Danio rerio
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA110937 | ENA |
REPOSITORIES: ENA
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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:Gene Expression Profile of Hematopoietic Stem Cells during Zebrafish Development
| PRJNA99755 | ENA
Project description:Expression data of kidney multiciliated cells from zebrafish embryos
| PRJNA202452 | ENA
Project description:Gene expression profile of zebrafish renal collecting ducts
| PRJNA147689 | ENA
Project description:Expression profile of zebrafish embryonal rhabdomyosarcoma
| PRJNA147915 | ENA
Project description:Gene expression data from myelomonocytes and whole kidney marrows in zebrafish adult kidney after deletion of miR-142-3p
| PRJNA253956 | ENA
Project description:RNAseq was performed on hcar1-4+/+ and hcar1-4-/- zebrafish larvae with (2 h and 4 h) or without (0 h) Pseudomonas aeruginosa (PA) ear infection. The transcriptome profile generated here reveals PA14 infection-induced differential gene expression patterns between hcar1-4-/- and hcar1-4+/+ siblings.
2022-10-31 | GSE201604 | GEO
Project description:The side population (SP), recently identified in several normal tissues and in a variety of tumors, may comprise cells endowed with stem cell features. In this study, we investigated the presence of SP in epithelial ovarian cancer (EOC) and found it in 4 out of 6 primary cultures from xenotransplants, as well as in 9 out of 25 clinical samples analyzed. SP cells from one xenograft bearing a large SP fraction were characterized in detail and they were capable of recreate the full repertoire of cancer cell populations observed in the parent tumor. Moreover, SP cells had higher proliferation rates, were much less apoptotic compared to non-SP cells, and generated tumors more rapidly than non-SP cells. We also investigated the effects of interferon-alfa (IFN-alpha), a cytokine which has been widely used to treat solid tumors, on EOC cells and observed that IFN-alpha exerts marked anti-proliferative and pro-apoptotic effects on primary cultures containing SP cells. IFN-alfa-treatment invariably caused a dramatic reduction in SP size in tumor cell lines of different origin and in normal bone-marrow SP cells, associated with a distinctive transcriptional profile. Gene therapy with human IFN-alpha resulted in regression of established tumors bearing a large SP fraction, which was not observed when tumors bearing low SP levels were treated. These findings could have relevant clinical implications since they imply that tumors bearing large SP numbers - albeit rare - could be sensitive to IFN-alpha treatment. Experiment Overall Design: 4 Affymetrix microarrays: Experiment Overall Design: 2 technical replicates: Ovarian cancer, untreated Side Population, rep1 Experiment Overall Design: Ovarian cancer, untreated Side Population, rep2 Experiment Overall Design: + Experiment Overall Design: 2 technical replicates: Ovarian cancer, IFN-alpha treated Side Population, rep1 Experiment Overall Design: Ovarian cancer, IFN-alpha treated Side Population, rep2
2008-11-13 | E-GEOD-9481 | biostudies-arrayexpress
Project description:Purpose: Construction of 3D zebrafish spatial transcriptomics data for studying the establishment of AP axis. Methods: We performed serial bulk RNA-seq data of zebrafish embryo at three development points. Using the published spatial transcriptomics data as references, we implemented Palette to infer spatial gene expression from bulk RNA-seq data and constructed 3D embryonic spatial transcriptomics. The constructed 3D transcriptomics data was then projected on zebrafish embryo images with 3D coordinates, establishing a spatial gene expression atlas named Danio rerio Asymmetrical Maps (DreAM). Results: DreAM provides a powerful platform for visualizing gene expression patterns on zebrafish morphology and investigating spatial cell-cell interactions. Conclusions: Our work used DreAM to explore the establishment of anteroposterior (AP) axis, and identified multiple morphogen gradients that played essential roles in determining cell AP positions. Finally, we difined a hox score, and comprehensively demonstrated the spatial collinearity of Hox genes at single-cell resolution during development.
2024-04-08 | GSE262578 | GEO