Project description:The present study was conducted in the frame of the EU-funded Graphene Flagship project. The aim is to evaluate the impact of graphene oxide (GO) on the (innate) immune system using zebrafish as a model. We previously performed single-cell RNA-sequencing of germ-free zebrafish embryos exposed to GO plus the microbial metabolite butyrate (BA). Here, we performed a follow up experiment using germ-free lck-GFP transgenic fish in which the zebrafish were exposed to GO plus BA at 5 dpf. The embryos were then dissociated and subsequently sorted on lck and submitted for single-cell RNA-sequencing using 10x Genomics.
Project description:Transcriptome data from individual lck:GFP expressing cells isolated from spleens of two adult Zebrafish. LCK is a marker of lymphocytes and here we identified two major subpopulations corresponding to T-cells and NK-like and a minor one of myeloid-like cells. Single cell transcriptomes are matched with FACS index sorting data (GFP, forward and side light scatter and dead cell staining)
Project description:Transcriptome data from zebrafish single and bulk cells from blood in five organs. Blood cells were collected from adult Tg(cd4-1:mCherry), Tg(lck:EGFP), Tg(mhc2dab:GFP, cd45:dsRed), AB.
Project description:Investigation of expression differences between melanomas harvested from MiniCoopR-GFP versus MiniCoopR-SETDB1 transgenic zebrafish.
Project description:Transcriptome data from zebrafish single cells from guts from either from Tg(lck:EGFP) rag1-/-mutant or wild-type zebrafish were isolated and single cell suspensions were prepared as described in protocol section. Three zebrafish, per each condition (i.e. zebrafish intraperitoneally injected with PBS, lyophilised Anisakis simplex or inactivated Vibrio anguillarum), were used to collect the total of 12,000 lck+ cells (4000 per zebrafish) for 10x experiment.
Project description:Single cell RNA-seq analysis was carried out for 1 normal sample from a control zebrafish line (lck-mCherry) and 5 non-tumor and 14 tumor samples from the IRF4 transgenic line (lck-IRF4). Tumor cells were harvested from the animals with or without heterozygous p53 mutation at different time points of tumor development.
Project description:Melanocytes of the skin have traditionally been viewed as a homogeneous population, however, recent findings suggest the existence of distinct cell states within the melanocyte population. To investigate this further, we employed the zebrafish as a valuable model system for studying melanocyte biology. The zebrafish offers advantages such as its transparent nature and the availability of transgenic lines that allow specific labeling of melanocytes. In our study, we utilized a transgenic zebrafish line, Tg(mifa:GFP), that expresses green fluorescent protein (GFP) under the control of a melanocyte-specific promoter, mitfa, labelling only those cells in which mitfa promoter is active. We then performed single-cell RNA sequencing (scRNA-seq) analysis to explore the diversity of mitfa:GFP-positive cells.
Project description:Investigation of expression differences between melanomas harvested from MiniCoopR-GFP versus MiniCoopR-SETDB1 transgenic zebrafish. An eight-chip study using total RNA prepared from four distinct melanomas from zebrafish injected with MiniCoopR-GFP (control) transposon and four distinct melanomas from zebrafish injected with MiniCoopR-SETDB1 transposon. Injected animals carried a p53 loss-of-function mutation, a mutation in nacre, and an mitf:BRAF-V600E transgene. Each chip measures the expression level of 32,292 genes.
Project description:To investigate the cell types involved in the gliovascular niche of the zebrafish brain, we performed single cell sequencing on cells sorted from fli1:gfp and her4: GFP transgenic animals in control and amyloid toxicity conditions.