KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Acetylated Tubulin (Guinea Pig, polyclonal, 1:1k) | Sigma | Cat #: T6793; RRID:AB_609894 |
| Islet1/2 (mouse, monoclonal, 1:25) | DSHB | Cat# 39.4D5; RRID:AB_2314683 |
| Calbindin (mouse, monoclonal, 1:500) | Swant | Cat# CB300PUR; RRID: AB_3542811 |
| MafB (rabbit, polyclonal, 1:4k) | Sigma | Cat# HPA005653; RRID:AB_1079293 |
| GFP (chicken, polyclonal, 1:30k) | Aves | Cat#GFP-1020; RRID:AB_10000240 |
| RFP (rabbit, polyclonal, 1:2k) | Rockland | Cat# 600-401-379; RRID:AB_2209751 |
| En1 (guinea pig, polyclonal, 1:10k) | Columbia University | Cat# CU1714; RRID:AB_3313271 |
| FoxP1 (rabbit, polyclonal, 1:16k) | Columbia University | Cat# CU1025; RRID:AB_2631297 |
| FoxP2 (goat, polyclonal, 1:500) | Santa Cruz Biotechnology | Cat# sc-21069; RRID:AB_2107124 |
| Hb9 (guinea pig, polyclonal, 1:5k) | Columbia University | Cat# CU1633; RRID: AB_3661722 |
| Lhx3 (mouse, monoclonal, 1:5k) | DSHB | Cat# 67.4E12; RRID:AB_2135805 |
| MafA (rabbit, polyclonal, 1:16k) | Columbia University | Cat# CU1755; RRID:AB_2941769 |
| Pou3f1/cScip (Guinea pig, polyclonal, 1:16k) | Columbia University | Cat# CU687/688; RRID:AB_2631305 |
| Pou6f2 (rat, polyclonal, 1:8k) | Columbia University | Cat# CU1796; RRID:AB_2665427 |
| Raldh2 (guinea pig, polyclonal, 1:32k) | Columbia University | Cat# CU1022; RRID: AB_3661741 |
| Sp8 (rat, polyclonal, 1:4k) | Columbia University | Cat# CU1944; RRID:AB_3644212 |
| Sp8 (rabbit, polyclonal, 1:64k) | Columbia University | Cat# CU1943; RRID:AB_3644213 |
| Sp8 (rabbit, polyclonal, 1:8k) | Millipore | Cat# AB-15260; RRID:AB_877304 |
| Myosin heavy chain (mouse, monoclonal, 1:200) | DSHB | Cat# MF20; AB_2147781 |
| Lhx3 (guinea pig, polyclonal, 1:4k) | Pfaff Lab | PMID: 9865699 |
| Lhx3 (rabbit, polyclonal, 1:20k) | Pfaff Lab | PMID: 9865699 |
| FoxP4 (rabbit, polyclonal, 1:32k) | Columbia University | Cat#: CU1797; RRID:AB_3644215 |
| FoxP4 (rat, polyclonal, 1:4k) | Columbia University | Cat#: CU1798; RRID:AB_3661716 |
| Nr3b3/Errg (mouse, monoclonal, 1:2k) | R&D Systems | Cat #: PP-H6812–00; RRID:AB_2100280 |
| Nr3b3 (rabbit, polyclonal, 1:4k) | Evans Lab, SALK | PMID: 19965931 |
| Otp (rat, polyclonal, 1:16k) | Columbia University | Cat#: CU1941; RRID:AB_3644216 |
| Otp (rabbit, polyclonal, 1:2k) | Abcam | Cat# ab50897; RRID: AB_881808 |
| Nr4a2 (Rabbit, polyclonal, 1:500) | Santa Cruz Biotechnology | Cat#: SC5568; RRID:AB_2267355 |
| Phospho-smad (Rabbit, polyclonal, 1:1k) | Columbia University | Cat# CU503; RRID:AB_2631311 |
| Donkey Anti-Mouse IgG (H+L), AF405-conjugated (donkey, polyclonal) | Abcam | Cat# ab175658; RRID:AB_2687445 |
| AffinitiPure Donkey Anti-Mouse IgG (H+L), AF488-conjugated (donkey, polyclonal) | Jackson ImmunoResearch | Cat# 715-545-151; RRID:AB_2341099 |
| AffinitiPure Donkey Anti-Mouse IgG (H+L), Cy3-conjugated (donkey, polyclonal) | Jackson ImmunoResearch | Cat# 715-165-151; RRID:AB_2315777 |
| AffinitiPure Donkey Anti-Mouse IgG (H+L), Cy5-conjugated (donkey, polyclonal) | Jackson ImmunoResearch | Cat# 715-175-151; RRID:AB_2340820 |
| AffinitiPure Donkey Anti-Rat IgG (H+L), Cy3-conjugated (donkey, polyclonal) | Jackson ImmunoResearch | Cat# 712-165-153; RRID:AB_2340667 |
| AffinitiPure Donkey Anti-Rat IgG (H+L), Cy5-conjugated (donkey, polyclonal) | Jackson ImmunoResearch | Cat# 712-175-153; RRID:AB_2340672 |
| AffinitiPure Donkey Anti-Guinea Pig IgG (H+L), 488-conjugated (donkey, polyclonal) | Jackson ImmunoResearch | Cat# 706-545-148; RRID:AB_2340472 |
| AffinitiPure Donkey Anti-Guinea Pig IgG (H+L), Cy3-conjugated (donkey, polyclonal) | Jackson ImmunoResearch | Cat#706-165-148; RRID:AB_2340460 |
| AffinitiPure Donkey Anti-Rabbit IgG (H+L), 488-conjugated (donkey, polyclonal) | Jackson ImmunoResearch | Cat# 711-545-152; RRID:AB_2313584 |
| AffinitiPure Donkey Anti-Rabbit IgG (H+L), Cy3-conjugated (donkey, polyclonal) | Jackson ImmunoResearch | Cat# 711-165-152; RRID:AB_2307443 |
| AffinitiPure Donkey Anti-Rabbit IgG (H+L), Cy5-conjugated (donkey, polyclonal) | Jackson ImmunoResearch | Cat# 711-175-152; RRID:AB_2340607 |
| Donkey Anti-Goat IgG (H+L), AF405-conjugated (donkey, polyclonal) | Abcam | Cat# ab175665; RRID:AB_2636888 |
| AffinitiPure Donkey Anti-Goat IgG (H+L), AF488-conjugated (donkey, polyclonal) | Jackson ImmunoResearch | Cat# 705-545-147; RRID:AB_2336933 |
| AffinitiPure Donkey Anti-Goat IgG (H+L), Cy3-conjugated (donkey, polyclonal) | Jackson ImmunoResearch | Cat# 705-165-147; RRID:AB_2307351 |
| AffinitiPure Donkey Anti-Goat IgG (H+L), Cy5-conjugated (donkey, polyclonal) | Jackson ImmunoResearch | Cat# 705-175-147; RRID: AB_2340415 |
| Bacterial and virus strains | ||
| None | None | None |
| Chemicals, peptides, and recombinant proteins | ||
| O.C.T | Fisher Scientific | Cat# 23730571 |
| Superfrost Plus slides | Fisher Scientific | Cat# 1367811E |
| Normal donkey serum | The Jackson Laboratory | Cat# 017-000-121 |
| Triton X-100 | Sigma-Aldrich | Cat# T8787 |
| L-Cysteine | Sigma-Aldrich | Cat# C7780-500G |
| ProLong Diamond | Invitrogen | Cat# P36970 |
| ProLong Diamond with DAPI | Invitrogen | Cat# P36971 |
| Cover glasses, 1.5 mm thickness | Fisher Scientific | Cat# 22266882 |
| 2-methylbutane | Sigma-Aldrich | Cat# M32631 |
| DAPI | Sigma-Aldrich | Cat# D9542-1MG |
| PVA Mounting Medium with DABCO | Millipore Sigma | Cat# 10981 |
| Paraformaldehyde (frog experiments) | Merck | Cat# 441344 |
| Paraformaldehyde (mouse experiments) | Electron Microscopy Sciences | Cat# 15714 |
| Triton X-100 | Merck | Cat# 72593 |
| TWEEN 20 (50% Solution) | Life Tech | Cat# 003005 |
| Benzyl alcohol | Sigma-Aldrich | Cat# 402834-500ML |
| Benzyl benzoate | Sigma-Aldrich | Cat# B6630-250ML |
| Cas9 protein with NLS | PnasBio | Cat# CP01-200 |
| Tissue freezing medium | Electron Microscopy Science | Cat# 72593 |
| Gentamicin Sulfate | Sigma-Aldrich | Cat# G1914-5G |
| Dextran, Tetramethylrhodamine, 3000 MW, Anionic, Lysine Fixable | Sigma-Aldrich | Cat# D-3308 |
| Cytiva Ficoll PM400 | Fisher Scientific | Cat# 11590724 |
| Gelatin from cold water fish skin | Sigma-Aldrich | Cat# G7041-500G |
| Pregnant Mare Serum Gonadotropin (PMSG) | Biozol | Cat# BVD-RP1782725000-5000 |
| Chorionic Gonadotropin Human, Lyophilize (hCG) | Sigma-Aldrich | Cat# CG5-10VL |
| Critical commercial assays | ||
| Phire Tissue Direct PCR Master | Mix Thermo Fisher | Cat# F-170S |
| Experimental models: Cell lines | ||
| None | None | None |
| Experimental models: Organisms/strains | ||
| Frog: wildtype pigmented Xenopus laevis | ISTA | N/A |
| Frog: Xla.Tg(218-2:GFP)Swee | This paper | 218-2:GFP |
| Frog: Xla.Tg(218-tdTomato; cry:tdTomato)Swee | This paper | 218-2:tdT |
| Frog: Xla.foxp1tmlSwee | This paper | N/A |
| Frog: Xla.en1tm1Swee | This paper | N/A |
| Mouse: En1::Cre | The Jackson Laboratory | RRID:IMSR_JAX:007916 |
| Mouse: RC.lsl.Sun1-sfGFP | The Jackson Laboratory | RRID:IMSR_JAX:021039 |
| Oligonucleotides | ||
| sgRNA sequences; See Table S2 | This paper | N/A |
| Genotyping primers; See Table S1 | This paper | N/A |
| Recombinant DNA | ||
| N1_Slit3peGFP | This paper | SO04 |
| Slit::tdT_Cry tdT | This paper | SO57 |
| Software and algorithms | ||
| Xenbase illustrations | Xenbase | http://www.xenbase.org/; RRID:SCR_003280 |
| Xenbase | Xenbase | http://www.xenbase.org/, RRID:SCR_003280 |
| Adobe Illustrator | Adobe | https://www.adobe.com/at/products/illustrator.html |
| Imaris 9.9.1 | Oxford Instruments | https://imaris.oxinst.com/ |
| MATLAB | Mathwords | https://www.mathworks.com/ |
| Fiji 2.14.0 | 119 | https://fiji.sc/ |
| Prism 10 | Graphpad Software, Inc. | https://www.graphpad.com/features |
| ZenBlue 3.7 | Carl Zeiss Microscopy | N/A |
| Custom code for plotting neuron distribution | GitHub | https://github.com/tamachado/rnakecontours |
| SMART sequence analysis | 120,121 | http://smart.embl-heidelberg.de/ |
| SequenceBuilder Pro | DNASTAR | https://www.dnastar.com/software/lasergene/seqbuilder-pro/ |
| BLAST | https://blast.ncbi.nlm.nih.gov/Blast.cgi | |
| OBS (Open Broadcaster Software) | https://obsproject.com/ | |
| MATLAB | Math Works | https://www.mathworks.com/products/matlab.html |
| Custom code for data analysis (including plotting neuron distribution, behavioral analysis, and Tadpose) | This paper | https://github.com/sweeneylab/MN_V1_analysis |
| Other | ||
| Automatic capillary puller | Sutter Instrument | P-97 |
| Cryostat microtome | Bright | OTF 6000 |
| Cryostat microtome | ThermoFisher | |
| PicoSpritzer injection setup | World Precision Instruments | PV820 |
| Standard Infusion Only Pump | Harvard Apparatus | 70–4501 |
| Glass capillaries | Drummond | 3-000-203-G/X |
| Nikon CSU-W1 | Nikon Instruments | CSU-W1 |
| ZEISS LSM800 | Carl Zeiss Microscopy | LSM800 |
| ZEISS Lightsheet Z.1 | Carl Zeiss Microscopy | Lightsheet Z.1 |
| ZEISS Lightsheet 7 | Carl Zeiss Microscopy | Lightsheet 7 |
| ZEISS Apotome | Carl Zeiss Microscopy | |
| Leica SP8 AOBS | Leica Microsystems | SP8 AOBS |