KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Mouse monoclonal anti-ABCA3 | Abcam | Cat#ab24751; RRID: AB_448287 |
| Rat monoclonal anti-LAMP1 | Abcam | Cat#ab25245; RRID: AB_449893 |
| Mouse monoclonal anti-LC3B | Cosmo Biometrics | Cat#CTB-LC3-2-IC: AB_10707197 |
| Mouse monoclonal anti-HSP90 | 3D Transduction Laboratories | Cat#610419; RRID: AB_397799 |
| Rabbit polyclonal anti-SPC | EMD Millipore | Cat#ABC99; RRID: AB_2755001 |
| Rabbit polyclonal anti-SPB | EMD Millipore | Cat#07-614; RRID: AB_310753 |
| Rabbit polyclonal anti-p62 | MBL | Cat#PM045; RRID: AB_1279301 |
| Mouse monoclonal anti-HOPX | Santa Cruz Biotechnology | Cat#sc-398703; RRID: AB_2687966 |
| Alexa Fluor 488-conjugated anti-mouse IgG | Thermo Fisher Scientific | Cat#A-11001; RRID: AB_2534069 |
| Alexa Fluor 568-conjugated anti-rabbit IgG | Thermo Fisher Scientific | Cat#A-11011; RRID: AB_143157 |
| Alexa Fluor 568-conjugated anti-rat IgG | Thermo Fisher Scientific | Cat#A-11077; RRID: AB_141874 |
| Alexa Fluor 660-conjugated anti-mouse IgG | Thermo Fisher Scientific | Cat#A-21055; RRID: AB_2535722 |
| Alexa Fluor 633-conjugated anti-rat IgG | Thermo Fisher Scientific | Cat#A-21094; RRID: AB_141553 |
| Alexa Fluor 660-conjugated anti-rabbit IgG | Thermo Fisher Scientific | Cat#A-21074; RRID: AB_2535735 |
| HRP-conjugated goat polyclonal anti-rabbit IgG | Jackson ImmunoResearch Laboratories | Cat#111-035-144; RRID: AB_2307391 |
| HRP-conjugated goat polyclonal anti-mouse IgG | Jackson ImmunoResearch Laboratories | Cat#115-035-003; RRID: AB_10015289 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Alt-R S.p. Cas9 Nuclease 3NLS | IDT | Cat#1074181 |
| PrimeSTAR Max DNA polymerase | Takara Bio Inc. | Cat#R045A |
| Hoechst33342 | Dojindo Molecular Technologies | Cat#H342 |
| SlowFade antifade reagents | Thermo Fisher Scientific | Cat#S36936 |
| 1-phenyl 2-thiourea | Sigma-Aldrich | Cat#P7629 |
| tricaine | Sigma-Aldrich | Cat#A5040 |
| Critical Commercial Assays | ||
| mMESSAGE mMACHINE SP6 Transcription Kit | Thermo Fisher Scientific | Cat#AM1340 |
| MEGAshortscript T7 Transcription Kit | Thermo Fisher Scientific | Cat#AM1354 |
| mirVana miRNA Isolation Kit | Thermo Fisher Scientific | Cat#AM1560 |
| RNeasy Mini Kit | QIAGEN | Cat#74104 |
| Experimental Models: Organisms/Strains | ||
| Zebrafish: RIKEN Wako wild-type strain | Zebrafish National Bioresource | ZFIN ID: ZDB-GENO-070802-4 |
| Zebrafish: atg101+/− | This study | N/A |
| Zebrafish: atg13+/− | This study | N/A |
| Zebrafish: atg14+/− | This study | N/A |
| Zebrafish: atg2a+/− | This study | N/A |
| Zebrafish: atg2b+/− | This study | N/A |
| Zebrafish: atg5+/− | This study | N/A |
| Zebrafish: atg9a+/− | This study | N/A |
| Zebrafish: atg9b+/− | This study | N/A |
| Zebrafish: atg16l1+/− | This study | N/A |
| Zebrafish: fip200/rb1cc1+/− | (Kaizuka et al., 2016) | ZFIN ID: ZDB-ALT-171018-3 |
| Zebrafish: vmp1+/− | (Morishita et al., 2019) | ZFIN ID: ZDB-ALT-200609-11 |
| Mouse: C57BL/6J | Sankyo Labo Service | N/A |
| Mouse: Afg101+/− | This study | N/A |
| Mouse: Afg5+/− | (Kuma et al., 2004) | BRC No.: RBRC02231 |
| Mouse: Fip200flox/+ | (Gan et al., 2006) | N/A |
| Mouse: Afg5flox/+ | (Hara et al., 2006) | BRC No.: RBRC02975 |
| Mouse: SPC-Cre | (Hato et al., 2009) | CARD ID: 2191 |
| Mouse: GFP-LC3-RFP-LC3ΔG | (Kaizuka et al., 2016) | BRC No: RBRC09930 |
| Recombinant DNA | ||
| pMXs-IP-GFP-LC3B | (Hara et al., 2008) | Addgene #38195 |
| pCS2-LAMP1-GFP | This study | N/A |
| pCS2-LAMP1-RFP | This study | N/A |
| Software and Algorithms | ||
| CRISPRscan | (Moreno-Mateos et al., 2015) | https://www.crisprscan.org/ |
| ImageJ | (Schindelin et al., 2012) | RRID: SCR_002285 |
| Photoshop CS6 | Adobe Systems | N/A |
| GraphPad Prism 8 software | GraphPad software | N/A |