Gene expression analysis of hematopoietic niche cells in the zebrafish kidney
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ABSTRACT:
PROVIDER: PRJNA773247 | ENA |
REPOSITORIES: ENA
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Project description:The zebrafish is an excellent model for the study of hematopoiesis. The use of fluorescently labeled transgenic lines allows us to isolate various hematopoietic cell types. Moreover, transplantation and cell culture assays enable to test the ability for hematopoietic repopulation and differentiation in isolated hematopoietic cells. The zebrafish counterpart of the mammalian bone marrow is the kidney, termed the "kidney marrow", providing an attractive tool for studying hematopoietic niches. Here, we isolated two candidate niche cell populations from the zebrafish kidney, pericytes and sinusoidal endothelial cells. Sinusoidal endothelial cells have been shown to endocytose acetylated low-density lipoprotein (Ac-LDL), whereas pericytes can be labeled by pdgfrb expression. Therefore, pericytes and sinusoidal endothelial cells were isolated by using pdfgrb:GFP and kdrl:Cerulean injected with Alexa Fluor 488-conjugated Ac-LDL, respectively. In addition, we also utilized a cell line generated from the zebrafish kidney, zebrafish kidney stromal (ZKS), which have been shown to support proliferation of various hematopoietic precursors (Stachula et al., 2009). In this study, we performed RNA-seq analysis using these three fractions to investigate the gene expression profile of each niche cell fraction. Three distinct conditions of gata2a:GFP+ runx1:mCherry+ (DP) hematopoietic stem/progenitor cells were also analyzed: uncultured gata2a+ runx1+ cells (DP_uncul), gata2a+ runx1+ cells co-cultured with ZKS cells (DP_cocul), and gata2a+ runx1+ cells co-cultured with ZKS cells in the presence of both IWR-1-endo and Thpo (DP_IW+Th).
2022-10-21 | GSE186298 | GEO
Project description:The kidney is the main hematopoietic organ in teleost fish. Various stages of hematopoietic cells were observed in the interstitial tissue of the kidney. We recently demonstrated that zebrafish hematopoietic stem cells (HSCs) expressing jam1a were specifically localized along the renal collecting ducts in the adult kidney. Interestingly, most of HSCs invaded into the intracellular spaces of the epithelium in collecting ducts, suggesting that collecting ducts provide a specific microenvironment for HSCs. In order to identify niche factors in collecting ducts, we performed microarray analysis in collecting ducts isolated from the Tg(jam1a:EGFP) zebrafish kidney. Collecting ducts were isolated from Tg(jam1a:EGFP) zebrafish under a fluorescent microscope. To examine the effect of X-ray irradiation on the niche, collecting ducts were isolated from the fish irradiated with 25Gy. The whole kidney tissues were also used for a comparison analysis. Two independent replicates consisting of five zebrafish were prepared for each sample.
2012-08-24 | E-GEOD-32363 | biostudies-arrayexpress
Project description:Hematopoietic stem cells (HSCs) maintain the entire blood system throughout the life and are utilized for a therapeutic component of blood diseases. The zebrafish is an elegant genetic model for the study of hematopoiesis due to its many unique advantages. We have developed the method to isolate zebrafish HSCs by a combination of two HSC-related transgenic lines, gata2a:GFP and runx1:mCherry. In this study, we performed RNA-seq analysis in three distinct hematopoietic cell populations in the adult kidney, gata2a+ runx1+ cells (HSCs), gata2a− runx1+ cells (erythroid- and/or myeloid-primed progenitors), and gata2a+ runx1− cells (lymphoid-primed progenitors).
2019-10-15 | GSE132927 | GEO
Project description:The kidney is the main hematopoietic organ in teleost fish. Various stages of hematopoietic cells were observed in the interstitial tissue of the kidney. We recently demonstrated that zebrafish hematopoietic stem cells (HSCs) expressing jam1a were specifically localized along the renal collecting ducts in the adult kidney. Interestingly, most of HSCs invaded into the intracellular spaces of the epithelium in collecting ducts, suggesting that collecting ducts provide a specific microenvironment for HSCs. In order to identify niche factors in collecting ducts, we performed microarray analysis in collecting ducts isolated from the Tg(jam1a:EGFP) zebrafish kidney.
2012-08-24 | GSE32363 | GEO
Project description:Gene expression analysis of hematopoietic stem/progenitor cells in the zebrafish kidney
| PRJNA549478 | ENA
Project description:Side population (SP) cells are identified based on their capacity to efflux of the fluorescent dye Hoechst 33342, and are enriched for hematopoietic stem cells (HSCs) in mammalian bone marrow. We recently demonstrated that SP cells were present in the teleost kidney, the main hematopoietic organ in teleosts, and were enriched for HSCs. In this analysis, to identify the regulated genes in teleost HSCs, gene expression analysis of zebrafish kidney SP cells were performed using the GeneChip Zebrafish Genome Array.
2008-10-10 | GSE12955 | GEO
Project description:Side population (SP) cells are identified based on their capacity to efflux of the fluorescent dye Hoechst 33342, and are enriched for hematopoietic stem cells (HSCs) in mammalian bone marrow. We recently demonstrated that SP cells were present in the teleost kidney, the main hematopoietic organ in teleosts, and were enriched for HSCs. In this analysis, to identify the regulated genes in teleost HSCs, gene expression analysis of zebrafish kidney SP cells were performed using the GeneChip Zebrafish Genome Array. Experiment Overall Design: Based on their Hoechst fluorescence intensity, lymphoid cells (FS-low, SS-low) from zebrafish kidney were subdivided into SP and MP populations (referred to as âzSPâ and âzMPâ). To minimize the biological variability, 20 zebrafish were used for 3 independent cell sorting experiments and lysates from these 3 experiments were pooled by cell type. Each RNA sample was split into two aliquots and used for amplification, labeling, and hybridization to independent arrays.
2008-10-26 | E-GEOD-12955 | biostudies-arrayexpress
Project description:Comprehensive Analysis of Hematopoietic Stem Cell Niche
| PRJEB7266 | ENA
Project description:To profile the developmental landscape of fetal HSPCs and their local niche, here, by using single-cell RNA-sequencing, we decoded the expanding hematopoietic organ in zebrafish
2021-03-18 | GSE146404 | GEO
Project description:Zebrafish hematopoietic cells from kidney marrow from zebrafish tet2 mutants were compared to wild-type
2020-09-01 | GSE136349 | GEO