KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Rabbit polyclonal anti-β-actin | Cell Signaling Technology | Cat#4967S; RRID: AB_330288 |
| Rabbit polyclonal anti-ATG5 | Novus | Cat#NB110-53818; RRID: AB_828587 |
| Rabbit polyclonal anti-Histone 3 (monomethyl K9) | abcam | Cat#ab8896; RRID: AB_732929 |
| Rabbit monoclonal anti-MTMR5 | abcam | Cat#ab181106 |
| Mouse monoclonal anti-MTMR5 | Santa Cruz | Cat#sc-393488 |
| Mouse monoclonal anti-MTMR2 | Santa Cruz | Cat#sc-365184 |
| Mouse monoclonal anti-SQSTM1/p62 | Novus | Cat#H00008878-M01; RRID: AB_437085 |
| Mouse monoclonal anti-TFEB | MyBioSource | Cat#MBS120432; RRID: AB_2271743 |
| Goat anti-mouse Atto488 | Rockland Immunochemicals | Cat#610-152-121; RRID: AB_10893825 |
| Goat anti-mouse Alexa Fluor 594 | ThermoFisher Scientific | Cat#A11032; RRID: AB_2534091 |
| Goat anti-rabbit Alexa Fluor 647 | ThermoFisher Scientific | Cat#A32733; RRID: AB_2633282 |
| Chemicals, peptides, and recombinant proteins | ||
| Dimethyl sulfoxide (DMSO) | Sigma-Aldrich | Cat#D8418 |
| TeSR-E8 | STEMCELL | Cat#05990 |
| Torin1 | Tocris | Cat#4247 |
| Bafilomycin A1 | Cayman | Cat#NC135138 |
| Ammonium chloride (NH4Cl) | Sigma-Aldrich | Cat#A9434 |
| Bortezomib | Sigma-Aldrich | Cat#179324-69-7 |
| Experimental models: Cell lines | ||
| Human: mono-allelic mEGFP-tagged MAP1LC3 WTC iPSC line (tag at N-term) | Coriell Institute | Cat#AICS-0030-022 |
| Human: TDP-43-Dendra2 iPSC line (tag at C-term) | This paper | N/A |
| Human: GAPDH-2A-Dendra2 iPSC line | This paper | N/A |
| Rat: primary cortical neurons | This paper | N/A |
| Rat: primary cortical glia | This paper | N/A |
| Oligonucleotides | ||
| Primer: human ATG5 RT-PCR; Forward: GACTGGACTTGTGGTGCGCT; Reverse: AGCCGCAAAAAGCACCG | This paper | N/A |
| Primer: rat Atg5 RT-PCR; Forward: CTGTGATCCCGGTAGACCCA; Reverse: CCGTCCAAACCACACGTCTC | This paper | N/A |
| Primer: human GAPDH RT-PCR; Forward: AAGGTGAAGGTCGGAGTCAA; Reverse: AATGAAGGGGTCATTGATGG | This paper | N/A |
| Primer: rat Gapdh RT-PCR; Forward: CATCTCCCTCACAATTCCATCC; Reverse: GAGGGTGCAGCGAACTTTAT | This paper | N/A |
| Primer: human MTMR2 RT-PCR; Forward: GCCAGCACGGAGAGTCGAT; Reverse: AGCAGTCTTCGCGGCTACAG | This paper | N/A |
| Primer: rat Mtmr2 RT-PCR; Forward: CCACCTCCACCCCCAAAATG; Reverse: CAGGGAAGAGATCCGTGTGC | This paper | N/A |
| Primer: human MTMR9 RT-PCR; Forward: GAGGCGGCTTTCTCCTACTG; Reverse: CTAGGACTCGGCCACAGAGA | This paper | N/A |
| Primer: rat Mtmr9 RT-PCR; Forward: GCCTTGACCTTGGCTGTAGG; Reverse: CAGCACAGGGCACAGGTATC | This paper | N/A |
| Primer: human SBF1 RT-PCR; Forward: GAGGAGAGCACGGTGTTCAG; Reverse: CGCTCTCCGTGTCATAGCTC | This paper | N/A |
| Primer: rat Sbf1 RT-PCR; Forward: GCTGTAGTGTAGCCCTGCTC; Reverse: GACGTTGGTAGCTCCTGGAC | This paper | N/A |
| Primer: human SQSTM1 RT-PCR; Forward: GTACCAGGACAGCGAGAGGA; Reverse: CTCAAGCCCCATGTTGCACG | This paper | N/A |
| Primer: rat Sqstm1 RT-PCR; Forward: CTGATCCCCGGCTGATTGAG; Reverse: GAGGTGGGTTGTGGGACTTG | This paper | N/A |
| Primer: human TFEB RT-PCR; Forward: GAGAATGATGCCTCCGCACC; Reverse: GCGCAACCCTATGCGTGA | This paper | N/A |
| Primer: rat Tfeb RT-PCR; Forward: CGGCAGTCCTATGATGGGGA; Reverse: CCCCCTTCTCCAAAATGCCC | This paper | N/A |
| Recombinant DNA | ||
| pX335-U6-Chimeric_BB-CBh-hSpCas9n(D10A) plasmid | Addgene | Cat#42335 |
| pUCM-TDP-43-Dendra2 HDR plasmid | Blue Heron, LLC | N/A |
| pUCM-GAPDH-2A-Dendra2 HDR plasmid | Blue Heron, LLC | N/A |
| pUCM-CLYBL-NGN1&2 HDR plasmid | Michael Ward (NINDS) | N/A |
| pUCM-CLYBL-hNIL HDR plasmid | Michael Ward (NINDS) | N/A |
| PB-MYOD-shOCT4 plasmid | Michael Ward (NINDS) | N/A |
| TRC lentiviral human SBF1 shRNA | Horizon | Cat#RHS3979-201739167 |
| TRC lentiviral human MTMR2 shRNA | Horizon | Cat#RHS3979-224867040 |
| TRC lentiviral human MTMR9 shRNA | Horizon | Cat#RHS3979-201908246 |
| TRC lentiviral human TFEB shRNA | Horizon | Cat#RHS3979-201744686 |
| TRC lentiviral human SQSTM1 shRNA | Horizon | Cat#RHS3979-201739507 |
| TRC lentiviral human non-targeted shRNA | Horizon | Cat#RHS6848 |
| Software and algorithms | ||
| Prism | GraphPad | https://www.graphpad.com/scientific-software/prism/ |
| Fiji/ImageJ | NIH, open-source | https://fiji.sc/ |
| ImagePro | Mediacy | https://www.mediacy.com/imagepro |
| μManager | Vale Lab (UCSF) | https://micro-manager.org |
| Bowtie | SourceForge | http://bowtie-bio.sourceforge.net/bowtie2/index.shtml |
| TopHat | Center for Computational Biology (Johns Hopkins) | https://ccb.jhu.edu/software/tophat/index.shtml |
| DESeq | Huber Group (EMBL) | https://www.huber.embl.de/users/anders/DESeq/ |
| R | R Core Team | https://www.r-project.org |
| Collaborative Discovery platform (CODI) | ONI | http://alto.codi.bio |