Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Deciphering Endoderm-derived Macrophage-like Metaphocytes in Zebrafish Gill and Intestine

ABSTRACT: In order to have a comprehensive understanding of endoderm derived mpeg1+ cells in zebrafish gill and intestine, we isolated endoderm-derived GFP+ cells and remaining DsRedx+ cells (hematopoiesis-derived macrophages) from the gill (sox17_gill_GFP, sox17_gill_DsRedx) and intestine (sox17_intestine_GFP, sox17_intestine_DsRedx) of 4-OHT treated Tg(sox17:CreERT2;mpeg1:loxP-DsRedx-loxP-GFP) fish and performed RNA-seq. Both T-SNE analysis and feature gene comparison indicate that the endoderm-derived mpeg1+ cells in the gill and intestine are highly similar to the metaphocytes in the epidermis. We hence also refer to these endoderm-derived mpeg1+ cells as metaphocytes.

ORGANISM(S): Danio rerio

PROVIDER: GSE155287 | GEO | 2020/11/24

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Deciphering Endoderm-derived Macrophage-like Metaphocytes in Zebrafish Gill and Intestine

Project description:Deciphering Endoderm-derived Macrophage-like Metaphocytes in Zebrafish Gill and Intestine

| PRJNA649247 | ENA

Whole-transcriptome RNA-seq analysis of zebrafish epidemal MLCs

Project description:In order to have a comprehensive comparison of locally restricted mpeg1+ cells (MLCs) and cLCs, we isolated locally restricted mpeg1+ cells and cLCs from heat-shock labeled zebrafish epidermis and performed whole-transcriptome RNA-sequencing. As the controls, keratinocytes, T cells and neutrophils isolated from the epidermis were also included in this experiment. Both T-SNE analysis and feature gene comparison indicate that locally restricted mpeg1+ cells indeed share the highest similarity with cLCs in transcriptome profile.

2019-05-20 | GSE126763 | GEO

Spic is required for the differentiation of metaphocyte progenitor cells

Project description:Metaphocytes are tissue-resident myeloid-like cells of non-hematopoietic origin in zebrafish barrier tissues. How metaphocytes acquire myeloid cell properties from non-hematopoietic precursors during the development remains unknown. Here we show that metaphocytes are in situ generated from local progenitors guided by the ETS transcription factor Spic. Tg(spic:EGFP) transgenic fish were found to label both metaphocytes and their progenitor cells. While spic is dispensable for the formation of the metaphocyte progenitors, it is required for the progenitors to differentiate into immature metaphocytes. To decipher the molecular basis underlying the developmental arrest of metaphocytes in spic mutants, we sorted the metaphocyte progenitor cells from the epidermis and gill of the mutants and siblings and performed bulk RNA-seq analysis. The data suggests that Spic orchestrates the development of metaphocytes by promoting the expression of myeloid-associated genes, either directly or indirectly through downstream transcription factors.

2023-04-08 | GSE228732 | GEO

single-cell RNA sequencing analysis of metaphocytes and epidermal cells

Project description:Metaphocytes are tissue-resident myeloid-like cells of non-hematopoietic origin in zebrafish barrier tissues. How metaphocytes acquire myeloid cell properties from non-hematopoietic precursors during the development remains unknown. Here we show that metaphocytes are in situ generated from local progenitors guided by the ETS transcription factor Spic. Tg(spic:EGFP) transgenic fish were found to label both metaphocytes and their progenitor cells. To reveal the genetic programs underlying the development of metaphocytes, we performed single-cell RNA sequencing analysis of spic:GFP+ cells in the epidermis of adult Tg(spic:EGFP) fish. The result further supports that mature metaphocytes are generated from spic+ progenitors via an intermediate immature state and gradually obtain their myeloid characteristics during this process.

2023-04-08 | GSE228737 | GEO

RNA-Seq analysis of mouse small intestine enteroendocrine cells

Project description:We generated knock-in mice expressing GFP under the control of the endogenous GIP (Glucose-dependent Insulinotropic Polypeptide) promoter that enable the isolation of a purified population of small intestine K cells. Using RNA-Seq, we comprehensively characterized the transcriptomes of GIP-GFP cells as well as the entire enteroendocrine lineage derived from Neurogenin3 (Ngn3)-expressing progenitors. We interrogated the whole transcriptome of FACS-isolated small intestine GIPGFP cells using high-throughput mRNA sequencing. We also obtained the global gene expression patterns of the entire enteroendocrine cell lineage as well as the non-enteroendocrine cell population, comprising enterocytes, goblet cells and Paneth cells. To achieve this, small intestine epithelial cells from male mice resulting from the breeding of Neurogenin3 (Ngn3)-Cre mice with ROSA26-LoxP-STOP-LoxP-tomato indicator mice were isolated based on Tomato fluorescence and negative staining for CD45. Due to the small cell numbers, we constructed each of the three RNA-Seq libraries (GIPGFP, Ngn3TOMATO, and Ngn3-) using a pool of equal amounts of individual RNA samples without RNA amplification.

2015-01-01 | E-GEOD-61250 | biostudies-arrayexpress

Endothelial Brg1-Notch Signaling Regulates Zebrafish Heart Regeneration

Project description:The goal of this study is to compare the NGS-derived heart transcriptome profiling (RNA-seq) between kdrl GFP positive endothelial cells of 4-HT induced Tg(ubi:loxp-DsRed-stop-loxp-DN-xBrg1; kdrl:CreER; kdrl:eGFP) (DNK) and Tg(ubi:loxp-DsRed-stop-loxp-DN-xBrg1; kdrl:eGFP) (CtrlK) injured hearts.

2022-07-09 | GSE154193 | GEO

Gene expression profiling of osterix-derived cells from control and PTH1R knockout mice in osteoprogenitors

Project description:We used Osx-Cre:GFP / ROSA26-loxP-stop-loxP-tdTomato mice with or without PTH1Rfl/fl. Bone marrow and bone were digested to make single cell suspension, and sorted by fluorescence. Bulk cell RNA sequencing were performed to identify specific transcripts from osterix-derived cells.

2022-04-27 | GSE185944 | GEO

Gene expression profiling of Nodal versus Activin-derived endoderm from mouse ES cells

2013-01-01 | GSE41086 | GEO

Gene expression profiling of Nodal versus Activin-derived endoderm from mouse ES cells

Project description:To explore the molecular basis of functional differences observed between Nodal versus Activin-derived endoderm, we compared their respective gene expression profiles. Sox17-GFP mouse ES cells were differentiated in the presence of Nodal or Activin for 7 days, after which GFP(+) cells were purified by FACs. Undifferentiated ES cells were also included for comparison as a control. Results indicate that the two endoderm populations are nearly identical at the level of global transcription. Subtle differences suggest a difference in the degree of endoderm progression. Total RNA obtained from SOX17-GFP (+) mouse ES cells, Sox17-GFP treated with Nodal, Sox17-GFP treated with Activin. Two replicates for each sample; Sample data table contains average values of two replicates. The non_normalized.txt file contains individual signal values for each replicate.

2013-01-01 | E-GEOD-41086 | biostudies-arrayexpress

R-spondin 1 and noggin facilitate expansion of resident stem cells from non-damaged gallbladders.

Project description:Pioneering studies within the last few years have allowed the in vitro expansion of tissue-specific adult stem cells from a variety of endoderm-derived organs, including the stomach, small intestine and colon. Here we derived organoids from mouse gallbladder tissue (gallbladder organoids), from mouse liver (including the extrahepatic biliary ducts and gallbladder; liver organoids) and from mouse small intestine tissue (intestinal organoids). RNA was prepared from these organoids and used to assay expression of 21,258 genes using Affymetrix gene expression arrays. RNA was also prepared from mouse gallbladder, liver and small intestine tissues and used to assay gene expression in these tissues. Finally, gallbladder organoids were induced to differentiate by removing R-spondin 1 and noggin from the culture media and subjected to gene expression array analysis. RNA was extracted from mouse gallbladder organoids, differentiated gallbladder organoids, liver organoids, small intestine organoids, gallbladder tissue, liver tissue and small intestine tissue and then used for hybridization of Affymetrix gene expression microarrays.

2016-04-06 | E-GEOD-77461 | biostudies-arrayexpress

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