Key resources table.
| Reagent type (species) or resource |
Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Strain, strain background (Danio rerio) | cldnb:lyn-EGFP | doi:10.1016/j.devcel.2006.02.019 | ZFIN ID:ZDB-TGCONSTRCT-070117–15 | |
| Strain, strain background (Danio rerio) | cxcr4b:NLS-tdTomato | doi:10.1038/nature12635 | ZFIN ID:ZDB-TGCONSTRCT-141217–3 | |
| Strain, strain background (Danio rerio) | Actb2:mKate2-Rab11a | This paper | made with tol2kit, see section ‘Transgenic Fish Lines’ | |
| Strain, strain background (Danio rerio) | LexOP:CDMPR-tagRFPt | This paper | made with tol2kit, see section ‘Transgenic Fish Lines’ | |
| Strain, strain background (Danio rerio) | LexOP:B4GalT1(1-55Q)-tagRFPt; cxcr4b:LexPR | This paper | made with tol2kit, see section ‘Transgenic Fish Lines’ |
|
| Strain, strain background (Danio rerio) | atoh1a:dtomato | doi:10.1016/j.ydbio.2010.02.017 | ZFIN ID:ZDB-TGCONSTRCT-100928–4 | |
| Strain, strain background (Danio rerio) | 6xUAS:tagRFPt-UtrCH | This paper | made with tol2kit, see section ‘Transgenic Fish Lines’ | |
| Strain, strain background (Danio rerio) | cxcr4b:LexPR | doi:10.1038/nature13852 | ZFIN ID:ZDB-TGCONSTRCT-170105–4 | LexOP chemically inducible driver line |
| Strain, strain background (Danio rerio) | ETL GA346 | doi:10.1073/pnas.0903060106 | Gal4-UAS driver line | |
| Recombinant DNA reagent | sp6:mKate2-Rab5a (plasmid) | This paper | made with tol2kit, see section ‘Transgenic Fish Lines’ | |
| Recombinant DNA reagent | sp6:mKate2-GM130(rat) (plasmid) | doi:10.1242/jcs.026849 | made with tol2kit, see section ‘Transgenic Fish Lines’ | |
| Sequence-based reagent | CDMPR FOR (D. rerio, full-length) | This paper | PCR primers | GGGGACAAGTTTGTACAAAAAAGCAGGCTGGATGTTGCTGTCTGTGAGAATAATCACT |
| Sequence-based reagent | CDMPR REV (D. rerio, full-length) | This paper | PCR primers | GGGGACCACTTTGTACAAGAAAGCTGGGTCCATGGGAAGTAAATGGTCATCTCTTTCCTC |
| Sequence-based reagent | B4GalT1 FOR (D. rerio, 1-55Q) |
This paper | PCR primers | GGGGACAAGTTTGTACAAAAAAGCAGGCTGGATGTCGGAGTCGGTGGGATTCTTC |
| Sequence-based reagent | B4GalT1 REV (D. rerio, 1-55Q) |
This paper | PCR primers | GGGGACCACTTTGTACAAGAAAGCTGGGTCTTGTGAATTAACCATATCAGAGATAAATGAAATGTGTCG |
| Sequence-based reagent | Rab5a FOR (D. rerio, full-length) |
This paper | PCR primers | GGGGACAGCTTTCTTGTACAAAGTGGCTATGGCCAATAGGGGAGGAGCAACAC |
| Sequence-based reagent | Rab5a REV (D. rerio, full-length) |
This paper | PCR primers | GGGGACAACTTTGTATAATAAAGTTGCTTAGTTGCTGCAGCAGGGGGCT |
| Sequence-based reagent | Rab11 FOR (D. rerio, full-length) |
This paper | PCR primers | GGGGACAGCTTTCTTGTACAAAGTGGCTATGGGGACACGAGACGACGAATACG |
| Sequence-based reagent | Rab11 REV (D. rerio, full-length) |
This paper | PCR primers | GGGGACAACTTTGTATAATAAAGTTGCCTAGATGCTCTGGCAGCACTGC |
| Sequence-based reagent | Quasar 670-conjugated Stellaris smFISH probes | LGC, Biosearch Technologies | smFISH probes | Targeted at D. rerio pea3 gene, see section ‘smFISH: Fixation, Staining and Imaging’ |
| Commercial assay or kit | RNeasy Mini Kit | Qiagen | Cat#:74106 | |
| Commercial assay or kit | QIAshredder | Qiagen | Cat#:79654 | |
| Commercial assay or kit |
SuperScript III Reverse Transcriptase | Thermo Fisher Scientifc | Cat#:18080044 | |
| Commercial assay or kit | mMESSAGEmMACHINESP6 Transcription Kit | Thermo Fisher Scientific | Cat#:AM1340 | |
| Commercial assay or kit | MultiSite Gateway Pro | Invitrogen | Cat#:12537 | |
| Chemical compound, drug | LysoTrackerDeep Red | Thermo Fisher Scientific | Cat#:L12492 | |
| Chemical compound, drug | RU486 | Sigma-Aldrich | Cat#:M8046 | |
| Chemical compound, drug | N-phenylthiourea (PTU) | Sigma-Aldrich | Cat#:P7629 | |
| Chemical compound, drug | Tricaine (MESAB) | Sigma-Aldrich | Cat#:A5040 | |
| Software, algorithm | fiji | doi:10.1038/nmeth.2019 | RRID:SCR_002285 | imagej.net/Fiji |
| Software, algorithm | Anaconda | Anaconda, Inc | RRID:SCR_018317 | www.anaconda.com |
| Software, algorithm | python 2.7 | Python Software Foundation | RRID:SCR_008394 | www.python.org/psf |
| Software, algorithm | ISLA | This paper | github.com/WhoIsJack/data-driven-analysis-lateralline (Hartmann, 2020; copy archived at https://github.com/elifesciences-publications/data-driven-analysis-lateralline) | See section ‘Data and Code Availability’ |
| Software, algorithm | CBE | This paper | github.com/WhoIsJack/data-driven-analysis-lateralline | See section ‘Data and Code Availability’ |