Key resources table.
| Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Gene (Xenopus laevis) | aRCA3 | NCBI | NCBI:XM_018246573.1 | |
| Gene (Xenopus laevis) | VAMP2 | Xenbase | Xenbase:vamp2.S | |
| Gene (Xenopus laevis) | C3 | Xenbase | Xenbase:c3.L | |
| Strain, strain background (Escherichia coli) | DH5α competent cells | Invitrogen | Cat#:18265017 | |
| Biological sample (Xenopus laevis) | Albino Xenopus laevis tadpoles | Nasco | RRID:XEP_Xla200 | |
| Recombinant DNA reagent | pEGFP-N1 | Clontech | Cat#: 6085–1 | |
| Recombinant DNA reagent | pFA6a pH-tdGFP | PMID:27324986 | RRID:Addgene_74322 | |
| Recombinant DNA reagent | pEF1α P2A-pHtdGFP | This paper | Available from Edward Ruthazer upon request | |
| Recombinant DNA reagent | SYP-GFP plasmid | PMID:16571768 | ||
| Recombinant DNA reagent | pEF1α SYP-pHtdGFP | This paper | Available from Edward Ruthazer upon request | |
| Recombinant DNA reagent | pEF1α aRCA3-Myc-P2A-pHtdGFP | This paper | Available from Edward Ruthazer upon request | |
| Recombinant DNA reagent | pEF1α aRCA3-mCherry-Myc-P2A-SYP-pHtdGFP | This paper | Available from Edward Ruthazer upon request | |
| Recombinant DNA reagent | pEF1α pHtdGFP-P2A-VAMP2 | This paper | Available from Edward Ruthazer upon request | |
| Recombinant DNA reagent | pEF1α pHtdGFP-P2A-Myc-VAMP2-C3 | This paper | Available from Edward Ruthazer upon request | |
| Sequenced-based reagent | RNAscope Probe against Xenopus laevis polr2a.L | Advanced Cell Diagnostics | RNAscope probe: Xl-polr2aL | |
| Sequenced-based reagent | RNAscope Probe against Xenopus laevis aRCA3 | Advanced Cell Diagnostics | RNAscope probe: Xl-LOC108708165 | |
| Commercial assay or kit | RNAscope Multiplex Fluorescent Reagent Kit v2 | Advanced Cell Diagnostics | Cat#:323136 | |
| Chemical compound, drug | PLX5622 | Plexxikon | N/A | |
| Chemical compound, drug | Polyethylene glycol 400 | Sigma | SKU:P3265 | |
| Chemical compound, drug | Poloxamer 407 | Sigma | SKU:16758 | |
| Chemical compound, drug | D-α-Tocopherol polyethylene glycol 1000 succinate | Sigma | SKU:57668 | |
| Chemical compound, drug | Isolectin GS-IB4 FromGriffonia simplicifolia, Alexa Fluor 594 Conjugate | Thermo Fisher Scientific | Cat#:I21413 | |
| Chemical compound, drug | CellTracker Green BODIPY | Thermo Fisher Scientific | Cat#:C2102 | |
| Software, algorithm | STRING v11.0 protein-protein association networks | PMID:30476243 | RRID:SCR_005223 | |
| Software, algorithm | SMART protein domain annotation resource 8.0 | PMID:29040681 | RRID:SCR_005026 | |
| Software, algorithm | Phobius transmembrane topology tool | PMID:17483518 | RRID:SCR_015643 | |
| Software, algorithm | PyMOL 2.4 | Schrödinger, LLC. | RRID:SCR_000305 | Schrödinger, LLC, 2020 |
| Software, algorithm | trRosetta | PMID:31896580 | ||
| Software, algorithm | ProBLM | PMID:25126110 | ||
| Software, algorithm | NetPhos 3.1 | PMID:15174133 | RRID:SCR_017975 | |
| Software, algorithm | R 4.0.0 | R Core Team | RRID:SCR_001905 | |
| Software, algorithm | RColorBrewer | Erich Neuwirth | RRID:SCR_016697 | |
| Software, algorithm | ComplexHeatmap | PMID:27207943 | RRID:SCR_017270 | |
| Software, algorithm | Bioconductor 3.11 | PMID:25633503 | RRID:SCR_006442 | |
| Software, algorithm | Serial Cloner 2.6.1 | SerialBasics | RRID:SCR_014513 | |
| Software, algorithm | Imaris 6 | Oxford Instruments | RRID:SCR_007370 | |
| Software, algorithm | Fluoview 5.0 | Olympus | RRID:SCR_014215 | |
| Software, algorithm | ThorImage LS | Thorlabs | ||
| Software, algorithm | Leica LAS X | Leica | RRID:SCR_013673 | |
| Software, algorithm | FIJI ImageJ | PMID:22743772 | RRID:SCR_002285 | Schindelin et al., 2012 |
| Software, algorithm | 3D Objects Counter plugin | PMID:17210054 | RRID:SCR_017066 | |
| Software, algorithm | 3D ROI Manager plugin | PMID:23681123 | RRID:SCR_017065 | |
| Software, algorithm | TrackMate plugin | PMID:27713081 | ||
| Software, algorithm | Descriptor-based series registration plugin | PMID:20508634 | ||
| Software, algorithm | 3D hybrid median filter plugin | Christopher Philip Mauer and Vytas Bindokas | ||
| Software, algorithm | ScatterJ plugin | PMID:25515182 | ||
| Software, algorithm | MATLAB | MathWorks | RRID:SCR_001622 | |
| Software, algorithm | CANDLE | PMID:22341767 | ||
| Software, algorithm | Graphpad Prism 9 | GraphPad Software | RRID:SCR_002798 | |
| Software, algorithm | Fisher r-to-z transformation calculator | VassarStats | RRID:SCR_010263 | |
| Software, algorithm | Cura 4 | Ultimaker | RRID:SCR_018898 | |
| Software, algorithm | TinkerCAD | Autodesk | ||
| Software, algorithm | Psychopy 3.0 | PMID:30734206 | RRID:SCR_006571 | |
| Software, algorithm | XenLoom (beta): Looming Stimulus Presentation and Tracking of Xenopus laevis tadpoles |
This paper | github.com/tonykylim/XenLoom_beta; Lim, 2021; copy archived at swh:1:rev:b487791d1d91a5950eebfd1e7640e0c3db761cf5 | |
| Other | Allen Brain Map Human Multiple Cortical Areas SMART-seq data set | Allen Institute for Brain Science | ||
| Other | Estink 2000 lumens mini LED projector | Amazon.ca | ASIN#:B07F7RT9XZ | |
| Other | 96 white 20 lb bond copy paper | Staples.ca | Item#:380480 | |
| Other | Custom 3D printed mount for projector lens | This paper | http://www.thingiverse.com/thing:4335379 | |
| Other | Custom 3D printed stage for Xenopus laevis behavior | This paper | http://www.thingiverse.com/thing:4335395 | |
| Other | 8-inch soda lime 1500 ml culture dish | Carolina | Item#:741006 | |
| Other | 60 mm petri dish | Fisher Scientific Canada | Cat#:FB0875713A | |
| Other | PLA 1.75 mm 3D printing filament | iPrint-3D | Transparent purple | |
| Other | Logitech C920 webcam | Logitech | Model#:960–000764 | |
| Other | Anycubic i3 mega 3D printer | Amazon.ca | ASIN#:B07NY5T1LJ |