GEO DataSets

(Submitter supplied) The development of single-cell RNA-Sequencing (scRNA-Seq) has allowed high resolution analysis of cell type diversity and transcriptional networks controlling cell fate specification. To identify the transcriptional networks governing human retinal development, we performed scRNA-Seq over retinal organoid and in vivo retinal development, across 20 timepoints. Using both pseudotemporal and cross-species analyses, we examined the conservation of gene expression across retinal progenitor maturation and specification of all seven major retinal cell types. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

2 Samples

Download data: MTX, TSV

(Submitter supplied) Time-series of single-cell RNA-sequencing performed on stem cell derived retinal organoids or post-mortem tissue from the developing and adult retina

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

12 Samples

Download data: CSV, MTX

(Submitter supplied) The development of single-cell RNA-Sequencing (scRNA-Seq) has allowed high resolution analysis of cell type diversity and transcriptional networks controlling cell fate specification. To identify the transcriptional networks governing human retinal development, we performed scRNA-Seq over retinal organoid and in vivo retinal development, across 20 timepoints. Using both pseudotemporal and cross-species analyses, we examined the conservation of gene expression across retinal progenitor maturation and specification of all seven major retinal cell types. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

10 Samples

Download data: MTX, TSV

(Submitter supplied) Cis-regulatory elements (CREs) play a critical role in the development, maintenance, and disease-states of all human cell types. In the human retina, CREs have been implicated in a variety of inherited retinal disorders. To characterize cell-class-specific CREs in the human retina and elucidate their potential functions in development and disease, we performed single-nucleus (sn)ATAC-seq and snRNA-seq on the developing and adult human retina and on human retinal organoids. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platform:

GPL24676

51 Samples

Download data: MTX, TSV

(Submitter supplied) Gene regulatory networks (GRNs), consisting of transcription factors and their target cis-regulatory sequences, control neurogenesis and cell fate specification in the developing central nervous system, but their organization is poorly characterized. In this study, we performed integrated scRNA-seq and scATAC-seq analysis from both mouse and human retina to profile dynamic changes in gene expression, chromatin accessibility and transcription factor footprinting during retinal neurogenesis and gliogenesis. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platform:

GPL19057

38 Samples

Download data: MTX, TXT

(Submitter supplied) Application of single-cell sequencing C1 to obtain neural retinal transcriptomes.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

800 Samples

Download data: CSV

(Submitter supplied) Application of single-cell sequencing technology "10X" to obtain neural retinal transcriptomes. This resource highlight transcriptional sequences that establish the hierarchical ordering of early cell fate specification in the retina.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

2 Samples

Download data: CSV

(Submitter supplied) Background: The vertebrate retina consists of six major classes of neuronal cells. During development, these cells are generated from a pool of multipotent retinal progenitor cells (RPCs) that express the gene Vsx2. Fate-restricted RPCs have recently been identified, with limited mitotic potential and cell fate possibilities compared to multipotent RPCs. One population of fate-restricted RPCs, marked by activity of the regulatory element ThrbCRM1, gives rise to both cone photoreceptors and horizontal cells. more...

Organism:

Gallus gallus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19005

2 Samples

Download data: BIGWIG

(Submitter supplied) Single cell RNA sequencing using either an adapted Smart-seq2 protocol on Chx10-GFP (+) retinal progenitor cells; 10x Genomics Chromium Single Cell system across 10 timepoints of mouse retinal development to examine retinal progenitor cell heterogeneity across retinal development and global changes in gene expression from early retinal neuroepithelial cells through specification and differentiation of retinal cell types; 10X Genomics Chromium Single Cell on P14 Nfia/b/x het control or Nfia/b/x tCKO (Chx10-Cre-GFP) retinas

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

882 Samples

Download data: MTX, TSV

(Submitter supplied) While dysfunction and/or death of light-detecting photoreceptor cells underlies most inherited retinal dystrophies, knowledge of the species-specific details of human rod and cone photoreceptor cell development remains limited. Here, we generate retinal organoids using induced pluripotent stem cells (iPSC) derived from a patient with genetic photoreceptor disease, an isogenic control, and an unrelated control. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL24676

29 Samples

Download data: CSV

(Submitter supplied) We used single-cell RNA-sequencing (scRNA-seq) on human embryonic stem cell (hESC)-derived retinal organoid to deconstruct RPC developmental trajectory in the early retinogenesis, which revealed the fate branchpoint in RPC progression.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

451 Samples

Download data: TXT

(Submitter supplied) The rapid improvements in single cell sequencing technologies and analyses methods afford greater scope for dissecting organoid cultures composed of multiple cell types and create an opportunity to interrogate these models to understand tissue biology, cellular behaviour and interactions. To this end, retinal organoids generated from human embryonic stem cells (hESCs) were analysed by single cell RNA-Sequencing at three time points of differentiation. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

79 Samples

Download data: CSV

(Submitter supplied) Transcription factors have been implicated in the specification and differentiation of all cells in the mammalian retina with several transcription factors controlling the development of multiple neuronal subclasses. Horizontal cells and cone photoreceptors share a particularly intimate functional relationship but have been previously thought to develop through separate and distinct intrinsic molecular processes. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6096

6 Samples

Download data: CEL, CHP

(Submitter supplied) To generate an unbiased view of changes to the retinal gene network in Neurog2 retinal mutants, we generated and compared the P2 transcriptomes from control, heterozygote and mutant mice. A pair of P2 retinas from each biologic replicate were used to produce libraries for high throughput sequencing (n = 5 biologic replicates/genotype). Reads were aligned with BWA and Bowtie programs to the mm10 genome. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

15 Samples

Download data: XLSX

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

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

11 Samples

Download data

(Submitter supplied) Here we perform massively parallel single-cell RNA sequencing (scRNA-seq) of human retinas using two independent platforms, and report the single-cell transcriptomic atlas of the human retina. Using a multi-resolution network-based analysis, we identify all major retinal cell types, and their corresponding gene expression signatures. 

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

5 Samples

Download data: MTX, TXT

(Submitter supplied) Here we perform massively parallel single-cell RNA sequencing (scRNA-seq) of human retinas using two independent platforms, and report the single-cell transcriptomic atlas of the human retina. Using a multi-resolution network-based analysis, we identify all major retinal cell types, and their corresponding gene expression signatures. 

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

6 Samples

Download data: MTX, TSV, TXT

(Submitter supplied) Single cell transcriptomics reveals lineage trajectory of the retinal ganglion cells in wild-type and Atoh7-null retinas

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

7 Samples

Download data: H5, TXT

(Submitter supplied) Here we report a transcriptomic analysis of fate-restricted progenitor cells biased to produce cone photoreceptors and horizontal cells, marked by the THRB cis-regulatory element ThrbCRM1. Comparison to a control population enriched in multipotent progenitor cells identified several genes considered to be pan-progenitor, such as VSX2, LHX2, and PAX6, as downregulated in these fate-restricted retinal progenitor cells

Organism:

Gallus gallus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16133

4 Samples

Download data: TSV, XLSX

(Submitter supplied) How the diverse neural cell types emerge from multipotent neural progenitor cells during central nervous system development remains poorly understood. Recent scRNA-seq studies have delineated the developmental trajectories of individual neural cell types in many neural systems including the neural retina. Further understanding of the formation of neural cell diversity requires knowledge about how the epigenetic landscape shifts along individual cell lineages and how key transcription factors regulate these changes. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24247

25 Samples

Download data: H5, NARROWPEAK, TSV