E-PROT-76
Ontology highlight
ABSTRACT:
PROVIDER: E-PROT-76 | ExpressionAtlas | 2022-01-14
REPOSITORIES: ExpressionAtlas
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Project description:Diverse groups of proteins play integral roles in both the physiology and pathophysiology of the mouse retina. A comprehensive mouse retina proteome has been developed using a discovery-based proteomic approach.
2019-02-16 | PXD009909 | Pride
Project description:A comprehensive mouse retina proteome including six development stages (E13.5, E15.5, P0, P6, and P21, mixed sample).
2021-07-11 | PXD023439 | Pride
Project description:Diverse groups of proteins play integral roles in both the physiology and pathophysiology of the mouse retina. A comprehensive mouse retina phosphoproteome has been developed using a discovery-based proteomic approach in conjunction with an enrichment procedure for phosphopeptides.
2019-02-16 | PXD009981 | Pride
Project description:A comparative analysis of the proteome of mouse retina with and without ischemic injury and hypoxia conditioning was achieved through discovery-based quantitative proteomics. Retina from each mouse were harvested immediately for Quantitative Discovery-Based Proteomic Workflow. A 10plex TMT experiment was performed comparing each condition of retina proteomes.
2021-09-08 | PXD014769 | Pride
Project description:There is a growing need to better characterise senescent cells in the CNS and retina. The recently published SenMayo gene panel was developed to identify transcriptomic signatures of senescence across multiple organ systems, but the retina was not included. While other approaches have identified senescent signatures in the retina, these have largely focused on experimental models in young animals. We therefore conducted a detailed single-cell RNA-seq analysis to identify senescent cell populations in the retina of different aged mice and compared these with five comprehensive human and mouse retina and brain transcriptome datasets. Transcriptomic signatures of senescence were most apparent in mouse and human retinal glial cells, with IL4, 13 and 10 and the AP1 pathway being the most prominent markers involved. Similar levels of transcriptional senescence were observed in the retinal glia of young and old mice, whereas the human retina showed significantly increased enrichment scores with advancing age.
2024-12-06 | GSE268463 | GEO
Project description:To enrich mouse rod and cone photoreceptors for mass spectrometric analysis, we optimized our previously established trituration-based fluorescence-activated cell sorting (FACS) strategy (see Lux et al., 2024 for details; PMID: 38481472). For quantitative mass spectrometry, we utilized an ion mobility-enhanced version of a data-independent acquisition (DIA) workflow with alternating low and elevated energy (referred to as UDMSE). Label-free protein quantification of rod and cone photoreceptor in comparison with retina samples revealed an enrichment of photoreceptor-specific proteins. More importantly, established photoreceptor markers were significantly enriched in the respective photoreceptor samples, which confirms the quality and specificity of our proteome resource. Among the proteins highly enriched in the cone photoreceptor samples, we identified Mpp6/Pals2, a protein uncharacterized in photoreceptors so far, and established it as a novel pan-cone photoreceptor marker by immunocytochemistry. As an example of the use of our resource for the characterization of retina- and photoreceptor-specific protein isoforms, we assessed the expression of the two known isoforms of Mpp6/Pals2, the canonical Pals2β and the 14 aa shorter splice variant Pals2α. We confidently identified a tryptic peptide that only occurs upon splicing, indicating the expression of the non-canonical Pals2α in cone photoreceptors. In summary, our proteome resource provides comprehensive details on the protein (isoform) composition of mouse rod and cone photoreceptors, making it a valuable research tool for the study of retina biology and pathology.
2025-12-08 | PXD066755 | Pride
Project description:Otx2 has been shown to be non cell autonomously required for photoreceptor cell survival in the adult mouse RPE. This study aims to identify Otx2 DNA binding profile in both RPE and neural retina to i) identify direct targets of Otx2 in the RPE ii) compare Otx2 binding profile in neural retina and RPE to unveil hidden functions in the neural retina. WT and GFP antibodies were used to perform two independent ChIP-seq experiments using Illumina GAIIx.
2014-01-15 | E-GEOD-54084 | 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:Control of neural organogenesis is a complex process and the epigenetic contribution is largely unknown. Here we have followed the genome-wide distribution of two important histone H3 modifications, H3K4me2 and H3K27me3 during late mouse retina development. We found that genes expressed only in mature rod photoreceptors, have a unique signature consisting of de-novo accumulation of H3K4me2 both at the transcription start site (TSS) and over the whole gene that correlates with the increase in transcription, but no accumulation of H3K27me3 at any stage. We also found that distribution of H3K4me2 and H3K27me3 on the genes widely expressed is not always associated with their transcriptional levels. Genes without H3K4me2 and H3K27me3 accumulation at any stage represent a group of transcripts never expressed in retina. The epigenetic signatures defined by H3K4me2 and H3K27me3 can distinguish cell-type specific genes from widespread transcripts and may be reflective of cell specificity during retina maturation. Examination of 2 different histone modifications during late mouse retina development.
2012-12-13 | E-GEOD-38500 | biostudies-arrayexpress
Project description:Mouse retina m6A epitranscriptome
| PRJNA749619 | ENA