known roles in small intestinal regulation of type 2 cytokine producing Group 2 innate lymphoid cells. To understand the phenotype of tuft cells in another tissue, the extrahepatic biliary tree, we performed RNAseq analysis on tuft cells and non-tuft epithelial cells from small intestine and gallbladder of the mouse.

2022-03-01 | GSE194035 | GEO

Peptide YY: a Paneth cell antimicrobial peptide that maintains Candida gut commensalism.

Project description:The mammalian gut secretes a family of multifunctional peptides that affect appetite, intestinal secretions, and motility, while some regulate the microbiota. We report peptide YY (PYY1-36), but not endocrine PYY3-36, is an antimicrobial peptide (AMP) expressed by gut epithelial Paneth Cells (PC). PC-PYY has limited antibacterial activity, but shows selective activity against virulent hyphal, but not yeast forms, of Candida albicans. 5 PC-PYY is a cationic molecule that interacts with the anionic surfaces of fungal hyphae to cause membrane disruption and transcriptional reprogramming to maintain the yeast phenotype of the fungus. PC-PYY is packaged into secretory granules and is secreted into and retained by surface mucus, which optimizes PC-PYY activity. Hence, PC-PYY acts as a selective antifungal AMP that contributes to the maintenance of gut fungal commensalism.

2024-02-28 | GSE229566 | GEO

The taste receptor TAS1R3 regulates small intestinal tuft cell homeostasis

Project description:Tuft cells are an epithelial cell subset critical for initiating type 2 immune responses to parasites and protozoa in the small intestine. To respond to these stimuli, intestinal tuft cells use taste chemosensory signaling pathways, but the role of taste receptors in type 2 immunity is poorly understood. Here, we show that the taste receptor TAS1R3, which detects sweet and umami in the tongue, also regulates tuft cell responses in the distal small intestine. BALB/c mice, which have an inactive form of TAS1R3, as well as Tas1r3-deficient C57BL6/J mice both have severely impaired responses to tuft cell-inducing signals in the ileum including the protozoa Tritrichomonas muris and succinate. In contrast, TAS1R3 is not required to mount an immune response to the helminth Heligmosomoides polygyrus, which infects the proximal small intestine. Examination of uninfected Tas1r3-/- mice revealed a modest reduction in the number of tuft cells in the proximal small intestine but a severe decrease in the distal small intestine at homeostasis. Together, these results suggest that TAS1R3 influences intestinal immunity by shaping the epithelial cell landscape at steady state.

2020-01-09 | GSE140395 | GEO

A proximal-to-distal survey of healthy adult human small intestine and colon epithelium by single-cell transcriptomics

Project description:Background and Aims: Single-cell transcriptomics offer unprecedented resolution of tissue function at the cellular level, yet studies analyzing healthy adult human small intestine and colon are sparse. Here, we present single-cell transcriptomics covering the duodenum, jejunum, ileum, and ascending, transverse, and descending colon from 3 humans. Methods: 12,590 single epithelial cells from three independently processed organ donors were evaluated for organ-specific lineage biomarkers, differentially regulated genes, receptors, and drug targets. Analyses focused on intrinsic cell properties and capacity for response to extrinsic signals along the gut axis across different humans. Results: Cells were assigned to 25 epithelial lineage clusters. Human intestinal stem cells (ISCs) are not specifically marked by many murine ISC markers. Lysozyme expression is not unique to human Paneth cells (PCs), and PCs lack expression of expected niche-factors. BEST4+ cells express NPY and show maturational differences between SI and colon. Tuft cells possess a broad ability to interact with the innate and adaptive immune systems through previously unreported receptors. Some classes of mucins, hormones, cell-junction, and nutrient absorption genes show unappreciated regional expression differences across lineages. Differential expression of receptors and drug targets across lineages reveals biological variation and potential for variegated responses. Conclusions: Our study identifies novel lineage marker genes; covers regional differences; shows important differences between mouse and human gut epithelium; and reveals insight into how the epithelium responds to the environment and drugs. This comprehensive cell atlas of the healthy adult human intestinal epithelium resolves likely functional differences across anatomical regions along the gastrointestinal tract and advances our understanding of human intestinal physiology.

2022-02-21 | GSE185224 | GEO

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