KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Goat polyclonal anti-Sox2 | Santa Cruz | Cat# sc17320; RRID:AB_2286684 |
| Mouse monoclonal anti-RLBP1 | Abcam | Cat# ab15051; RRID:AB_2269474 |
| Mouse monoclonal anti-Opsin, Unconjugated, Clone RET-P1 | Sigma-Aldrich | Cat# O4886; RRID:AB_260838 |
| Rabbit Polyclonal anti-Ki-67 | Millipore | Cat# AB9260; RRID:AB_2142366 |
| Mouse monoclonal anti-Brn3a (POU-domain protein), Unconjugated | Millipore | Cat# MAB1585; RRID:AB_94166 |
| Mouse polyclonal anti-S-Opsin | Millipore | Cat# AB5407; RRID:AB_177457 |
| Mouse polyclonal anti-L/M-Opsin | Millipore | Cat# AB5405 RRID:AB_177456 |
| Mouse monoclonal anti-calbindin | Abcam | Cat# ab9481–500; RRID:AB_2811302 |
| Goat Polyclonal anti-Calretinin | Millipore | Cat# AB1550; RRID:AB_90764 |
| Sheep polyclonal anti-CHX10(VSX2) | Exalpha Biologicals | Cat# x1179p; RRID:AB_2314191 |
| PKC alpha antibody [Y124] | Abcam | Cat#ab32376; RRID:AB_777294 |
| MCM2 (D7G11) XP(tm) Rabbit mAb antibody | Cell Signaling Technology | Cat# 3619s; RRID:AB_2142137 |
| Human ONECUT2/OC-2 Affinity Purified Polyclonal Ab antibody | R&D Systems | Cat#AF6294; RRID:AB_10640365 |
| Mouse monoclonal anti-LHX1 | DSHB | Cat#4F2; RRID: AB_531784 |
| Human Otx2 Affinity Purified Polyclonal Ab antibody | R&D Systems | Cat# AF1979; RRID:AB_2157172 |
| Mouse Anti-Human CRX Monoclonal Antibody, Unconjugated, Clone 4G11 | Abnova Corporation | Cat# H00001406-M02; RRID:AB_606098 |
| Rabbit polyclonal anti-ATOH7 | Novus | Cat# NBP1–88639; RRID:AB_11034390 |
| Mouse monoclonal – β-ACTIN | Sigma-Aldrich | Cat# A5441; RRID:AB_476744 |
| Goat polyclonal anti-GFP | Abcam | Cat# Ab6673; RRID:AB_305643 |
| Rabbit polyclonal anti-GFP | Life Technologies | Cat# A11122; RRID:AB_221569 |
| Rabbit polyclonal anti-GNAT2 | LifeSpan BioSciences | Cat# LS-C321680; RRID:AB_2811301 |
| Chicken polyclonal anti-mCherry | Novus Biologicals | Cat# NBP2–25158; RRID:AB_2636881 |
| Goat polyclonal anti-NRL | R&D Systems | Cat# AF2945; RRID:AB_2155098 |
| Rabbit polyclonal anti-RFP | Abcam | Cat# Ab62341; RRID:AB_945213 |
| Mouse monoclonal anti-RXRγ | Santa Cruz Biotechnology | Cat# Sc-365252; RRID:AB_10850062 |
| Alexa Fluor 488 Conjugated Donkey anti-Mouse IgG(H+L) | Invitrogen | Cat# A-21202; RRID:AB_141607 |
| Alexa Fluor 488 Conjugated Donkey anti-Rabbit IgG(H+L) | Invitrogen | Cat# A-21206; RRID:AB_141708 |
| Alexa Fluor 594 Conjugated Donkey anti-Rabbit IgG(H+L) | Invitrogen | Cat# A21207; RRID:AB_141637 |
| Alexa Fluor 594 Conjugated Donkey anti-Mouse IgG(H+L) | Invitrogen | Cat# A-21203; RRID:AB_141633 |
| Alexa Fluor 594 Conjugated Donkey anti-Goat IgG(H+L) | Invitrogen | Cat# A-11058; RRID:AB_142540 |
| Alexa Fluor 647 Conjugated Donkey anti-Goat IgG(H+L) | Invitrogen | Cat# A21447; RRID:AB_10584487 |
| Alexa Fluor 647 Conjugated Donkey anti-Mouse IgG(H+L) | Invitrogen | Cat# A-31571; RRID:AB_162542 |
| Alexa Fluor 488 Conjugated Donkey anti-Goat IgG(H+L) | Invitrogen | Cat# A11055; RRID:AB_2534102 |
| Alexa Fluor 647 Conjugated Donkey anti-Rabbit IgG(H+L) | Invitrogen | Cat# A31573; RRID:AB_2536183 |
| Alexa Fluor 568 Conjugated Donkey anti-Rabbit IgG(H+L) | Invitrogen | Cat# A10042; RRID:AB_2534017 |
| Alexa Fluor 568 Conjugated Goat anti-Chicken | Molecular Probes | Cat# A11041; RRID:AB_2534098 |
| Biological Samples | ||
| Human retinal samples | Anzhen Hospital of Capital Medical University and The First Affiliated Hospital of University of Science and Technology of China | N/A, materials available on request from Dr. Xiaoqun Wang |
| Human retinal samples | Morgentaler Clinic, Mount Sinai Hospital, Toronto, Canada | |
| Human retinal sample | Alabama Eye Bank, Birmingham, AL | 86-year-old Female without retinal disease; Cause of death: mitral regurgitation Death to enucleation: 3.3 hr |
| Human retinal organoids | ATCC | Generated from iPSCs derived from IMR-90 cell line (RRID: CVCL_C437) |
| Chemicals, Peptides, and Recombinant Proteins | ||
| RNAscope® Multiplex Fluorescent Reagent Kit v2 | ACD | Cat# 323100 |
| RNAscope® Probe- Hs-CYP26A1 | ACD | Cat#487741 |
| RNAscope® Probe- Hs-SFRP1-C2 | ACD | Cat#429381 |
| RNAscope® Probe- Hs-RLBP1-C2 | ACD | Cat#414221-C2 |
| RNAscope® Probe- Hs-DIO2-C3 | ACD | Cat#562211-C3 |
| RNAscope® Probe- Hs-LHX1 | ACD | Cat#493021 |
| RNAscope® Probe- Hs-ISL1-C2 | ACD | Cat#478591-C2 |
| 4’,6-Diamidino-2-Phenylindole, Dihydrochloride (DAPI) | Thermo Fisher | Cat# D1306; RRID: AB_2629482 |
| Triton X-100 | Sigma-Aldrich | Cat# T9284 |
| Critical Commercial Assays | ||
| Chromium Single Cell 3′ Library and Gel Bead Kit v2 | 10x Genomics | Cat# PN-120237 |
| Chromium Single Cell 3′ Chip Kit v2 | 10x Genomics | Cat# PN-120236 |
| Chromium i7 Multiplex Kit | 10x Genomics | Cat# PN-120262 |
| Deposited Data | ||
| Single-cell RNA sequencing Visualization of processed data available at: https://proteinpaint.stjude.org/?genome=hg38&singlecell=files/hg38/NEI.AGI.retina/singlecell/Human_Retina_Development.json |
This paper | GEO: GSE118614 GEO: GSE116106 GEO: GSE122970 |
| Mouse retinal development single-cell RNA-sequencing | Clark et al., 2019 | GEO: GSE138002 |
| Software and Algorithms | ||
| GraphPad Prism 5.0/7 | GraphPad Software | http://www.graphpad.com/scientific-software/prism/ |
| ImageJ | NIH | https://imagej.nih.gov/ij/ |
| Adobe Photoshop CC2015 | Adobe Systems | http://www.adobe.com |
| Cell ranger 2.0.1 | 10x Genomics | http://10xgenomics.com |
| R version 3.6.0 | The R project | https://www.r-project.org/ |
| CoGAPS v3.5 | (Sherman et al., 2019; Stein-O’Brien et al., 2019) | https://doi.org/10.18129/B9.bioc.CoGAPS |
| projectR | (Stein-O’Brien et al., 2019) | https://doi.org/10.18129/B9.bioc.projectR |
| umap | (Becht et al., 2018) | https://github.com/lmcinnes/umap/archive/0.2.4.tar.gz. |
| scanpy | (Wolf et al., 2018) | https://scanpy.readthedocs.io/ |
| Monocle (multiple version; 2.6.1, 2.99.3) | Cole Trapnell | https://github.com/cole-trapnell-lab/monocle-release |
| Monocle3_0.1.0 | Cole Trapnell | https://cole-trapnell-lab.github.io/monocle3/ |
| Seurat | (Butler et al., 2018) | https://satijalab.org/seurat/ |
| largeVis | (Tang et al., 2016) | https://github.com/lferry007/LargeVis |
| BBKNN | (Polański et al., 2020) | https://bbknn.readthedocs.io/ |
| Combat | (Leek et al., 2012) | https://github.com/brentp/combat.py |
| BioMart | (Durinck et al., 2005, 2009) | https://doi.org/10.18129/B9.bioc.biomaRt |
| ComplexHeatmap | (Gu et al., 2016) | https://github.com/jokergoo/ComplexHeatmap |
| genesorteR | (Ibrahim and Kramann, 2019) | https://github.com/mahmoudibrahim/genesorteR |
| pheatmap_1.0.12 | Raivo Kolde | https://CRAN.R-project.org/package=pheatmap |