Project description:In order to obtain the transcriptomic information about roof/dorsal and floor/ventral endothelial cells (ECs) of the dorsal aorta (DA) in zebrafish, we isolated single ECs from the DA roof and the floor respectively using the Tg(flk1:eGFP;flk1:NLS-Eos) zebrafish after photoconversion, and then performed scRNA sequencing. These single ECs were isolated at two different time points, 21 hpf and 28 hpf, when the lumen of the DA is established and the EHT begins , respectively.
Project description:scRNA-seq on GFP + cells sorted from the Tg(mitfa:GFP) transgenic zebrafish embryos at 28 hours post fertilization (hpf) using the 10x Chromium system
Project description:Transcriptional profiling of 28 hpf zebrafish transgenic expressing human KIT-D816V mutant gene versus wild-type embryos was performed. The aim of this experiment was to determine the expression changes caused by expression of KIT-D816V oncogene. This transgenic zebrafish represents a model of systemic mastocytosis with many features of this disease present in adults, but no very clear phenotypes in embryos. Thus, we attempted to determine if there are certain expression changes, which can be used as molecular features of active KIT expressed in these embryos.
Project description:RNA-seq transcriptome analysis identified a functional requirement for zebrafish Rfx4 in the developing neural floor plate and roof plate.
Project description:Transcriptional profiling of 28 hpf zebrafish transgenic expressing human KIT-D816V mutant gene versus wild-type embryos was performed. The aim of this experiment was to determine the expression changes caused by expression of KIT-D816V oncogene. This transgenic zebrafish represents a model of systemic mastocytosis with many features of this disease present in adults, but no very clear phenotypes in embryos. Thus, we attempted to determine if there are certain expression changes, which can be used as molecular features of active KIT expressed in these embryos. Two-condition experiment, Tg(actb2:KIT-D816V) versus wild-type(AB), 4 replicate experiments with a dye-swap each time
Project description:In our previous study, we found zebrafish embryos treated with 5uM 11,12-EET (epoxyeicosatrienoic acid) had increased stem cell marker, runx1, expression in the AGM. EET also induced ectopic runx1 expression in the tail. To systematically study how EET regulates gene expression, we performed microarray analysis on EET-treated embryos. Zebrafish whole embryos were synchronized at fertilization. Embryos were grown at 28 degree overnight. 25 embryos per group were treated with DMSO or 5uM 11,12-EET starting from 24 hpf (hour post fertilization) until 36 hpf at 28 degree. The triplicates were from three different clutches of embryos, and split into DMSO v.s. EET for each clutch.
Project description:Plasmodium-specific CD4+ T cells from mice infected with Plasmodium chabaudi chabaudi AS parasites were recovered at Days 0, 7, and 28 to undergo processing and generate scRNA-seq dataset. At Day 28, mice were administered with either saline or artesunate (intermittent artesunate therapy - IAT). scRNA-seq dataset was analysed to investigate transcriptome dynamics of CD4+ T cells from effector to memory states.
Project description:In our previous study, we found zebrafish embryos treated with 5uM 11,12-EET (epoxyeicosatrienoic acid) had increased stem cell marker, runx1, expression in the AGM. EET also induced ectopic runx1 expression in the tail. To systematically study how EET regulates gene expression, we performed microarray analysis on EET-treated embryos. Zebrafish whole embryos were synchronized at fertilization. Embryos were grown at 28 degree overnight. 25 embryos per group were treated with DMSO or 5uM 11,12-EET starting from 24 hpf (hour post fertilization) until 36 hpf at 28 degree. The triplicates were from three different clutches of embryos, and split into DMSO v.s. EET for each clutch. EET vs. DMSO