Gene Expression
Nebulas
Gene Expression NebulasSummary: 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. Furthermore, we examined gene expression differences between developing macula and periphery and between two distinct populations of horizontal cells. We also identify both shared and species-specific patterns of gene expression during human and mouse retinal development. Finally, we identify an unexpected role for ATOH7 expression in regulation of photoreceptor specification during late retinogenesis. These results provide a roadmap to future studies of human retinal development, and may help guide the design of cell-based therapies for treating retinal dystrophies.
Overall Design: More than 45000 single cells from the developing human retina, ranging from gestational weeks (GW)12-27, and postnatal retina on day 8 were analyzed via single cell RNA-sequencing.
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| Growth Protocol: | - |
| Treatment Protocol: | - |
| Extract Protocol: | Fetal retina tissue samples were collected in ice-cold artificial cerebrospinal fluid (ACSF), single cell was selected by FACS |
| Library Construction Protocol: | Single-cell R--seq using 10X genomics platform was performed using Chromium™ Single Cell 3' v2 Reagent Kits following the manufacturer's protocol. Libraries were constructed using Chromium™ Single Cell 3' v2 Reagent Kits following the manufacturer's protocol Libraries were sequenced on Illumi- HiSeq X Ten platform to obtain 100 and 32-bp paired end reads using the following read length; read 1, 26 cycles, read 2, 98 cycles and i7 index, 8 cycles. |
| Molecule Type: | poly(A)+ RNA |
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| Library Layout: | PAIRED |
| Library Strand: | Forward |
| Platform: | ILLUMINA |
| Instrument Model: | Illumina HiSeq 4000 |
| Strand-Specific: | Specific |
| Data Resource | GEN Sample ID | GEN Dataset ID | Project ID | BioProject ID | Sample ID | Sample Name | BioSample ID | Sample Accession | Experiment Accession | Release Date | Submission Date | Update Date | Species | Race | Ethnicity | Age | Age Unit | Gender | Source Name | Tissue | Cell Type | Cell Subtype | Cell Line | Disease | Disease State | Development Stage | Mutation | Phenotype | Case Detail | Control Detail | Growth Protocol | Treatment Protocol | Extract Protocol | Library Construction Protocol | Molecule Type | Library Layout | Strand-Specific | Library Strand | Spike-In | Strategy | Platform | Instrument Model | Cell Number | Reads Number | Gbases | AvgSpotLen1 | AvgSpotLen2 | Uniq Mapping Rate | Multiple Mapping Rate | Coverage Rate |
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