PROJECT ID: GSE122680

Data source GEO: GSE122680
Description It provides an opportunity to make the first comparative study of molecular programs used by embryonic and post-embryonic neurogenic programs in the vertebrate retina.
Key word developmental state; retinal progenitor cells; retinal stem cells; single-cell RNA sequencing; zebrafish
Publication Xu B, Tang X, Jin M, Zhang H et al. Unifying developmental programs for embryonic and postembryonic neurogenesis in the zebrafish retina. Development 2020 Jun 19;147(12). PMID: 32467236
Abstract The zebrafish retina grows for a lifetime. Whether embryonic and postembryonic retinogenesis conform to the same developmental program is an outstanding question that remains under debate. Using single-cell RNA sequencing of 20,000 cells of the developing zebrafish retina at four different stages, we identified seven distinct developmental states. Each state explicitly expresses a gene set. Disruption of individual state-specific marker genes results in various defects ranging from small eyes to the loss of distinct retinal cell types. Using a similar approach, we further characterized the developmental states of postembryonic retinal stem cells (RSCs) and their progeny in the ciliary marginal zone. Expression pattern analysis of state-specific marker genes showed that the developmental states of postembryonic RSCs largely recapitulated those of their embryonic counterparts, except for some differences in rod photoreceptor genesis. Thus, our findings reveal the unifying developmental program used by the embryonic and postembryonic retinogenesis in zebrafish.


Dataset Information

Dataset ID Species Tissue / Organ Experiment type Sample Source dataset ID
1. GSE122680 (24hpf) Danio rerio retina baseline 24hpf, WT, untreatment GEO: GSM3478013
2. GSE122680 (1.5dpf) Danio rerio retina baseline 1.5dpf, WT, untreatment GEO: GSM3478014
3. GSE122680 (3dpf) Danio rerio retina baseline 3dpf, WT, untreatment GEO: GSM3478018
4. GSE122680 (14dpf) Danio rerio retina baseline 14dpf, WT, untreatment GEO: GSM3478019
5. GSE122680 (2dpf) Danio rerio retina baseline 2dpf, WT, untreatment GEO: GSM4233148

Clustering Result

Cluster Cell type Gene id (symbol) Marker class Evidence
1 Retinal progenitors ENSDARG00000054155 (pcna) marker DOI:10.1242/dev.185660
2 Retinal progenitors ENSDARG00000014329 (npm1a) marker DOI:10.1242/dev.185660
3 Retinal progenitors ENSDARG00000091150 (mki67) marker DOI:10.1242/dev.185660
3 Retinal progenitors ENSDARG00000087554 (cdk1) marker DOI:10.1242/dev.185660
4 Horizontal cells ENSDARG00000055158 (prox1a) marker DOI:10.1242/dev.185660
5 Muller glia cells ENSDARG00000012504 (rlbp1a) marker DOI:10.1242/dev.185660
7 Amacrine cells ENSDARG00000059279 (tfap2a) marker DOI:10.1242/dev.185660

Cluster Cell type Gene id (symbol) Marker class Evidence
1 Retinal progenitors ENSDARG00000056732 (her4.1) marker DOI:10.1242/dev.185660
2 Retinal progenitors ENSDARG00000014329 (npm1a) marker DOI:10.1242/dev.185660
3 Retinal progenitors ENSDARG00000091150 (mki67) marker DOI:10.1242/dev.185660
3 Retinal progenitors ENSDARG00000087554 (cdk1) marker DOI:10.1242/dev.185660
4 Muller glia cells ENSDARG00000025301 (gfap) marker DOI:10.1242/dev.185660
5 Bipolar cells ENSDARG00000003469 (neurod4) marker DOI:10.1242/dev.185660
6 Retinal ganglion cells ENSDARG00000099744 (gap43) marker DOI:10.1242/dev.185660
6 Retinal ganglion cells ENSDARG00000014420 (elavl3) marker DOI:10.1242/dev.185660
9 Horizontal cells ENSDARG00000055158 (prox1a) marker DOI:10.1242/dev.185660
10 Muller glia cells ENSDARG00000012504 (rlbp1a) marker DOI:10.1242/dev.185660

Cluster Cell type Gene id (symbol) Marker class Evidence
1 Retinal progenitors ENSDARG00000054155 (pcna) marker DOI:10.1242/dev.185660
1 Retinal progenitors ENSDARG00000091150 (mki67) marker DOI:10.1242/dev.185660
2 Amacrine cells ENSDARG00000059279 (tfap2a) marker DOI:10.1242/dev.185660
3 Photoreceptor cells ENSDARG00000019902 (rcvrn2) marker DOI:10.1242/dev.185660
5 Retinal ganglion cells ENSDARG00000099744 (gap43) marker DOI:10.1242/dev.185660
6 Bipolar cells ENSDARG00000056292 (vsx1) marker DOI:10.1242/dev.185660
8 Photoreceptor cells ENSDARG00000019902 (rcvrn2) marker DOI:10.1242/dev.185660
9 Muller glia cells ENSDARG00000025301 (gfap) marker DOI:10.1242/dev.185660
10 Horizontal cells ENSDARG00000020544 (rem1) marker DOI:10.1242/dev.185660
13 Horizontal cells ENSDARG00000020544 (rem1) marker DOI:10.1242/dev.185660

Cluster Cell type Gene id (symbol) Marker class Evidence
1 Amacrine cells ENSDARG00000058039 (bhlhe22) marker DOI:10.1242/dev.185660
2 Bipolar cells ENSDARG00000056292 (vsx1) marker DOI:10.1242/dev.185660
3 Retinal progenitors ENSDARG00000054155 (pcna) marker DOI:10.1242/dev.185660
5 Photoreceptor cells ENSDARG00000011989 (crx) marker DOI:10.1242/dev.185660
5 Photoreceptor cells ENSDARG00000019902 (rcvrn2) marker DOI:10.1242/dev.185660
6 Retinal ganglion cells ENSDARG00000014420 (elavl3) marker DOI:10.1242/dev.185660
8 Retinal ganglion cells ENSDARG00000099744 (gap43) marker DOI:10.1242/dev.185660
8 Retinal ganglion cells ENSDARG00000014420 (elavl3) marker DOI:10.1242/dev.185660
9 Horizontal cells ENSDARG00000020544 (rem1) marker DOI:10.1242/dev.185660

Cluster Cell type Gene id (symbol) Marker class Evidence
1 Bipolar cells ENSDARG00000056292 (vsx1) marker DOI:10.1242/dev.185660
1 Bipolar cells ENSDARG00000056292 (vsx1) marker DOI:10.1242/dev.185660
2 Amacrine cells ENSDARG00000059279 (tfap2a) marker DOI:10.1242/dev.185660
2 Amacrine cells ENSDARG00000103379 (pax6a) marker DOI:10.1242/dev.185660
2 Amacrine cells ENSDARG00000059279 (tfap2a) marker DOI:10.1242/dev.185660
2 Amacrine cells ENSDARG00000103379 (pax6a) marker DOI:10.1242/dev.185660
3 Retinal progenitors ENSDARG00000091150 (mki67) marker DOI:10.1242/dev.185660
3 Retinal progenitors ENSDARG00000087554 (cdk1) marker DOI:10.1242/dev.185660
3 Retinal progenitors ENSDARG00000091150 (mki67) marker DOI:10.1242/dev.185660
3 Retinal progenitors ENSDARG00000087554 (cdk1) marker DOI:10.1242/dev.185660
4 Retinal progenitors ENSDARG00000087554 (cdk1) marker DOI:10.1242/dev.185660
4 Retinal progenitors ENSDARG00000087554 (cdk1) marker DOI:10.1242/dev.185660
6 Retinal progenitors ENSDARG00000054155 (pcna) marker DOI:10.1242/dev.185660
6 Retinal progenitors ENSDARG00000054155 (pcna) marker DOI:10.1242/dev.185660
7 Photoreceptor cells ENSDARG00000019902 (rcvrn2) marker DOI:10.1242/dev.185660
7 Photoreceptor cells ENSDARG00000019902 (rcvrn2) marker DOI:10.1242/dev.185660
8 Retinal ganglion cells ENSDARG00000099744 (gap43) marker DOI:10.1242/dev.185660
8 Retinal ganglion cells ENSDARG00000014420 (elavl3) marker DOI:10.1242/dev.185660
8 Retinal ganglion cells ENSDARG00000099744 (gap43) marker DOI:10.1242/dev.185660
8 Retinal ganglion cells ENSDARG00000014420 (elavl3) marker DOI:10.1242/dev.185660
10 Amacrine cells ENSDARG00000059279 (tfap2a) marker DOI:10.1242/dev.185660
10 Amacrine cells ENSDARG00000059279 (tfap2a) marker DOI:10.1242/dev.185660
11 Photoreceptor cells ENSDARG00000019902 (rcvrn2) marker DOI:10.1242/dev.185660
11 Photoreceptor cells ENSDARG00000019902 (rcvrn2) marker DOI:10.1242/dev.185660
12 Horizontal cells ENSDARG00000020544 (rem1) marker DOI:10.1242/dev.185660
12 Horizontal cells ENSDARG00000020544 (rem1) marker DOI:10.1242/dev.185660