Key Resources Table
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies: | ||
| goat anti-Brn3 (1:200) | Santa Cruz Biotechnology | Cat. # SC-6026; RRID:AB_673441 |
| mouse anti calbindin-D-28K; Calb1 (1:200) | Sigma-Aldrich | Cat. # C9848 (clone CB-955); RRID:AB_476894 |
| sheep anti-Chx10 (1:500) | Exalpha Biologicals | Cat. # X1180P; RRID:AB_2314191 |
| rabbit anti-GFP (1:1000) | Thermo Fisher Scientific | Cat. # A6455; RRID:AB_221570 |
| mouse anti-Glutamine synthetase; Glul (1:200) | BD Biosciences | Cat. # 610518 (Clone6); RRID:AB_397880 |
| mouse anti-Islet1 (1:200) | Developmental Studies Hybridoma Bank |
Cat. # 40.2D6; RRID:AB_528315 |
| mouse anti-Ki67 (1:200) | BD Biosciences | Cat. # 550609 (Clone B56); RRID:AB_393778 |
| rabbit anti-Lhx2 (1:1000) | generated in house with Covance; (de Melo et al., 2012) | RRID:AB_2783882 |
| mouse anti-P27Kip1 (1:500) | BD Transduction Labs | Cat. # 610241 (clone57/Kip1/p27); RRID:AB_397636 |
| mouse anti-Pax6 (1:200) | Developmental Studies Hybridoma Bank |
Cat. # Pax6a.a 1-223; RRID:AB_528427 |
| mouse anti-Nfia/b (1:200) | CDI Labs | Cat. # R1356.1.2C6; RRID:AB_2618885 |
| mouse anti-Tfap2a (1:200) | Abnova | Cat. # Clone 2G5; RRID:AB_490092 |
| rabbit anti-Recoverin (1:200) | Millipore | Cat. # AB5585; Lot LV1480447; RRID:AB_2253622 |
| mouse anti-Pkca (1:200) | Millipore | Cat. # Clone M4; RRID:AB_2284233 |
| rabbit anti-GFAP (1:500) | DakoCytomation | Cat. # Z0334; RRID:AB_10013382 |
| mouse anti-Rho4D2 (Rhodopsin; 1:200) | Dr. Robert Molday; (Laird and Molday, 1988) | RRID:AB_2315273 |
| rabbit anti-b-catenin (Ctnnb1; 1:200) | Sigma | Cat. # C2206; RRID:AB_476831 |
| rabbit anti-Iba1 (1:400) | Wako | Cat. # 019-19741; RRID:AB_839504 |
| donkey anti rabbit 488 (1:500) | Jackson ImmunoResearch | Cat. # 711-485-152; RRID:AB_2492289 |
| goat anti-rabbit 555 (1:500) | Thermo Fisher Scientific | Cat. # A-21428; RRID:AB_141784 |
| donkey anti-rabbit 594 (1:500) | Thermo Fisher Scientific | Cat. # A-21207; RRID:AB_141637 |
| goat anti-rabbit 633 (1:500) | Thermo Fisher Scientific | Cat. # A-21070; RRID:AB_2535731 |
| donkey anti-rabbit 647 (1:500) | Jackson ImmunoResearch | Cat. # 711-605-152; RRID:AB_2492288 |
| donkey anti-mouse 555 (1:500) | Thermo Fisher Scientific | Cat. # A-31570; RRID:AB_2536180 |
| donkey anti-mouse 594 (1:500) | Jackson ImmunoResearch | Cat. # 715-585-150; RRID:AB_2340854 |
| donkey anti-mouse 647 (1:500) | Jackson ImmunoResearch | Cat. # 715-605-150; RRID:AB_2340862 |
| donkey anti-goat 594 (1:500) | Thermo Fisher Scientific | Cat. # A-11058; RRID:AB_2534105 |
| donkey anti-goat 633 (1:500) | Thermo Fisher Scientific | Cat. # A-21082; RRID:AB_2535739 |
| donkey anti-sheep 568 (1:500) | Thermo Fisher Scientific | Cat. # A-21099; RRID:AB_2535753 |
| donkey anti-sheep 647 (1:500) | Jackson ImmunoResearch | Cat. # 713-605-003; RRID:AB_2340750 |
| Critical Commercial Assays: | ||
| Chromium Single Cell 3’ Library & Gel Bead Kit v2 | 10× Genomics | Cat. # 120237 |
| Chromium i7 Multiplex Kit | 10× Genomics | Cat. # 120262 |
| Chromium Single Cell A Chip Kit | 10× Genomics | Cat. # 1000009 |
| Chromium Controller & Accessory Kit | 10× Genomics | Cat. # 120223 |
| Click-iT EdU Alexa Fluor 647 Imaging Kit | Thermo FIsher Scientific | Cat. # C10340 |
| In Situ Cell Death Detection Kit, TMR red | Sigma | Cat. # 12156792910 |
| Experimental Models: Organisms/Strains | ||
| Mouse:CD1.Tg(Chx10-EGFP/cre/-ALPP)2Clc | Dr. Connie Cepko; (Rowan and Cepko, 2004) | RRID:MGI:3838985 |
| Mouse:Nfiafl/fl | Dr. Richard Gronostajski; This study |
N/A |
| Mouse:Nfibfl/fl | Dr. Richard Gronostajski; (Hsu et al., 2011) | N/A |
| Mouse:Nfixfl/fl | Dr. Richard Gronostajski; (Campbell et al., 2008) |
N/A |
| Deposited Data: | ||
| Retinal Development Smart-Seq2 Data | This Paper | GEO: GSE118614 |
| Retinal Development 10× Data | This Paper | GEO: GSE118614 |
| P14 Nfia/b/x Mutant and control retina 10× Data | This Paper | GEO: GSE118614 |
| Software: | ||
| Cell Ranger - 2.1.0 | 10× Genomics | https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest |
| GraphPad Prism 7 | GraphPad | www.graphpad.com |
| Monocle2 | Cole Trapnell | http://cole-trapnell-lab.github.io/monocle-release/docs/ |
| R version 3.4.1 | The R project | https://www.r-project.org/ |
| scCoGAPS | Bioconductor; This Paper | https://bioconductor.org/packages/release/bioc/hyml/CoGAPS.html |
| EVAsc | (Davis-Marcisak et al., 2018) | https://bioconductor.org/packages/release/bioc/html/GSReg.html |
| MAGIC | (van Dijk et al., 2018) |
https://github.com/DpeerLab/magic, https://github.com/KrishnaswamyLab/magic |
| umap | (McInnes and Healy, 2018) | https://github.com/lmcinnes/umap |
| largeVis | (Tang et al., 2016) | https://github.com/lferry007/LargeVis |
| Mclust | (Scrucca et al., 2016) | https://cran.r-project.org/web/packages/mclust/index.html |