"Table S1. gRNA, RNAi, and primer sequences" gRNAs gRNAs that were inserted into the pX330 plamids. Note that each gene was deleted with three mixed gRNAs targeting distinct regions in the first half of each gene. "Also note that some gRNAs are 21 bases, as we added a G at the 5' end to enable U6 promoter driven expression." Gene 1 2 3 VPS29 GGACATCAAGTTATTCCATG GGACATCAAGTTATTCCATG GGCAAACTGTTGCACCGGTG VPS35 GTGGTGTGCAACATCCCTTG GAAAAGGATTCAAAGTCTGG GTTTGCTAAAGGAAGGAAAG TBC1D5 GATGCATTACCCATTCATCG GAGTTACTCTAACAAGTCTGG GACTAGCATATTACCAACCCG SNX1 GAGCCTACAAAGTTACAACAC GGCCGGGGGATCAGAACCCG GTCTTTGGAGCCATTGTTGAT SNX2 GCAGCACTGTCTCCACCCTAG GTGGGCTTCCCGTCCCCCAG GAAGGGAACCTATCCTATCCT SNX5 GCTCTGAAACGTGGGCAGTG GGTATGTCAATCTGAAGCGA GCAGGAGGAGGACCGCAGCA SNX6 GATGTGCTGCCACACGACAC GATTATATTCCAAGAAGACA GGAGTATCATAACCGAGTTA FAM21 GTGGCAGTATTGTGGACACTG GAAATCAAGAAACAAGTGGA GTCTCATTCCTAAAGTCCAGG VARP GTGGCGCCCTTGGAAACCAGG GACCAAGAAGGACTACAGAG GCAGACAAGCTTCTGCTGTG ANKRD50 GATGATGGAAGAAATGCACTG GAAGGGTGTAACATTACTGA GATCCTTGGAGTAGTCCACTG RAB7a GGGACACAGCAGGACAGGAA GGGAAGTTTTCAGGATCTCG GAGCTGACTTTCTGACCAAGG VPS39 GGGCCAGGATGATCTCACCG GATGTAGCATCACCTGAAAG GGAGGTGTTACGGATGTGTG NPRL2 GGTTGAAGAGGAGAGCATT GACTTGAAGGTGATTGAGCAG GAGCAGCTTCGTGTCCATGG DEPDC5 GAGCACAAGGAAACTACCTGG GGATCAGTATATTGGCCGTG GCACCAGGGAGGTTTCACGT CCZ1 GATGTGCCTTGGAAAAAGGG GCCGCATACCTGTCCTTCGCG GCAGTGCTACAGCATGTACA TBC1D2 GGGTATTTAAGTAAGTTCGG GACAGGTTCTGATGCTCACCA GGCGTCCAGCGCATACCTGG TBC1D15 GGCACGCGCAGGAAACATGG GGAAAGACCAATGACCAAGA GAAGCAGATGATATTTAGAG VPS35L/C16ORF62 GAAGTCAAGAGCCTACCTTG GGAGCTGGATGACTTTGAGG GGATTACGTGAACCGCATAG CCDC22 GCCTGCGTGTGATCAACCCTG GAGAAGAGAAGCAGGTCTCGG GACTTCTCTGAGTGCGTGAAG siRNA sequences VPS35 AAATACCAGTTGACACTTA SNX27 GAGGGTGTTCTGCGAGCTCAA GGAACAACGGTTACAGTCA SNX1 CCACGTGATCAAGTACCTT SNX27 GAU AGA CCA GUU ACA UCA A Primer Sequences for cloning of ORFs from HeLa cDNA Gene/protein plasmid backbone Restriction sites forward primer reverse primer LC3b pLVX puro GFP (N-term) EcoR1/Kpn1 gattatgaattctatgccgtcggagaagaccttc gat tat ggt acc ttacactgacaatttcatccc TFEB pEGFP-N1 EcoR1/Kpn1 gattatgaattcGccaccatggcgtcacgcatagggttg Gattatggtacccagcacatcgccctcctccatgctgaag HA-VPS35 pLVX puro Xho1/Kpn1 gat ta tctc gag gcc atg tac cca tac gac gtc cca gac tac gct cctacaacacagcagtcccctc gat tat ggt acc ttaaaggatgagaccttcataaattg VPS29 pLVX puro EcoR1/Kpn1 atg aat tct atg gct ggg cac aga ttg gtg at ggt acc ttaaggttttttgtattcgattc RAGA pLVX puro GFP (N-term) Xho1/Kpn1 gat ta tct cga gtt atgccaaatacagccatgaag gat tat ggt acc tcaacgcataaggagactgtg RAGB pLVX puro GFP (N-term) Xho1/Kpn1 gat ta tct cga gtt atggaagaatctgactctgag gat tat ggt acc ttagcgcatgagaagacactg LAMTOR1 pLVX puro GFP (C-term) EcoR1/Kpn1 gat tat gaa ttc ccggccatggggtgctgctacag gat tat ggt accaa tgggatcccaaactgtacaac myc-RAGA pLVX puro Xho1/Kpn1 ta tct cga gccggccatg GAACAAAAACTTATTTCTGAAGAAGATCTG atgccaaatacagccatgaagaaaaagg gat tat ggt acc tcaacgcataaggagactgtgcttg SNX27 pEGFP-C1 Xho1/Kpn1 ta tct cga gtt atg gcg gac gag gac ggg gaa g at ggt acc cta ctcttttctccacttgagctc VPS26 pEGFP-C1 Xho1/Kpn1 atg aat tct atg agt ttt ctt gga ggc ttt ttt g at ggt acc tcacatttcaggctgttcggcag VPS35 pEGFP-C1 Kpn1/BamH1 at ggt acc atg cct aca aca cag cag tc at gga tcc aaggatgagaccttcataaattg FAM21 pEGFP-C1 Xho1/BamH1 ta tct cga gtt atgatgaaccggacgacccccg tat gga tcc ctactggcctccaaaggcattc WASH1 pEGFP-C1 EcoR1/Kpn1 tatg aat tct atgactcctgtgaggatgcagtat ggt acc ctacgattcccagtcgtcctc tat ggt acc ctacgattcccagtcgtcctc TBC1D5 pLVX puro GFP (N-term) Xho1/Kpn1 gattatctcgagttatgtatcattccttatctgaaactagacatc gattatggtacctcagatgtccaggggactcacaatggtgaag Primer Sequences for site directed mutagenesis (Quickchange II protocol) RAGA-Q66L ccatgaaggtgtccagaccgccacagtcc ggactgtggcggtctggacaccttcatgg RAB7 T22N Ctggttcatgagtgaattcttcccgactccagaatctcc Ggagattctggagtcgggaagaattcactcatgaaccag RAB7 Q67L Actggaaccgttccagtcctgctgtgtcc Ggacacagcaggactggaacggttccagt VPS29 L152E Ctgtagaagcctggatatccatctccacaaatgatggaataatgtttgt acaaacattattccatcatttgtggagatggatatccaggcttctacag TBC1D5 L142E Actcccttcatcctgtgactcaggattattgatcatcaaatcttgttggcc Ggccaacaagatttgatgatcaataatcctgagtcacaggatgaagggagt