MERFISH profiling of mouse retinal ganglion cell layer on wholemount
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ABSTRACT:
PROVIDER: PRJNA1295347 | ENA |
REPOSITORIES: ENA
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Project description:We optimized a workflow combining imaging-based spatial transcriptomics (MERFISH) and immunostaining on ganglion cell layer retinal flatmounts of C57/Bl6J mice.The MERFISH data shows molecularly-defined retinal ganglion cell types types exhibited non-uniform distributions. We also analyzed local neighborhoods for each cell and registered several RGC types as enriched in the perivascular niche.
2025-07-23 | GSE303399 | GEO
Project description:During development of the central nervous system (CNS), cycling uncommitted progenitor cells give rise to a variety of distinct neuronal and glial cell types. As these different cell types are born, they progress from newly specified cells to fully differentiated neurons and glia. In order to define the developmental processes of individual cell types, single cell expression profiling was carried out on developing ganglion and amacrine cells of the murine retina. Individual cells from multiple developmental stages were isolated and profiled on Affymetrix oligonucleotide arrays. These experiments have yielded an expanded view of the processes underway in developing retinal ganglion and amacrine cells, as well as several hundred new marker genes for these cell types. In addition, this study has allowed for the definition of some of the molecular heterogeneity both between developing ganglion and amacrine cells and among subclasses of each cell type. Experiment Overall Design: Single retinal cells were isolated in tubes containing lysis buffer, their mRNAs were reverse transcribed, and the resulting cDNAs were PCR amplified for 35 cycles. Labeled cDNA samples were hybridized to Affymetrix 430 2.0 microarrays and the data was normalized using MAS5.0 software. Cells were identified post hoc as either developing retinal ganglion cells, amacrine cells or rod photoreceptor cells.
2008-06-16 | E-GEOD-9812 | biostudies-arrayexpress
Project description:Cue-directed axon guidance depends partly on local translation in growth cones. Many mRNA transcripts are known to reside in developing axons yet little is known about their subcellular distribution or, specifically, which transcripts are in growth cones. Laser capture microdissection (LCM) was used to isolate the growth cones of retinal ganglion cell (RGC) axons of two vertebrate species, mouse and Xenopus, coupled with unbiased genome-wide microarray profiling. Localized mRNA from the isolated growth cones of Xenopus laevis and Mus musculus retinal ganglion cells were subjected to microarray analysis
2010-11-23 | E-GEOD-25166 | biostudies-arrayexpress
Project description:Demyelination and loss of oligodendrocytes deprives neurons of crucial metabolic and trophic support and contributes to neurodegeneration. However, the precise mechanisms that trigger neurodegeneration during demyelination remain unclear. Here, we examine transcriptional differences in neurons that have been demyelinated relative to myelinated neurons. Demyelination is induced by the knockout of Myrf, a transcription factor essential for myelin gene expression and oligodendrocyte identity, from oligodendrocyte lineage cells using Myrffl/fl Sox10 CreERT mice. We performed laser capture microdissection of the ganglion cell layer, which contains the majority of the retinal ganglion cells (RGC), a nearly ubiquitously myelinated population of neurons. We find that dissection of the ganglion cell layer greatly enriches for RGC transcripts relative to controls. Demyelinated Myrffl/fl Sox10 CreERT mice have upregulation of Hrk and Ecel1 in the ganglion cell layer, which are known to be upregulated during axonal injury and driven by dual leucine zipper kinase (DLK) signaling. These data suggest that demyelination may activate a DLK-mediated signaling cascade that culminates in transcriptional changes that are often associated with apoptosis of neurons in the central nervous system.
2024-09-11 | GSE245362 | GEO
Project description:Epigenetic mark deposition during embryonic development contribute to postnatal homeostasis and tissue stability. Previously, we found out that Ezh2 contributes critically to the function and postnatal cell survival in bipolar cells but not in retinal ganglion cells in the retina. (Yan et al. Postnatal onset of retinal degeneration by loss of embryonic Ezh2 repression of Six1. Sci Report. doi:10.1038/srep33887; (Cheng L, Wong LJ, Yan N, Han RC et al. Ezh2 does not mediate retinal ganglion cell homeostasis or their susceptibility to injury. PLoS One 2018;13(2):e0191853.). In this study, we used RNA-seq to define up- and down regulated genes in both Ezh2 and G9a deficient (Math5Cre; Ezh2f/fG9af/+; dKO) retinal ganglion cells (RGC) to evaluate the hypothesis of Ezh2 and G9a interaction that has been discussed in other tissues but in the retina. ChIP-Seq was applied to evaluate H3K27me3 histone marks in retinal ganglion cells in wild type (WT), Ezh2 (Math5Cre; Ezh2-/-, sKO) and combined G9a-Ezh2 (Math5Cre; G9a+/-Ezh2-/-, dKO) knockout mutant mice at P1.
2022-07-26 | GSE136360 | GEO
Project description:RNA-seq analysis from young and pre-glaucomatous DBA/2J retinal ganglion cells and control (age and sex-matched, D2-Gpnmb+) retinal ganglion cells
2017-03-07 | GSE90654 | GEO
Project description:Identification of genes regulated by ATH5 in a dose-dependent manner.; Identification of retinal ganglion cells (RGC)-specific genes.
2009-01-14 | E-TABM-417 | biostudies-arrayexpress
Project description:The goal of this study was to characterize the transcriptomes of intrinsically-photosenstive retinal ganglion cells that innervate different retinorecipient target regions in the brain
2023-05-01 | GSE224600 | GEO
Project description:This study aimed to characterize the transcriptomes of adult retinal ganglion cells (RGCs). The physiological properties of these cells were characterized first in non-dissociated retinal tissue. With that information recorded, the cells were isolated for transcriptome profiling.
2019-11-01 | GSE115379 | GEO
Project description:Diabetic retinopathy (DR), caused by hypo- and hyperglycemia, is a leading cause of blindness. Hypoglycemia induces endoplasmic reticulum stress and retinal cell death in mice, and low glucose conditions induce macroautophagy/autophagy defects in 661W photoreceptor cells and retinal explants. To further understand the effect of hypoglycemia on the mouse retina, we studied autophagy in vivo. Retinal explants cultured under low glucose conditions exhibited autophagy activation; a similar pattern was observed in the presence of autophagy modulators. Intraocular injection of rapamycin and 5 h hypoglycemia had similar effects, specifically in the ganglion cell layer, as shown by green fluorescence protein (GFP) colocalization with different ganglion cell markers. We then isolated retinal ganglion cells (RGCs) from two mouse lines and cultured them at different glucose concentrations. We also assessed autophagosome/lysosome fusion in C57BL/6 RGCs infected with the RFP-GFP-LC3 lentivirus and cultured under different conditions. p62 protein expression and GFP fluorescence increased when RGCs were cultured with 1 or 25 mM glucose in the presence of rapamycin, whereas no sign of autophagy was detected with 5 or 25 mM glucose alone. The fusion process was defective at 1 and 25 mM glucose in the presence of chloroquine, but normal with 5 and 25 mM glucose alone. This study showed that 5 h hypoglycemia induces autophagosome formation in mouse RGCs; however, a defect in the fusion process inhibits the protective effect of autophagy. Therefore, the modulation of both autophagic and apoptotic pathways might be important to avoid complications associated with DR.
2025-11-27 | GSE292784 | GEO