Key resource table
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Chicken polyclonal anti-GFP | Invitrogen | CAT# A10262 |
| Rabbit polyclonal anti-tagRFP | Invitrogen | CAT# R10367 |
| Mouse monoclonal anti-synaptotagmin 2 (syt2) | ZIRC | AB_10013783 |
| Goat anti-chicken A488 | Invitrogen | CAT# A32931 |
| Goat anti-rabbit A555 | Invitrogen | CAT# A32732 |
| Goat anti-mouse A647 | Invitrogen | CAT# A32728 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| AMES’ Medium | Sigma | CAT# A1420 |
| BSA (Bovine Serum Albumin) | Sigma | CAT# A9418 |
| Calcein Blue | ThermoFisher | CAT# C1429 |
| DAPI | Invitrogen | CAT# D1306 |
| DNAseI | Sigma | CAT# D4527 |
| L-cysteine | Sigma | CAT# C1276 |
| Low melting point agarose | Invitrogen | CAT# 10143954 |
| Metronidazole | Sigma | CAT# M1547 |
| Ovomucoid | Worthington | CAT# LS003087 |
| Papain | Worthington | CAT# LS003126 |
| Paraformaldehyde | Alfa Aesar | CAT# 43368 |
| PBS (for single cell transcriptomics) | Gibco | CAT# 10010001 |
| PTU (Phenylthiourea) | Sigma | CAT# P7629 |
| TissueTek | Sakura | CAT# 4583 |
| Tricaine – MS222 | Sigma | CAT# E10521 |
| Critical Commercial Assays | ||
| Chromium Single Cell 30 Library & Gel Bead Kit v2 | 10X Genomics | CAT# 120237 |
| Chromium Single Cell A Chip Kit | 10X Genomics | CAT# 1000009 |
| Chromium i7 Multiplex Kit | 10X Genomics | CAT# 120262 |
| Deposited Data | ||
| Raw data files for RNA-sequencing | GEO | GSE152842 |
| Visualized zebrafish RGC atlas | https://portals.broadinstitute.org/single_cell | SCP992 |
| Guide for reproduction of key results | https://github.com/shekharlab/ZebrafishRGC | |
| Experimental Models: Organisms/Strains | ||
| isl2b:tagRFP | Chien lab (Poulain and Chien, 2013) | zc80Tg |
| isl2b:GFP | Chien lab (Pittman et al., 2008) | zc7Tg |
| isl2b:Gal4 | Bonkowsky lab (Fujimoto et al., 2011) | zc65Tg |
| tbx20:Gal4 | Baier lab (Förster et al., 2017) | mpn220 |
| ath5:Cre | Baier lab (Förster et al., 2017) | mpn221 |
| UAS:GCaMP6s | Baier lab (Thiele et al., 2014) | mpn101 |
| UAS:NTR-mCherry | Halpern lab (Davison et al., 2007) | c264Tg |
| UAS:Dendra | Baier lab (Arrenberg et al., 2009) | s1998 |
| ath5:QF2 | Baier lab (Fernandes et al., 2019) | mpn405 |
| eomesa:QF2 | This study | mpn406 |
| mafaa:QF2 | This study | mpn408 |
| tbr1b:QF2 | This study | mpn409 |
| tbx3a:QF2 | This study | mpn410 |
| QUAS:epNTR-tagRFP | Baier lab (Fernandes et al., 2019) | mpn165 |
| QUAS:switchNTR (QUAS:loxP-GFPcaax-loxP-epNTR-tagRFP) | This study | mpn168 |
| QUAS:switchG6s (QUAS:loxP-tdTomatocaax-loxP-GCamP6s) | This study | mpn169 |
| actb2:loxP-eGFP-loxP-lynTagRFPT | Burgess lab (Marquart et al., 2015) | y272 |
| CRISPR-Cas9 reagents & gRNA’s | ||
| Alt-R® S.p. HiFi Cas9 Nuclease V3 | IDT | CAT# 1081060 |
| Alt-R® CRISPR-Cas9 tracrRNA | IDT | CAT# 1072533 |
| Alt-R® CRISPR-Cas9 crRNA | IDT | customized |
| Nuclease-free Duplex Buffer | IDT | CAT# 11-05-01-12 |
| Recombinant DNA | ||
| pTol2 - QUAS:loxP-GFPcaax-loxP-epNTR-tagRFP | This paper | |
| pTol2 - QUAS:loxP-tdTomatocaax-loxP-GCaMP6s | This paper | |
| pGGEV-1 | This paper | |
| pGGEV-2 (locus-specific gRNA target sequence) | This paper | |
| pGGEV-3 e1b | This paper | |
| pGGEV-4 QF2-polyA | This paper | |
| pGGEV-5’ polyA | This paper | |
| Software and Algorithms | ||
| Cell Ranger v2.1.0 | 10X Genomics | www.support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome |
| FIJI | (Schindelin et al., 2012) | www.fiji.sc |
| Zen | Zeiss | www.zeiss.com/microscopy/int/products/microscope-software/zen.html |
| LAS X | Leica | www.leica-microsystems.com/products/microscope-software/p/leica-las-x-ls/ |
| Psychopy2 | (Peirce et al., 2019) | www.psychopy.org |
| R | R version 3.6 | www.r-project.org/ |
| Python 2.7.12 | Anaconda2 | www.anaconda.com |
| Python 3.7. | Anaconda3 | www.anaconda.com |
| CCTop | (Stemmer et al., 2015) | https://crispr.cos.uni-heidelberg.de |
| The Real Fish Tracker | N/A | http://www.dgp.toronto.edu/~mccrae/projects/FishTracker/ |
| Other | ||
| Camera | IDS | UI-3370CP-NIR |
| Chromium Controller | 10X Genomics | N/A |
| Film Polarizer | Thorlabs | LPVISE2X2 |
| HiSeq 2500 System | Illumina | N/A |
| Leica SP8 confocal microscope | Leica | N/A |
| Lens | Edmund Optics | 86-572 |
| ZebraBox | ViewPoint | N/A |