Project description:Cell-based therapy is a promising treatment for neurodegenerative diseases such as Parkinson’s disease or cardiac disease. Similarly, reconstruction of the corticospinal tract by cell transplantation is expected as a treatment for stroke and degenerative disease. For efficient cell integration to the corticospinal tract after transplantation, the induction or selection of corticofugal projection neuron (CFuPN) is important. However, no CFuPN specific surface markers for the purification are known. Recently, miRNAs have been reported as alternatives to surface markers; microRNA responsive switch. In order to separate CFuPN at the axon extension stage, which is optimal for regenerative medicine, by using miRNA switches, we used microarrays to identify miRNAs that are specifically expressed in CFuPN during cerebral cortex V-VI layer formation.
Project description:In order to understand the relationship between cellular diversity and pallium regions, single-nucleus RNA-seq (snRNA-seq) was performed in 3 microdissected regions from the axolotl pallium: medial, dorsal, and lateral.
Project description:A comparative RNA-SEQ analysis of control total RNA preparations from pooled E14.5 dorsal root ganglia was carried out to determine the performance of the RNAseq reactions at differing concentrations (3ng, 10ng & 30ng in high or low volumes) and concordance among different institutions using the same source of RNA. RNA was extracted from E14.5 dorsal root ganglia dissected from wild type C57BL/6J embryos and sequenced using Illumina Hiseq 2500 platform.
Project description:This experiment aims at characterizing the transcriptome of embryonic mouse dorsal spinal cord. Dorsal spinal cords dissected from litters of E14.5 wild type embryos of unknown sex were processed for RNA extraction using Trizol and RNeasy Mini kit (Qiagen) extraction procedures. Five replicates of wild type embryos were analyzed, each sample with tissue pooled from three embryos.
Project description:The goal of this experiment is to track cellular regeneration after a dorsal injury to the axolotl pallium. To this end, we employed Div-seq, that is, performed snRNA-seq on cells labelled with EdU, which have thus recently replicated. We performed this in a time course, in order to observed the cell populations that were generated as regeneration progressed.
Project description:The medial pallium (MP) is the major forebrain region underlying learning and memory, spatial navigation, and emotion; however, the mechanisms underlying the specification of its principal neuron subtypes remain largely unexplored. Here, by postmitotic deletion of FOXG1 (a transcription factor linked to autism and FOXG1 syndrome) and single-cell RNA sequencing, we found that FOXG1 controls the specification of upper-layer retrosplenial cortical pyramidal neurons (RSC-PyNs (UL)), subiculum PyNs (SubC-PyNs), CA1-PyNs, CA3-PyNs and dentate gyrus granule cells (DG-GCs) in the mouse MP. We uncovered subtype-specific and subtype-shared FOXG1-regulated transcriptomic networks orchestrating MP neuron specification.
Project description:In the urinary tract, smooth muscle (SM) is present in the renal pelvis, the ureter, the bladder and the urethra and plays a crucial role in the functional and structural integrity of these organs. In Tshz3 mutant ureters the myogenic program is not activated in the proximal region due to the absence of expression of myocardin (Myocd), a key regulator of SM differentiation. We set out to characterize TSHZ3-dependent mechanisms that participate to the process of ureteric smooth muscle cells (SMC) differentiation. To this aim, we used microarrays to identify distinct classes of up- and down-regulated genes in Tshz3LAcZ/LacZ mutant ureters at two different time points; at E14.5, which corresponds to the onset of the myogenic program and at E16.5, when SMC express the full repertoire of differentiation marker genes. Mouse embryonic (E14.5 and E16.5) wild type and Tshz3LacZ/LacZ mutant ureters were dissected for RNA extraction and hybridization on Affymetrix microarrays.
Project description:In the adult mouse, distinct morphological and transcriptional differences separate stomach from intestinal epithelium. Remarkably, the epithelial boundary between these two organs is literally one cell thick. This discrete junction is established suddenly and precisely at embryonic day (E) 16.5, by sharpening a previously diffuse intermediate zone. In the present study, we define the dynamic transcriptome of stomach, pylorus and intestinal tissues between E14.5 and E16.5. We show that establishment of this boundary is concomitant with the induction of over a thousand genes in intestinal epithelium, and these gene products provide intestinal character. Hence, we call this process intestinalization. We identify specific transcription factors (Hnf4g, Creb3l3 and Tcfec) and examine signaling pathways (Hedgehog and Wnt) that may play a role in this process. Finally, we define a unique expression domain at the pylorus itself and detect novel pylorus-specific patterns for the transcription factor Gata3 and the secreted protein nephrocan. Experiment Overall Design: Stomach, pylorus and duodenum tissue from E14.5 and E16.5 mouse embryos were collected for RNA extraction and hybridization on Affymetrix microarrays. We sought to study the gene expression profiles and identify genes and pathways enriched in these three tissues at two important developmental times.
Project description:Our study examined a population of radial glial-like cells (RGLCs) in the dorsal spinal cord midline that we showed provide long-distance growth support for longitudinal rapidly adapting (RA) mechanoreceptor axons during development of spinal cord dorsal column. To evaluate potential molecular markers of these cells, we isolated the RGLCs using hematoxylin and eosin staining to visualize the cell bodies in the dorsal column midline from E14.5 mouse embryos, and used laser capture microdissection for each sample ("LCM"). To compare transcript expression to the adjacent RA mechanoreceptive axons, we performed FACS of dorsal root ganglion of E14.5 Ret-Tdtomato+ RA mechanoreceptors. Our analyses revealed a high enrichment of radial glial-specific markers in the LCM replicates compared to Ret-Tdt samples. In contrast, neuronal-specific markers were more highly enriched in the Ret-Tdt samples, as expected. These data suggest the midline RGLCs are of radial glial identity. Others may find these data helpful in determining potential RGLC-mechanoreceptor molecular interactions in subsequent studies.
Project description:A comparative RNA-SEQ analysis of control total RNA preparations from pooled E14.5 dorsal root ganglia was carried out to determine the performance of the RNAseq reactions at differing concentrations (3ng, 10ng & 30ng in high or low volumes) and concordance among different institutions using the same source of RNA.