Project description:The data revealed differential expression between floor plate and ventral lateral region in E10.5 mouse embryo midbrain. Several differentially expressed genes in these regions have been reported in the literature, demonstrating reliability of tissue dissection. Midbrain floor plate and non-overlapping adjacent ventral lateral region of mouse E10.5 embryo midbrain was dissected. Each sample was a pool from 6 embryos. Three replicates for each region were used for the experiment.
Project description:The data revealed differential expression between floor plate and ventral lateral region in E10.5 mouse embryo midbrain. Several differentially expressed genes in these regions have been reported in the literature, demonstrating reliability of tissue dissection.
Project description:Regional specificity of stem cell-derived astrocytes is believed to be an important prerequisite for their applications in disease modelling and cell-based therapies. The regional identity of these astrocytes is often defined by the positional characteristics of their antecedent, stem cell-derived neural progenitors patterned to a fate of interest, with the assumption that the positional specification is to be preserved by the derived astrocytes. Using a human iPSC line designed for tracing midbrain floor plate derivatives, here we show that lineage composition of the derived astrocytes is not a faithful recapitulation of the founder progenitor population, as demonstrated by the loss of floor plate differentiated progeny in the final astrocyte products. Using deep single cell RNA sequencing, we identified distinct transcriptomic signatures of midbrain floor plate-derived astrocytes. Our study highlights the need for rigorous characterisation of PSC-derived regional astrocytes and provides a valuable resource for assessing midbrain floor plate-derived human astrocytes.
Project description:Embryonic stem (ES) cells were differentiated in culture to midbrain dopaminergic (mDA) progenitors and subjected to ChIP-seq analysis to resolve genome-wide binding sites of forkhead box protein A2 (Foxa2). Foxa2 was found to directly regulate multiple lineage pathways to specify midbrain dopaminergic and floor plate progenitor identity.
Project description:Investigations into the roles for Pbx1 and its transcriptional network in dopaminergic neuron development and Parkinson's Disease Three samples each from dorsal midbrain, forebrain, hindbrain, Alar plate, and ventral midbrain
Project description:In the developing embryo, haematopoietic stem cells (HSCs) emerge from the aorta-gonad-mesonephros (AGM) region but the molecular regulation of this process is poorly understood. Recently, the progression from E9.5 to E10.5 and polarity along the dorso-ventral axis have been identified as clear demarcations of the supportive HSC niche. To identify novel secreted regulators of HSC maturation, we performed RNA-sequencing over these spatio-temporal transitions in the AGM region, and supportive OP9 cell line.
Project description:In the developing embryo, haematopoietic stem cells (HSCs) emerge from the aorta-gonad-mesonephros (AGM) region but the molecular regulation of this process is poorly understood. Recently, the progression from E9.5 to E10.5 and polarity along the dorso-ventral axis have been identified as clear demarcations of the supportive HSC niche. To identify novel secreted regulators of HSC maturation, we performed RNA-sequencing over these spatio-temporal transitions in the AGM region, and supportive OP9 cell line.
Project description:Floor plate-derived extracellular signaling molecules, including canonical axon guidance cues of the Netrin family, control neuronal circuit organization. Despite the importance of the floor plate as an essential signaling centre in the developing vertebrate central nervous system, no systematic approach to identify binding partners for floor plate-expressed cellsurface and secreted proteins has been carried out. Here, we used a high-throughput assay to discover extracellular protein-protein interactions, which likely take place in the zebrafish floor plate microenvironment. The assembled floor plate network contains 47 interactions including the hitherto not reported interaction between Netrin-1 and Draxin. We further characterized this interaction, narrowed down the binding interface, and demonstrated that Draxin competes with Netrin receptors for binding to Netrin-1. Our results suggest that Draxin functions as an extracellular Netrin signaling modulator in vertebrates. A reciprocal gradient of Draxin might shape or sharpen the active Netrin gradient, thereby critically modulating its effect.
Project description:E12.5 wild-type and NestinCre Foxa1/2 Flox/ Flox mutant embryos were quickly snap-frozen, then 10um-thick cryostat coronal sections of the midbrain were cut and mounted on membrane slides (Zeiss) and the floor plate was Laser Capture Microdissected. RNA was extracted using the Picopure RNA Isolation Kit RNA sequencing library was prepared using the Ovation RNA-Seq system (Nugen). RNA-Seq libraries were sequenced on the Illumina GAIIx.
