KEY RESOURCES TABLE
| REAGENT or RESOURCE Antibodies | SOURCE | IDENTIFIER |
|---|---|---|
| Mouse anti-acetylated Tubulin | Abcam | Cat# ab11323 RRID:AB_297928 |
| Mouse anti-β-Actin (loading control) | Abcam | Cat#ab8227 RRID:AB_2305186 |
| Rabbit anti-β-Catenin (H-102)- total | Santa Cruz | Cat# sc7199 RRID:AB_634603 |
| Rabbit anti-β-Catenin Non-phospho (Active)(Ser33/37/Thr41) (D13A1) | Cell Signaling Technology | Cat# 8814 RRID:AB_11127203 |
| Rabbit anti-β-Galactosidase | Chemicon (Millipore Sigma) | Cat# AB986 RRID:AB_92401 |
| Rabbit anti-Calretinin | Swant | Cat# 76699/4 RRID: N/A |
| Rabbit anti-CD9 | Santa Cruz | Cat# sc9148 RRID:AB_2075905 |
| Mouse anti-CD63 | BD Pharmingen | Cat# 556019 RRID:AB_396297 |
| Goat anti-ChAT (choline acetyltransferase) | Chemicon | Cat# AB144P RRID:AB_2079751 |
| Goat anti-human DSCAM Affinity Purified Polyclonal | R&D Systems | Cat# AF3666 RRID:AB_2230818 |
| Rabbit anti-DSCAM Polyclonal | Thermo Fisher Scientific | Cat# PA5–42698 RRID:AB_2610175 |
| Rabbit anti-DSCAM (Biotin conjugated) | Bioss | Cat# bs-11456R-Biotin RRID: N/A |
| Rabbit anti-Dynamin 1 polyclonal antibody (DNM1) | Thermo Fisher Scientific | Cat# PA1–660 RRID:AB_325845 |
| Rabbit anti-FAT3 (E—12) | Santa Cruz | Cat# sc-133366 RRID:AB_10655386 |
| Rabbit anti-FAT3 (Biotin-conjugaged) | Antibodies-Online | Cat# ABIN6882377 RRID: N/A |
| Goat anti-GFP | Abcam | Cat# ab5450 RRID:AB_304897 |
| Mouse anti-HNK-1/N-CAM (CD57) clone Vc1.1 | Sigma-Aldrich | Cat# C6680 RRID:AB_1078474 |
| Rabbit anti-MEGF10 | Millipore | Cat# ABC10 RRID:AB_11204003 |
| Rabbit anti-MEGF10 (Biotin-conjugated) | Thermo Fisher Scientific | Cat# BS-24335R-BIOTIN RRID: N/A |
| Rabbit anti-PAX6 | Covance Research | Cat# PRB-278P RRID:AB_291612 |
| Rabbit anti- Phospho-Akt (Ser473) (D9E) | Cell Signaling Technology | Cat# 4060 RRID:AB_2315049 |
| Rabbit anti-PTEN | Cell Signaling | Cat# 9559 RRID:AB_390810 |
| Mouse anti-RAB4 | Novus Biologicals | Cat# NBP2–37485 RRID: N/A |
| Mouse anti-RAB5A | Proteintech | Cat# 66339–1-IG 66339–1-IG |
| Rabbit anti-RAB10 antibody [4E2] | Abcam | Cat# Ab104859 RRID:AB_10711207 |
| Rabbit anti-SCAMP1 | Synaptic Systems | Cat# 121 002 RRID:AB_887780 |
| Rabbit anti-TH | Millipore | Cat# AB152 RRID: AB_390204 |
| Rabbit anti-TSG101 | Sigma-Aldrich | Cat# HPA006161 RRID:AB_1080408 |
| Rabbit anti-Tubulin, gamma (DQ-19) | Sigma-Aldrich | Cat# T3195 RRID:AB_261651 |
| αMouse IgG Alexa Flour 647 | Life Tech. | Cat# A-31571 RRID:AB_162542 |
| αMouse IgG Alexa Flour 555 | Life Tech. | Cat# A32773 RRID:AB_2762848 |
| αMouse IgG Alexa Flour 488 | Life Tech. | Cat# A32766 RRID:AB_2762823 |
| αGoat IgG Alexa Flour 488 | Life Tech. | Cat# A11055 RRID:AB_2534102 |
| αGoat IgG Alexa Flour 568 | Life Tech. | Cat# A11057 RRID:AB_2534104 |
| αRabbit IgG Alexa Flour 488 | Life Tech. | Cat# A-21206 RRID:AB_2535792 |
| αRabbit IgG Alexa Flour 568 | Life Tech. | Cat# A10042 RRID:AB_2534017 |
| αRabbit IgG Alexa Flour 647 | Life Tech. | Cat# A-31573 RRID:AB_2536183 |
| αRat IgG Alexa Flour 568 | Jackson | Cat# 711–156-152 RRID:AB_2340603 |
| Streptavidin Cy3 | Thermo Fisher Scientific | Cat# 434315 RRID: N/A |
| Goat Anti-Rabbit IgG (H + L)-HRP Conjugate | Bio-Rad | Cat# #1721019 RRID: AB_11125143 |
| Goat Anti-Mouse IgG (H + L)-HRP Conjugate | Bio-Rad | Cat# #1721011 RRID: AB_11125936 |
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| Chemicals, peptides, and recombinant proteins | ||
|
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| Opal™ 690 reagent | Akoya | Cat# FP1497001KT RRID: N/A |
| Opal™ 570 reagent | Akoya | Cat# FP1488001KT RRID: N/A |
| Opal™ 520 reagent | Akoya | Cat# FP1487001KT RRID: N/A |
| XAV939 | Selleckchem | Cat# S1180 RRID: N/A |
| Cholera Toxin Subunit β-Alexa Fluor™ 555 Conjugate | Invitrogen/Life | Cat# C-34776 RRID:AB_2313636 |
| Papain dissociation kit | Worthington Biochemical Corp | Cat# LK003150 RRID: N/A |
| Micro BCA™ Protein Assay Kit | ThermoFisher Scientific | Cat# #23235 RRID: N/A |
| Amersham ECL Prime Western Blotting Detection Reagent | Cytiva | Cat#RPN2232 RRID: N/A |
| Anti mouse IgM MicroBeads | Miltenyi Biotec | Cat# 130–047-302 RRID:AB_244359 |
| Dead cell removal kit | Miltenyi Biotec | Cat# 130–090-101 RRID: N/A |
| Recombinant Wnt3a | R&D Systems | Cat# 5036 RRID: N/A |
| DMSO | Sigma | Cat# D8418 RRID: N/A |
| DMEM | Wisent | Cat# 319–005 RRID: N/A |
| HBSS | Gibco | Cat# 24020–117 RRID: N/A |
| Heat-inactivated horse serum | Gibco | Cat# 16050130 RRID: N/A |
| L-glutamine | Gibco | Cat# 35050–061 RRID: N/A |
| HEPES | Gibco | Cat# 15630–080 RRID: N/A |
| Pen-Strep | Wisent | Cat# 450–201 RRID: N/A |
| PBS | Wisent | Cat# 311–420 RRID: N/A |
| Trypsin | Wisent | Cat# 325–542 RRID: N/A |
| bpV(pic) | Selleckchem | Cat# S8651 |
| BDNF | Peprotech | Cat# 450–02 |
| CNTF | Peprotech | Cat# 450–13 |
| TGF-β1 | Peprotech | Cat# 100–21 |
| TGF-β2 | Peprotech | Cat# 100–35B |
| Forskolin | Sigma | Cat# F6886 |
| B27 | Thermo Fisher Scientific | Cat# 17504044 |
| N2 | Thermo Fisher Scientific | Cat# 17502048 |
| NAC | Sigma | Cat# A8199 |
| Insulin | Invitrogen | Cat# 12585–014 |
| Na Pyruvate | Invitrogen | Cat# 11360–070 |
| L-glutamine | Invitrogen | Cat# 25030–081 |
| T3 | Sigma | Cat# T6397 |
| Neurobasal | Invitrogen | Cat# 21103–049 |
| Paraformaldehyde Granular | Electron Microscopy Sciences | Cat# 19208 |
| Poly-D-Lysine | Corning | Cat# 354210 |
| Laminin | Corning | Cat# 354232 |
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| Critical commercial assays | ||
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| RNAscope® Multiplex Fluorescent Detection Kit v2 | ACD | Cat# 323110 RRID: N/A |
| Chromium Next GEM Single Cell 5′ Reagent Kit v2 | 10X Genomics | Cat# 1000263 |
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| Deposited data | ||
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| ProteomeXchange Consortium via the PRIDE [1] partner repository (mass spectrometry data) | This study |
Project accession: PXD036221 Project DOI: 10.6019/PXD036221 |
| Uncropped western blot images | This study | https://doi.org/10.17632/jf4pwztxrj |
| scRNA-seq data- P7 wt retinas | This study | GEO: GSE228191 |
|
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| Experimental models: Organisms/strains | ||
|
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| Mus musculus: CD-1 ® IGS mouse | Charles River | Strain Code: 022 RRID:IMSR_CRL:022 |
| Mus musculus: C57BL/6J | The Jackson Laboratory | Cat# 000664 RRID:IMSR_JAX:000664 |
| Ptenfl allele (Backman et al.)37 | The Jackson Laboratory | Strain #: 006440 |
| B6.129S4-Ptentm1Hwu/J | RRID:IMSR_JAX:006440 | |
| Pax6::Cre driver (Marquardt et al.)38 | The Jackson Laboratory | Strain #:024578 |
| Tg(Pax6-GFP/cre)1Rilm/J | RRID:IMSR_JAX:024578. | |
| fro/fro (Alebrahim et al.)58 | Monzur Murshed | (Alebrahim et al.)58 |
| Dscamdel17 (Fuerst et al.)34 | The Jackson Laboratory | Strain #:008000 |
| B6.CBy-Dscamdel17/RwbJ | RRID:IMSR_JAX:008000) | |
| Lef/Tcf-lacZ reporter mice | The Jackson Laboratory | Strain #:004623 |
| Tg(TCF/Lef1-lacZ)34Efu/J | RRID:IMSR_JAX:004623. | |
| Ctnnblfl mice | The Jackson Laboratory | Strain #022775 |
| B6(Cg)-Ctnnb1tm1Knw/J | RRID:IMSR_JAX:022775 | |
|
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| Oligonucleotides | ||
|
| ||
| RNAscope probe: Mm-Pten | ACD | Cat# 316301-C1 |
| RNAscope probe: Mm-Dscam | ACD | Cat# 834031-C2 |
| RNAscope probe: Mm-Th | ACD | Cat# 317621-C3 |
| RNAscope probe: Mm-lsl1 | ACD | Cat# 451931-C3 |
| RNAscope probe: Mm-Smpd3 | ACD | Cat# 815591-C3 |
| Genotyping Pax6::Cre mutant forward: | This study | N/A |
| 5′-CCACGACCAAGTGACAGCAATG-3′ and mutant reverse | ||
| 5′- CAGAGACGGAAATCCATCGCTC-3′ | ||
| Expected band size: MT: 373 bp | ||
| Genotyping primers: Dscam mutant forward | This study | N/A |
| 5′-CTTTGCGCGTTATGATCCT-3′ and Dscam mutant reverse | ||
| 5′-GTGGTGTCGATACTGATG-3′ | ||
| Expected band size: WT: 170 bp MT: 133 bp | ||
| Genotyping primers: Pten flox forward | This study | N/A |
| 5′-CTCCTCTACTCCATTCTTCCC-3′ and Pten flox reverse | ||
| 5′-ACTCCCACCAATGAACAAAC-3′ | ||
| Expected band size: WT: 288 bp MT: 335 bp | ||
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| Software and algorithms | ||
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| Fiji (ImageJ) | Schindelin et al.78 | https://imagej.net/Fiji |
| GraphPad Prism | GraphPad Software |
https://www.graphpad.com/ RRID:SCR_002798 |
| Seurat v.3.2.3 | Butler et al.79 | https://satijalab.org/seurat |
| MASCOT software version 2.6 (Matrix Science, UK) | Matrix Science | http://www.matrixscience.com/mascot_support_v2_6.html |
| Scaffold version 4.8.2 (USA) | Proteome Software | https://www.proteomesoftware.com/products/scaffold-5 |
| ClueGO Cytoscape plug-in | Bindea et al.80 | http://www.ici.upmc.fr/cluego/cluegoDownload.shtml |
| pathfind R Bioconductor package | Ulgen et al.81 | N/A |
| Qiagen Ingenuity Pathway Analysis (Qiagen IPA) | Qiagen | https://digitalinsights.qiagen.com/products-overview/discovery-insights-portfolio/analysis-and-visualization/qiagen-ipa/ |
| rrvgo Bioconductor package | https://bioconductor.org/packages/release/bioc/vignettes/rrvgo/inst/doc/rrvgo.html | |
| Leica Application Suite X (LASX) | Leica Microsystems | LAS X Life Science Microscope Software - Downloads | Products | Leica Microsystems (leica-microsystems.com) |
| Adobe Photoshop 2021 | Adobe Creative Cloud | Creative business solutions | Adobe Creative Cloud for teams |
| Biorender Science Figures Licence | Biorender | https://biorender.com/ |
| Image Lab | Bio-Rad | https://www.bio-rad.com/en-ca/product/image-lab-software?ID=KRE6P5E8Z |