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Characterization of an Eye Field-like State during Optic Vesicle Organoid Development [ATAC-seq]

ABSTRACT: Characterization of an Eye Field-like State during Optic Vesicle Organoid Development [ATAC-seq]

PROVIDER: PRJNA880307 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR21551685_1.fastq.gz	Fastqsanger.gz
	SRR21551685_2.fastq.gz	Fastqsanger.gz
	SRR21551686_1.fastq.gz	Fastqsanger.gz
	SRR21551686_2.fastq.gz	Fastqsanger.gz
	SRR21551687_1.fastq.gz	Fastqsanger.gz

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Characterization of an Eye Field-like State during Optic Vesicle Organoid Development

Project description:Characterization of an Eye Field-like State during Optic Vesicle Organoid Development

| PRJNA880304 | ENA

Characterization of an Eye Field-like State during Optic Vesicle Organoid Development [RNA-seq]

Project description:Specification of the eye field (EF) within the neural plate marks the earliest detectable stage of eye development. Experimental evidence, primarily from non-mammalian model systems, indicates that the stable formation of this group of cells requires the activation of a set of key transcription factors (TFs). This critical event is challenging to probe in mammals and, quantitatively, little is known regarding the regulation of the transition of cells to this ocular fate. Using optic vesicle organoids to model the onset of the EF, we generate timecourse transcriptomic data allowing us to identify dynamic gene-expression programs that characterise this cellular-state transition. Integrating this with chromatin accessibility data suggests a direct role of canonical EFTFs in regulating these gene-expression changes, and highlights candidate cis-regulatory elements through which these TFs act. Finally, we begin to test a subset of these candidate enhancer elements, within the organoid system, by perturbing the underlying DNA sequence and measuring transcriptomic changes during EF activation.

2023-07-06 | GSE213272 | GEO

Characterization of an Eye Field-like State during Optic Vesicle Organoid Development [ATAC-seq]

2023-07-06 | GSE213271 | GEO

Characterization of an Eye Field-like State during Optic Vesicle Organoid Development [RNA-seq]

Project description:Characterization of an Eye Field-like State during Optic Vesicle Organoid Development [RNA-seq]

| PRJNA880309 | ENA

Single-cell transcriptional analysis reveals developmental stage-dependent changes in retinal progenitors in the murine early optic vesicle

Project description:The optic vesicle in the developing embryonic eye contains a multitude of neuroepithelial progenitors that subsequently differentiate into functionally distinct domains of the optic cup, such as the neural retina, pigment epithelium, and optic stalk. To investigate cell-type diversity across early optic vesicles before regionalization of the optic cup, we performed single-cell RNA-sequencing (scRNA-seq) using 7,989 cells from the presumptive eye area in mouse embryos at the 12–26-somite stages at five developmental time points. We demonstrated the presence of seven optic vesicle populations, including three unique cell types located in the ventricular surface or dorsoventral areas of the optic vesicle structure. Moreover, the remaining four populations of retinal progenitor cells could be classified according to their stage-dependent time point, and these cells exhibited altered expression of several structural and metabolic key genes, such as Col9a1 and Ckb, just before regionalization of the optic cup. From these data, we provide the first report on stage-dependent transcriptional profiles during initial retinal specification at single-cell resolution and highlight the unexpected developmental heterogeneity of the murine optic vesicle structure.

2021-02-08 | GSE148063 | GEO

Whole transcriptomic sequencing of zebrafish rx3 mutants during optic vesicle morphogenesis

Project description:To identify genes regulated by Rx3 during optic vesicle morphogenesis, adult zebrafish carriers of a null rx3 mutation were mated. Before 13 hours post fertilization (hpf), the earliest time point at which optic vesicle evagination phenotypes could be reliably detected, offspring were phenotypically separated into pools comprising of mutants with an absence of optic vesicles or siblings exhibiting a wild-type phenotype. Three replicates of pooled RNA samples from 13 hpf eyeless mutants (rx3-/-) or phenotypically wild-type siblings (rx3+/+ or rx3+/-), and one replicate of 13 hpf wild-type zebrafish larva were collected for whole transcriptome sequencing. Whole transcriptome sequencing (RNA-seq) was performed on zebrafish rx3-/- mutants, wild-type siblings and wild-type AB strains at 13 hpf

2014-09-30 | E-GEOD-52652 | biostudies-arrayexpress

Characterization of an Eye Field-like State during Optic Vesicle Organoid Development

Project description:This SuperSeries is composed of the SubSeries listed below.

2023-07-06 | GSE213273 | GEO

Gene expression after deletion of Bmp4 in the mouse optic vesicle

Project description:Bmp4 was conditionally deleted from the mouse optic vesicle with Rx-Cre. The heads of wild type and knockout E10.5 mouse embryos were laser micodissected to isolate the lens ectoderm and prospective retina from three embryos of each genotype. Total RNA was purified and reverse transcribed and amplified using a NuGEN Ovation Pico WTA system V2 kit. cDNA was biotinylated and hybridized to Illumina Mouse6 V2 bead arrays. Three wild type and three knockout embryos were used. RNA obtained from the lens ectoderm or prospective retina (distal optic vesicle) was pooled, amplified and used for microarray analysis. Statistical analysis was performed using the values from the 25-50 beads on each array.

2015-02-20 | E-GEOD-62536 | biostudies-arrayexpress

Whole transcriptomic sequencing of zebrafish rx3 mutants during optic vesicle morphogenesis

2014-09-30 | GSE52652 | GEO

Eye development in mouse and rat

Project description:In this series the ocular primordium was microdissected from normal CD-1 (outbred) mouse embryos harvested days 8-10 post-coitus, corresponding to human development during the 3rd-4th weeks post-fertilization. The precise embryological age was ascertained by counting somite pairs to an accuracy of +/- 2 pairs per litter. Samples were pooled as follows: optic pit pooled from 48-50 embryos (6 litters) on 8 d.p.c. (4-8 somite pairs), optic vesicle pooled from 36-40 embryos (5 litters) on 9 d.p.c. (16-20 somite pairs), and optic cip pooled from 27-30 embryos (3 litters) on 10 d.p.c. (28-32 somite pairs). The common reference for this series was RNA collected from embryonic headfold microdissected on 8 d.p.c. RNA samples were collected from CD-1 rat embryos at equivalent somite stages for the headfold, optic vesicle, and opic cup. Keywords = embryo Keywords = eye development Keywords = mouse Keywords = rat

2010-06-09 | E-GEOD-1082 | biostudies-arrayexpress

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