GEO DataSets

(Submitter supplied) Photoreceptor cell death is a major cause of incurable vision loss in retinal degeneration, with little to no treatment options available. To identify drug candidates to maintain photoreceptor survival, we performed an unbiased high-throughput screening of over 6,000 bioactive small molecules using retinal organoids differentiated from induced pluripotent stem cells of rd16 mice, which phenocopy Leber congenital amaurosis (LCA) 10 caused by CEP290 mutations. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

12 Samples

Download data: TSV

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL16791 GPL24676

43 Samples

Download data: H5

(Submitter supplied) Mutations in the cone-rod homeobox (CRX) transcription factor lead to distinct retinopathy phenotypes, including early-onset vision impairment in dominant Leber congenital amaurosis (LCA). Using induced pluripotent stem cells (iPSCs) from a patient with CRX-I138fs mutation, we established an in vitro model of CRX-LCA in retinal organoids that exhibit defective photoreceptor maturation by histology and gene profiling including diminished expression of visual opsins. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

5 Samples

Download data: H5

(Submitter supplied) Mutations in the cone-rod homeobox (CRX) transcription factor lead to distinct retinopathy phenotypes, including early-onset vision impairment in dominant Leber congenital amaurosis (LCA). Using induced pluripotent stem cells (iPSCs) from a patient with CRX-I138fs mutation, we established an in vitro model of CRX-LCA in retinal organoids that exhibit defective photoreceptor maturation by histology and gene profiling including diminished expression of visual opsins. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

38 Samples

Download data: TXT

(Submitter supplied) We generated iPSCs from control and ciliopathy cases and differentiated them into polarized 3D-adherent retinal sheets that could recapitulate normal photoreceptor development and disease state, respectively.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17303

14 Samples

Download data: TXT

(Submitter supplied) This experiment aimed to characterise the complete transcriptional profile of 661W cells to identify their origin as cone photoreceptor cells. Cells were either grown in complete media or subjected to 72 hours of serum starvation to encourage differentiation.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

6 Samples

Download data: XLSX

(Submitter supplied) In this study, we generated three-dimensional (3D) retinal organoids (ROs) from induced pluripotent stem cells (iPSCs) derived from an LCA4 patient carrying a Cys89Arg mutation in AIPL1. This study aimed to (i) explore whether the patient iPSC-derived ROs recapitulate LCA4 disease phenotype, and (ii) generate a clinically relevant resource to investigate the molecular mechanism of disease and safely test novel therapies for LCA4 in vitro.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

30 Samples

Download data: TXT, XLSX

(Submitter supplied) Death of photoreceptors and/or Retinal Pigment Epithelium (RPE) cells is a common cause of age related and inherited retinal dystrophies, thus their replenishment from renewable stem cell sources is a well sought therapeutic goal. Human pluripotent stem cells provide a useful cell source in view of their limitless self-renewal capacity and potential to differentiate into all key retinal cell types either in isolation or as part of three dimensional retinal organoids. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

96 Samples

Download data: TXT

(Submitter supplied) This study provides analysis of developing mouse retina organoids derived from induced pluripotent stem cells . RNA-seq profiling was performed on 2 time points during retinal organoids supplemented with docosahexaenoic acid (DHA), linoleic acid (LA), and/or FGF1. Alignment, transcript and gene quantitation, and normalization was performed.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

23 Samples

Download data: TSV

(Submitter supplied) Age-related macular degeneration (AMD) is a complex multifactorial disease with at least 34 loci contributing to genetic susceptibility. To gain functional understanding of AMD genetics, we generated transcriptional profiles of retina from 453 individuals including both controls and cases at distinct stages of AMD. We integrated retinal transcriptomes, covering 13,662 protein-coding and 1,462 noncoding genes, with genotypes at over 9 million common single nucleotide polymorphisms (SNPs) for expression quantitative trait loci (eQTL) analysis of a tissue not included in Genotype-Tissue Expression (GTEx) and other large datasets. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

523 Samples

Download data: TSV, TXT

(Submitter supplied) Clinical and genetic heterogeneity associated with retinal diseases makes stem cell-based therapies an attractive strategy for personalized medicine. However, we have limited understanding of the timing of key events in the developing human retina, and in particular the factors critical for generating the unique architecture of the fovea and surrounding macula. Here we define three key epochs in the transcriptome dynamics of human retina from fetal day (D) 52 to 150. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

25 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL17021 GPL11002

54 Samples

Download data

(Submitter supplied) This study provides analysis of developing mouse retina organoids derived from induced pluripotent stem cells . RNA-seq profiling was performed on 10 time points during retinal organoid development. Alignment, transcript and gene quantitation, and normalization was performed.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

30 Samples

Download data: TXT

(Submitter supplied) 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.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11002

24 Samples

Download data: TXT

(Submitter supplied) Mutations in RP2 lead to a severe form of X-linked retinitis pigmentosa (XLRP). RP2 functions as a GTPase activating protein (GAP) for the small GTPase ARL3, which is essential for cilia function and for photoreceptor development and maintenance. The mechanisms of RP2 associated retinal degeneration in humans are poorly understood, and genetically engineered animal models of RP2 XLRP present with differing retinal phenotypes and slow degeneration suggesting potential species differences. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

8 Samples

Download data: TXT

(Submitter supplied) To comprehensively capture changes in retinal transcriptome for the LCA7 organoids compared to control, we performed single cell RNA-sequencing (scRNAseq) using the 10X Genomics platform. Retinal organoids at D150 of differentiation were dissociated for scRNAseq analysis. scRNAseq data revealed significant dysregulation of specific photoreceptor genes between control and LCA7 organoids, as well as mutation-specific differences in various genes, including CRX, RCVRN, ARR3, and AIPL1.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

3 Samples

Download data: TAR

(Submitter supplied) Drug toxicity screening on retina is essential for the development of safe therapies for a large number of diseases, whilst preserving visual acuity and function. To this end, retinal organoids derived from human pluripotent stem cells (hPSCs) provide a suitable screening platform due to their similarity to human retina and the ease of generation in large-scale formats, offering almost unlimited excess of tissue. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

7 Samples

Download data: TXT

(Submitter supplied) mRNA transcript levels in embryonic day 15.5 (E15.5), E17.5 and postnatal day 1 (P1) mouse Crb1KOCrb2ΔRPC against mouse Crb1KO neuroretina (Run1), and in E15.5 mouse Crb1KOCrb2ΔRPC against wild type neuroretina (Run2) were analyzed. A comparison between Crb1KOCrb2ΔRPC and Crb1KO retina, at E15.5, or E17.5, or P1 on 100% C57BL/6JOlaHsd, yielded only subtle persistent changes at the transcriptional level over time (Figure 1 G-I, respectively), despite significant differences in morphology. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16790

48 Samples

Download data: TXT

(Submitter supplied) Mutations in CEP290, a large multidomain coiled coil protein, are associated with multiple cilia-associated syndromes. Over 130 CEP290 mutations have been linked to a wide spectrum of human ciliopathies, raising the question of how mutations in a single gene cause different disease syndromes. In zebrafish the expressivity of cep290 deficiencies were linked to the type of genetic ablation: acute cep290 morpholino knockdown caused severe cilia-related phenotypes while defects in a Crispr/Cas9 genetic mutant were restricted to photoreceptor defects. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14875

9 Samples

Download data: TXT, XLSX

(Submitter supplied) Subretinal transplantation of human retinal organoid-derived cells can potentially restore vision lost in photoreceptor dystrophies. Prior studies analyzed the maturation, integration, and function of transplanted organoid cells in the subretinal region, but detailed molecular analysis of transplanted photoreceptor and of cells that migrate to other retinal layers has not been conducted. Here, we characterized migratory and non-migratory organoid-derived cells following subretinal transplantation into a dystrophic host. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

5 Samples

Download data: CSV