Unifying Developmental Programs for Embryonic and Post-Embryonic Neurogenesis in the Zebrafish Retina
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ABSTRACT:
PROVIDER: PRJNA506002 | ENA |
REPOSITORIES: ENA
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Project description:It provides an opportunity to make the first comparative study of molecular programs used by embryonic and post-embryonic neurogenic programs in the vertebrate retina.
2020-05-19 | GSE122680 | GEO
Project description:Here, we apply differential transcriptome analysis on microscopically isolated cell populations, to define five transcriptional programs that represent each transient embryonic zone and the progression between these zones. The five transcriptional programs contain largely uncharacterized genes in addition to transcripts necessary for stem cell maintenance, neurogenesis, migration, and differentiation. Additionally, we found intergenic transcriptionally active regions that possibly encode novel zone-specific transcripts. Finally, we present a high-resolution transcriptome map of transient zones in the embryonic mouse forebrain. mRNAseq performed after laser microdissection of cells from transient embryonic zones in the mouse cortex
2011-08-22 | E-GEOD-30765 | biostudies-arrayexpress
Project description:To expedite gene discovery in eye development and its associated defects, we previously developed a bioinformatics resource-tool iSyTE (integrated Systems Tool for Eye gene discovery). However, iSyTE is presently limited to lens tissue and is predominantly based on transcriptomics datasets. Therefore, to extend the iSyTE approach to retina development on the proteome level, we performed high-throughput tandem mass spectrometry (MS/MS) on mouse embryonic day (E)14.5 retina and identified an average of 3,300 proteins per sample (n=5). High-throughput expression profiling-based gene discovery approaches–involving either transcriptomics or proteomics–pose a key challenge of prioritizing select candidates from thousands of RNA/proteins expressed in a particular cell/tissue type. To address this, we used MS/MS proteome data from mouse whole embryonic body (WB) as a reference dataset and performed comparative analysis–termed “in silico WB-subtraction”–with the retina proteome dataset. In silico WB-subtraction identified 90 high-priority proteins with retina-enriched expression at stringency criteria of 2.5 average spectral counts, 2.0 fold-enrichment, False Discovery Rate <0.01. These top candidates represent a pool of retina-enriched proteins, several of which are associated with retinal biology and/or defects (e.g., Aldh1a1, Ank2, Ank3, Dcn, Dync2h1, Egfr, Ephb2, Fbln5, Fbn2, Hras, Igf2bp1, Msi1, Rbp1, Rlbp1, Tenm3, Yap1, etc.), indicating the effectiveness of this approach. Importantly, in silico WB-subtraction also identified several new high-priority candidates with potential regulatory function in retina development. Finally, proteins exhibiting expression or enriched-expression in the retina are made accessible in a user-friendly manner at iSyTE (https://research.bioinformatics.udel.edu/iSyTE/), to allow effective visualization of this information by the research community to facilitate eye gene discovery.
2023-10-09 | PXD039490 | Pride
Project description:Regeneration of neurons has enormous implications for human health and is a topic of interest both from the biological and translational perspective. The retina poses an excellent system to study the potential of replacing neurons following injury and the impact different lesions can have on this process. We have established mouse models where proneural transcription factors are expressed in Müller glia to stimulate neurogenesis, which is analogous to how zebrafish regenerate the retina after injury. Our previous studies have shown that Müller glia overexpressing either Ascl1 or Ascl1-Atoh1 will respond to inner retinal damage, caused by a neurotoxic dose of NMDA, by acquiring a progenitor-like state and giving rise to bipolar cells or retinal ganglion-like cells, respectively. It was not known however whether neurogenesis would still occur if the retina suffered outer retinal injury and if the timing of injury relative to the expression of proneural factors was critical for the process. To address these questions, we explored whether timing or mode of injury affect the induced neurogenesis from MG. We show that reprogramming MG with Ascl1 is not impacted by the mode or timing of injury, since all paradigms resulted in similar ratios of new bipolar neurons. By contrast, MG that express Ascl1-Atoh1 respond to outer retinal damage by producing a new type of retinal ganglion-like cell that is not generated after NMDA injury. Therefore, although the fate of reprogrammed neurons is mostly dictated by the proneural transcription factors, there is a context-dependent effect of the injured retinal microenvironment.
2023-12-13 | GSE250019 | GEO
Project description:Regulation of embryonic and adult neurogenesis by Ars2
| PRJNA553785 | ENA
Project description:Here, we apply differential transcriptome analysis on microscopically isolated cell populations, to define five transcriptional programs that represent each transient embryonic zone and the progression between these zones. The five transcriptional programs contain largely uncharacterized genes in addition to transcripts necessary for stem cell maintenance, neurogenesis, migration, and differentiation. Additionally, we found intergenic transcriptionally active regions that possibly encode novel zone-specific transcripts. Finally, we present a high-resolution transcriptome map of transient zones in the embryonic mouse forebrain.
2011-08-22 | GSE30765 | GEO
Project description:The relative contribution of extrinsic and intrinsic mechanisms to cortical development is an intensely debated issue and an outstanding question in neurobiology. Currently, the emerging view is that interplay between intrinsic genetic mechanisms and extrinsic information shape different stages of cortical development. Yet, whereas the intrinsic program of early neocortical developmental events has been at least in part decoded, the exact nature and impact of extrinsic signaling are still elusive and controversial. We found that in the mouse developing visual system, acute pharmacological inhibition of spontaneous retinal activity (retinal waves-RWs) during embryonic stages increase the rate of corticogenesis (cell cycle withdrawal). Furthermore, early perturbation of retinal spontaneous activity leads to changes of cortical layer structure at a later time point. These data suggest that mouse embryonic retina delivers long-distance information capable of modulating cell genesis in the developing visual cortex and that spontaneous activity is the candidate long-distance acting extrinsic cue mediating this process. In addition, these data may support spontaneous activity to be a general signal coordinating neurogenesis in other developing sensory pathways or areas of the central nervous system.
| S-EPMC2999540 | biostudies-other
Project description:The microarray analysis was designed to test the effects of HES5.3 siRNAs, Atoh7 siRNAs and nt siRNAs on gene expression in embryonic chick retina.
2013-03-01 | E-MTAB-1430 | biostudies-arrayexpress
Project description:Subcellular RNA localization during Drosophila embryonic neurogenesis [fractionation-Seq]
| PRJNA415601 | ENA
Project description:To identify epigenetic programs underlying differentiation of mouse retina, we performed ATAC-Seq on bulk native retina (NaR) and iPSC-derived 3D retinal aggregates (3D-RA) at three matched stages of development: embryonic day (E)13 vs differentiation day (DD)13, postnatal day (P)0 vs DD21, and P5 vs DD25. We produced a total of 24 ATAC-seq libraries with two technical replicates (using either 1 ul or 2 ul of TDE1 enzyme) of two biological replicates, and two genomic DNA libraries to use for background controls.
2021-06-30 | E-MTAB-9440 | biostudies-arrayexpress