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| Status |
Public on Oct 21, 2022 |
| Title |
Gene expression analysis of hematopoietic niche cells in the zebrafish kidney |
| Organism |
Danio rerio |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
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).
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| Overall design |
mRNA profiles of isolated ZKS cells, pericytes, sinusoids, and gata2a+ runx1+ (DP) in the zebrafish kidney were generated by Quartz-seq using Illumina NextSeq500.
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| Contributor(s) |
Kimura K, Kondo M, Kobayashi I |
| Citation(s) |
35759948 |
| Submission date |
Oct 21, 2021 |
| Last update date |
Jan 20, 2023 |
| Contact name |
Isao Kobayashi |
| E-mail(s) |
ikobayashi@se.kanazawa-u.ac.jp
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| Organization name |
Kanazawa University
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| Street address |
Kakumamachi
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| City |
Kanazawa |
| State/province |
Ishikawa |
| ZIP/Postal code |
920-1192 |
| Country |
Japan |
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| Platforms (1) |
| GPL20828 |
Illumina NextSeq 500 (Danio rerio) |
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| Samples (12)
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| Relations |
| BioProject |
PRJNA773247 |
| SRA |
SRP342508 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE186298_RAW.tar |
1.4 Mb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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