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E-MTAB-1430

ABSTRACT: Transcription profiling by array of embryonic chick retina treated with HES5.3 siRNAs, Atoh siRNAs and nt siRNAs

PROVIDER: E-MTAB-1430 | ExpressionAtlas | 2015-10-23

REPOSITORIES: ExpressionAtlas

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Dataset's files

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			Action	DRS
	E-MTAB-1430-analysis-methods.tsv	Tabular
	E-MTAB-1430-atlasExperimentSummary.Rdata	Rdata
	E-MTAB-1430-configuration.xml	Xml
	E-MTAB-1430-percentile-ranks.tsv	Tabular
	E-MTAB-1430.condensed-sdrf.tsv	Tabular

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Transcription profiling by array of embryonic chick retina treated with Hes5.3 siRNAs, Atoh7 siRNAs and non-targeting siRNAs.

Project description:Transcription profiling by array of embryonic chick retina treated with Hes5.3 siRNAs, Atoh7 siRNAs and non-targeting siRNAs.

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[E-MTAB-366] Transcription profiling by array of chicken embryos at 15 different stages

Project description:Transcription profiling of chicken development The experiment were perfomed as a part of our Vertebrate Evo-Devo project. The aim of the project is to compare transcription profiles of normal (unmanipulated, wild-type, whole embryo) vertebrate embryos. Total RNA was collected from wild type G.gallus whole embryos at 15 different stages (Stages:HH1,2,4,6,8,9,11,14,16,19,24,27,32,34,38), and hybridized to the Affymetrix Chicken Genome Array. All the stages contains data from two biological replications. Each staged-samples consists of pooled total RNA from several whole embryos.

2011-04-05 | E-GEOD-28388 | biostudies-arrayexpress

Proteomic profiling of embryonic retina to facilitate ocular disease gene discovery

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

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Project description:Mouse liver transcription profiling by array

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Developmental Transcriptome Dynamics of the Murine Retina

Project description:This study provides a comprehensive transcript analysis of the developing mouse retina with a focus on normalization, differentially expression, cell-type specific gene expression, transcription factor co-expression, alternative splicing, and novel transcript discovery. RNA-seq profiling was performed on four embryonic and eight postnatal time points during mouse retinal development and maturation. Alignment, transcript quantitation, normalization and differential expression, alternative splice usage, and novel transcript discovery was performed. Quantitative analysis revealed that 25,901 total transcripts encoding for 13,714 genes were expressed in the mouse retina between embryonic day 11 and postnatal day 28. Of these expressed transcripts, 12,075 were significantly differentially expressed (10,069 genes) at some point during development corresponding to ~73% of the expressed genes.

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17β-Estradiol Delivered in Eye Drops: A Proteomics Study Focusing on the Rat Retina

Project description:Five ovariectomized (OVX) Brown Norway rats (Charles Rivers Laboratories, Wilmington, DE, USA) weighing 200-250 g received 10 µL of 17β-estradiol (E2) eye drops once daily in both eyes for three weeks [20]. The eye drops contained 0.1% (w/v) E2 in saline vehicle containing 20% (w/v) 2-hydroxypropyl-β-cyclodextrin. Five OVX control rats received 10 µL of this vehicle as eye drops for the same dosing regimen and duration. After 24 h of the last treatment, the animals were euthanized by CO2 overexposure, and their eyes were immediately enucleated followed by the isolation of the retina. The tissue samples were rinsed with saline and, then, blotted dry for preparation to label-free shotgun proteomic analyses. All procedures involving animals were reviewed and approved by the Institutional Animal Care and Use Committee at the University of North Texas Health Science Center before the initiation of the studies (approval number: 2018-0028). Directions to sample names CF1: Control (female) retina sample #1 CF2: Control (female) retina sample #2 CF3: Control (female) retina sample #3 CF4: Control (female) retina sample #4 CF5: Control (female) retina sample #5 EF1: E2-treated (female) retina sample #1 EF2: E2-treated (female) retina sample #2 EF3: E2-treated (female) retina sample #3 EF4: E2-treated (female) retina sample #4 EF5: E2-treated (female) retina sample #5

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Ciliary neurotrophic factor induces genes associated with inflammatory response and gliosis in the retina: A gene profiling study of flow-sorted, Muller (glial) cells

Project description:Our data suggest that CNTF remodels the transcription profile of Muller (glial) cells leading to induction of networks associated with transcription, cell cycle regulation and inflammatory response. CNTF also appears to function as an inducer of gliosis in the retina. These studies provide new insights into the biological functions of cytokines in the retina. Muller glial cells treated with CNTF for 1 and 3 days

2011-08-31 | E-GEOD-27195 | biostudies-arrayexpress

Gene specific signatures by H3K4me2 and H3K27me3 modifications during retina maturation

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.

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[E-MTAB-368] Transcription profiling by array of mouse embryos at 8 different stages

Project description:Transcription profiling of mouse development The experiment were perfomed as a part of our Vertebrate Evo-Devo project. The aim of the project is to compare transcription profiles of normal (unmanipulated, wild-type, whole embryo) vertebrate embryos.

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