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Single cell RNA sequencing analysis of germ free (GF) mouse Paneth cells and microbiome-transferred exGF mouse Paneth cells.

ABSTRACT: Single cell RNA sequencing analysis of germ free (GF) mouse Paneth cells and microbiome-transferred exGF mouse Paneth cells.

PROVIDER: PRJNA994583 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR25266965.fastq.gz	Fastqsanger.gz
	SRR25266966.fastq.gz	Fastqsanger.gz
	SRR25266967.fastq.gz	Fastqsanger.gz
	SRR25266968.fastq.gz	Fastqsanger.gz

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Similar Datasets

Single cell RNA sequencing analysis of germ free (GF) mouse Paneth cells and microbiome-transferred exGF mouse Paneth cells.

Project description:The single cell level Paneth cell transcriptome under gnotobiotic condition has not been resolved. How gut microbiome modulates Paneth cell transcriptome at single cell level in germ-free mice was not known. We used a flow cytometry method to isolate highly pure ileal Paneth cells from germ free (GF) Paneth cell reporter mice (Lyz1-3'UTR-IRES-CreER) and from exGF Paneth cell reporter mice that were transplanted with wild type C57B/l6 mouse gut microbiota (exGF+B6M). These isolated Paneth cells were subjected to single cell RNA sequencing by 10xGenomics.

2023-09-01 | GSE237328 | GEO

Proteomic profiling of mouse Paneth cells microdissected from small intestinal tissue

Project description:Paneth cells are antimicrobial peptide-secreting cells located at the base of the crypts of the small intestine. The proteome of Paneth cells is not well defined because of their co-existence with stem cells making it difficult to culture Panth cells alone in vitro. Using a simplied toluidine blue O method for staining mouse intestinal tissue, laser capture microdissection (LCM) to isolate cells from the crypt region and surfactant assisted one pot protein digestion, we identified more than 1,300 proteins from crypts equivalent to 18,000 cells. Compared with the proteomes of villi and smooth muscle regions, the crypt proteome is highly enriched in defensins, lysozymes and other antimicrobial peptides that are characteristic of Paneth cells. The sensitivity of the LCM-based proteomics approach was also assessed using a smaller number of cell equivalent tissues, a comparable proteomic coverage can be achieved with 3,600 cells. This work is the first proteomics study of intestinal tissue enriched with Paneth cells. The simplied workflow enables profiling of Paneth cell associated pathological changes at the proteome level directly from frozen intestinal tissue. It may also be useful for proteomics studies of other spatially resolved cell types from other tissues.

2022-10-12 | PXD034143 | Pride

Paneth cells

Project description:Paneth cells

| PRJNA994579 | ENA

Expression data from Germ-Free (GF) and L.NK2-colonized mice intestinal epithelial cells and Peyer's patches cells

Project description:Lactobacillus NK2 (L.NK2) is a commensal microbe, isolated from the mouse intestinal feces in our lab. To examine the potential role of L. NK2 in the gut immunity, we monocolonized GF mice with L.NK2. And, we conducted a microarray experiment to compare the transcriptomes of GF and L.NK2-colonized mice intestines under the same experimental condition We used microarrays to detail the global programme of gene expression in intestinal epithelial cells (IEC) and Peyer's patches cells (PP) of GF and L.NK2-colonized mice.

2018-03-01 | GSE111111 | GEO

Expression data from Germ-Free (GF) and L.NK318.1-colonized (NK318.1) mice intestinal epithelial cells and Peyer's patches cells

Project description:Lactobacillus NK318.1 is a commensal microbe isolated from the mouse intestinal feces in our lab. To examined the potential role of L. NK318.1 in the gut immunity, we monocolonized GF mice with L.NK318.1. And, we conducted a microarray experiment to compare the transcriptomes of GF and NK318.1 mice intestines under the same experimental condition We used microarrays to detail the global programme of gene expression in intestinal epithelial cells (IEC) and Peyer's patches cells (PP) of GF and NK318.1 mice.

2017-05-12 | GSE98819 | GEO

Shotgun proteomics on murine paneth cells after TNF-alpha treatment

Project description:Mouse were injected with TNF-alpha prior isolation of paneth cells with flow cytometry.

2024-07-18 | PXD053044 | Pride

Mouse duodenal and ileal Paneth cell single cell RNA sequencing

Project description:An indepth analysis of Paneth cell transcriptome at single cell level has not been available. Existing intestinal epithelial cell scRNA dataset contain many cell types, where Paneth cells represent a small portion. We used a flow cytometry based approach to enrich and isolate relatively pure Panethc cells from a newly developed Paneth cell reporter mouse line (Lyz1-3'UTR-IRES-CreER; Rosa26R-tdTomato). Single cell RNA sequencing was performed on purified duodenal and ileal Paneth cells of mice housed under specific pathogen free condition.

2023-09-01 | GSE237327 | GEO

Gene expression profiles in RAW264.7 cells with CpG and Gf

Project description:RAW264.7 cells were untreated or treated with CpG+/-Gf for 6 hours. Total RNA was analyzed via Illumina Mouse Ref-8 V2. CpG‐induced genes and their regulation by Gf were examined.

2018-03-15 | GSE97366 | GEO

RNA-seq of Paneth cells

Project description:The impact of removal of Mll1 in intestinal Paneth cells expressing an constitutively active form of beta-catenin (beta-cateninGOF) was analysed in 4 pairs of sorted Paneth cells of Lgr5-CreERT2; beta-cateninGOF;Mll1+/- (control) and Lgr5-CreERT2; beta-cateninGOF;Mll1-/- (knockout) mice at 10 days after tamoxifen-induced mutagenesis. Using 75-base-pair reads, around 30 million reads per sample with comparable unique mapped reads (52-93%) were obtained. To analyze differentially expressed genes, we applied DESeq2 analysis to the RNA-seq dataset. Differentially expressed genes in beta-cateninGOF; Mll1-/- versus beta-cateninGOF; Mll1+/- Paneth cells showed both up- and downregulation of genes at a false discovery rate (FDR) of 10%. This included a global increase in the expression of goblet cell-specific genes. Downregulated genes included specific markers of Paneth cells, indicating that ablation of Mll1 in Paneth cells shifted their identity towards a mixed Paneth-goblet cell fate.

2022-01-08 | GSE177047 | GEO

Paneth cells constitute the niche for Lgr5 stem cells in intestinal crypts

Project description:Homeostasis of self-renewing small intestinal crypts results from neutral competition between Lgr5 stem cells, small cycling cells located at crypt bottoms1, 2. Lgr5 stem cells are interspersed between terminally differentiated Paneth cells, that are known to produce bactericidal products such as lysozyme and cryptdins/defensins3. Single Lgr5-expressing stem cells can be cultured to form long-lived, self-organizing crypt-villus organoids in the absence of non-epithelial niche cells4. Here, we note a close physical association of Lgr5 stem cells with Paneth cells in vivo and in vitro. CD24+ Paneth cells express EGF, TGF?, Wnt3 and the Notch-ligand Dll4, all essential signals for stem cell maintenance in culture. Co-culturing of sorted stem cells with Paneth cells dramatically improves organoid formation. This Paneth cell requirement can be substituted by a pulse of exogenous Wnt. Genetic removal of Paneth cells in vivo results in the concomitant loss of Lgr5 stem cells. In colon crypts, CD24+ cells residing between Lgr5 stem cells may represent the Paneth cell equivalents. We conclude that Lgr5 stem cells compete for essential niche signals provided by a specialized daughter cell, the Paneth cell. We used intestinal cell fractions from Lgr5-EGFP-ires-CreERT2 mice, expressing GFP under the control of the Lgr5 promoter. RNA was isolated from two FACS sorted cell populations: stem cells were sorted based on high level of GFP expression (GFPhi) and Paneth cells were sorted based on high level of CD24 expression (CD24hi) and high side-scatter (SSChi). Differentially labelled cRNA from GFPhi and CD24hi/SSChi cells from two different sorts (each combining ten individual mice) were hybridized on 4X44K Agilent Whole Mouse Genome dual colour Microarrays (G4122F) in two dye swap experiments, resulting in four individual arrays.

2010-11-29 | E-GEOD-25109 | biostudies-arrayexpress

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