Key resources table.
| Reagent type (species) or resource |
Designation | Source or reference |
Identifiers | Additional information |
|---|---|---|---|---|
| Genetic reagent (Mus musculus) | GFP-LC3B | RIKEN BioResource Center in Japan; PMID: 14699058 | RRID:IMSR_RBRC00806 | |
| Genetic reagent (M. musculus) | C57BL/6J | Jackson Laboratory | Cat # 000664; RRID:IMSR_JAX:000664 | |
| Cell line (Homo sapiens) | HEK293 | Gibco (ThermoFisher) | Cat # R70507 | Authenticated by STR profiling; tested negative for mycoplasma |
| Cell line (H. sapiens) | HeLa-M | A. Peden (Cambridge Institute for Medical Research) | Authenticated by STR profiling; tested negative for mycoplasma | |
| Transfected construct (H. sapiens) | mCherry-ATG13 | This paper | Subcloned from RRID:Addgene_22875 | |
| Transfected construct (M. musculus) | mCherry-ATG5 | Addgene; PMID:16645637 | RRID:Addgene_13095 | |
| Transfected construct (H. sapiens) | Halo-ATG5 | This paper | Subcloned from RRID:Addgene_13095 | |
| Transfected construct (H. sapiens) | SNAP-ATG9 | This paper | Subcloned from RRID:Addgene_60609 | |
| Transfected construct (H. sapiens) | Halo-ATG9 | This paper | Subcloned from RRID:Addgene_60609 | |
| Transfected construct (H. sapiens) | SNAP-WIPI1A | This paper | Subcloned from RRID:Addgene_38272 | |
| Transfected construct (M. musculus) | Halo-DFCP1 | This paper | Subcloned from RRID:Addgene_38269 | |
| Transfected construct (H. sapiens) | mScarlet-LC3A | This paper | Subcloned from RRID:Addgene_73946 | |
| Transfected construct (H. sapiens) | mCherry-GABARAP | This paper | Subcloned from RRID:Addgene_73948 | |
| Transfected construct (H. sapiens) | mCherry-GEC1(GABARAPL1) | This paper | Subcloned from RRID:Addgene_73945 | |
| Transfected construct (H. sapiens) | mCherry-GATE16(GABARAPL2) | This paper | Subcloned from RRID:Addgene_73518 | |
| Transfected construct (H. sapiens) | SNAP-WIPI2B WT | This paper | Subcloned from GFP-WIPI2B, PMID: 24954904 | |
| Transfected construct (H. sapiens) | Halo-WIPI2B WT | This paper | Subcloned from GFP-WIPI2B, PMID: 24954904 | |
| Transfected construct (H. sapiens) | SNAP-WIPI2B (FTTG) | This paper | Generated via quick change from SNAP-WIPI2B WT | |
| Transfected construct (H. sapiens) | Halo-WIPI2B (FTTG) | This paper | Generated via quick change from Halo-WIPI2B WT | |
| Transfected construct (H. sapiens) | SNAP-WIPI2B (R108E) | This paper | Generated via quick change from SNAP-WIPI2B WT | |
| Transfected construct (H. sapiens) | Halo-WIPI2B (R108E) | This paper | Generated via quick change from Halo-WIPI2B WT | |
| Transfected construct (H. sapiens) | SNAP-WIPI2B (S395A) | This paper | Generated via quick change from SNAP-WIPI2B WT |
|
| Transfected construct (H. sapiens) | Halo-WIPI2B (S395A) | This paper | Generated via quick change from Halo-WIPI2B WT | |
| Transfected construct (H. sapiens) | SNAP-WIPI2B (S395E) | This paper | Generated via quick change from SNAP-WIPI2B WT |
|
| Transfected construct (H. sapiens) | Halo-WIPI2B (S395E) | This paper | Generated via quick change from Halo-WIPI2B WT | |
| Antibody | Anti-Actin, Mouse Polyclonal | EMD Millipore | Cat # MAB1501; RRID:AB_2223041 | WB (1:3000) |
| Antibody | Anti-ATG10, Rabbit Polyclonal | Novus | Cat # NBP2-38524 | WB (1:100) |
| Antibody | Anti-ATG12, Rabbit Polyclonal | Abcam | Cat # ab155589 | ICC (1:50) |
| Antibody | Anti-ATG13, Rabbit Polyclonal | Abcam | Cat # ab105392; RRID:AB_10892365 | ICC (1:50), IHC (1:100) |
| Antibody | Anti-ATG14, Rabbit Monoclonal | Cell Signaling Technology | Cat # 96752; RRID:AB_2737056 | WB (1:1000) |
| Antibody | Anti-ATG16L1, Rabbit Monoclonal | Abcam | Cat # ab187671 | WB (1:1000), ICC (1:50) |
| Antibody | Anti-ATG3, Rabbit Monoclonal | Abcam | Cat # ab108251; RRID:AB_10865145 | WB (1:3000), ICC (1:50) |
| Antibody | Anti-ATG5, Rabbit Monoclonal | Abcam | Cat # ab108327; RRID:AB_2650499 | WB (1:1000) |
| Antibody | Anti-ATG5-Alexa647, Rabbit Monoclonal | Abcam | Cat # ab206715 | ICC (1:50 ON) |
| Antibody | Anti-ATG7, Rabbit Monoclonal | Abcam | Cat # ab133528; RRID:AB_2532126 | WB (1:1000), ICC (1:50) |
| Antibody | Anti-ATG9, Armenian Hamster Monoclonal | Abcam | Cat # ab187823 | ICC (1:100), IHC (1:100) |
| Antibody | Anti-ATG9-Alexa488, Rabbit Monoclonal | Abcam | Cat # ab206252 | ICC (1:50 ON) |
| Antibody | Anti-Beclin1 (BECN1), Mouse Monoclonal | Santa Cruz | Cat # sc-48341; RRID:AB_626745 | WB (1:200) |
| Antibody | Anti-GABARAP, Rabbit Monoclonal | Cell Signaling Technology | Cat # 13733; RRID:AB_2798306 | WB (1:1000), ICC (1:50) |
| Antibody | Anti-GAPDH, Mouse Monoclonal | Abcam | Cat # ab9484; RRID:AB_307274 | WB (1:1000) |
| Antibody | Anti-GABARAPL1 (GEC1), Rabbit Monoclonal | Cell Signaling Technology | Cat # 26632; RRID:AB_2798928 | WB (1:1000), ICC (1:200) |
| Antibody | Anti-GABARAPL2 (GATE16), Rabbit Polyclonal | Abcam | Cat # ab137511 | ICC (1:50) |
| Antibody | Anti-GABARAPL2 (GATE16), Rabbit Monoclonal | Cell Signaling Technology | Cat # 14256; RRID:AB_2798436 | WB (1:1000) |
| Antibody | Anti-GABARAPs, Rabbit Monoclonal | Abcam | Cat # ab109364; RRID:AB_10861928 | ICC (1:100) |
| Antibody | Anti-Halo, Mouse Monoclonal | Promega | Cat # G9211 | WB (1:500), IP (3 μg) |
| Antibody | Anti-HSP90, Rabbit Monoclonal | Cell Signaling Technology | Cat # 4877; RRID:AB_2233307 | WB (1:1000) |
| Antibody | Anti-LC3, Rabbit Polyclonal | Abcam | Cat # ab48394; RRID:AB_881433 | IHC (1:200) |
| Antibody | Anti-LC3A, Rabbit Monoclonal | Cell Signaling Technology | Cat # 4599; RRID:AB_10548192 | WB (1:1000) |
| Antibody | Anti-LC3B, Mouse Monoclonal | Santa Cruz | Cat # sc-376404; RRID:AB_11150489 | WB (1:100), ICC (1:50) |
| Antibody | Anti-MEK1/2, Rabbit Monoclonal | Cell Signaling Technology | Cat # 8727; RRID:AB_10829473 | WB (1:1000) |
| Antibody | Anti-NFH, Chicken Polyclonal | Aves | Cat # NFH; RRID:AB_2313552 | IHC (1:400) |
| Antibody | Anti-p62, Mouse Monoclonal | Abcam | Cat # ab56416; RRID:AB_945626 | WB (1:200) |
| Antibody | Anti-phospho-ATG14(S29), Rabbit Polyclonal | Cell Signaling Technology | Cat # 13155; RRID:AB_2798133 | WB (1:1000) |
| Antibody | Anti-phospho-ULK1(S757), Rabbit Polyclonal | Cell Signaling Technology | Cat # 6888; RRID:AB_10829226 | WB (1:500) |
| Antibody | Anti-phospho-WIPI2(S395), Rabbit Polyclonal | Cell Signaling Technology | Cat # 13571; RRID:AB_2798259 | WB (1:1000) |
| Antibody | Anti-phospho-WIPI2(S395), Rabbit Polyclonal | This paper | # STO 316PB2 | WB (1:500), ICC (1:50) |
| Antibody | Anti-SV2, Mouse Monoclonal | Developmental Studies Hybridoma Bank, University of Iowa | Cat # SV2; RRID:AB_2315387 | IHC (1:100) |
| Antibody | Anti-ULK1, Rabbit Monoclonal | Cell Signaling Technology | Cat # 8054; RRID:AB_11178668 | WB (1:500) |
| Antibody | Anti-V-type H + ATPase, Rabbit Polyclonal | Synaptic Systems | Cat # 109–002; RRID:AB_887696 | WB (1:500) |
| Antibody | Anti-WIPI1, Rabbit Polyclonal | ThermoFisher | Cat # PA5-34973; RRID:AB_2552322 | WB (1:500) |
| Antibody | Anti-WIPI2, Mouse Monoclonal | Abcam | Cat # ab105459; RRID:AB_10860881 | WB (1:4000) |
| Antibody | Anti-WIPI3, Mouse IgM Monoclonal | Santa Cruz | Cat # sc-514194 | WB (1:100) |
| Antibody | Anti-WIPI4, Rabbit Polyclonal | ThermoFisher | Cat # PA5-71803; RRID:AB_2717657 | WB (1:250) |
| Antibody | Anti-Chicken IgY-AlexaFluor405, Goat Polyclonal | Abcam | Cat # ab175674 | IHC (1:200) |
| Antibody | Anti-Mouse IgG-AlexaFluor405, Goat Polyclonal | ThermoFisher | Cat # A31553; RRID:AB_221604 | IHC (1:200) |
| Antibody | Anti-Armenian Hamster-AlexaFluor647, Goat Polyclonal | Abcam | Cat # ab173004; RRID:AB_2732023 | IHC (1:200) |
| Antibody | Anti-Rabbit-AlexaFluor488,Goat Polyclonal | ThermoFisher | Cat # A11034; RRID:AB_2576217 | IHC (1:200) |
| Antibody | Anti-Armenian Hamster-AlexaFluor488, Goat Polyclonal | Abcam | Cat # ab173003 | ICC (1:200) |
| Antibody | Anti-Rabbit IgG-AlexaFluor546, Donkey Polyclonal | ThermoFisher | Cat # A10040; RRID:AB_2534016 | ICC (1:200) |
| Antibody | Anti-Mouse IgG-AlexaFluor546, Donkey Polyclonal | ThermoFisher | Cat # A10036; RRID:AB_2534012 | ICC (1:200) |
| Antibody | Anti-Rabbit IgG-AlexaFluor647, Donkey Polyclonal | ThermoFisher | Cat # A31573; RRID:AB_2536183 | ICC (1:200), IHC (1:200) |
| Antibody | Anti-Rabbit IgG-IRDye 800CW, Donkey Polyclonal | LI-COR Biosciences | Cat # 926–32213; RRID:AB_621848 | WB (1:20,000) |
| Antibody | Anti-Mouse IgG-IRDye 800CW, Donkey Polyclonal | LI-COR Biosciences | Cat # 926–32212; RRID:AB_621847 | WB (1:20,000) |
| Antibody | Anti-Mouse IgM-IRDye 800CW, Goat Polyclonal | LI-COR Biosciences | Cat # 926–32280 | WB (1:20,000) |
| Antibody | Anti-Rabbit IgG-IRDye 680RD, Donkey Polyclonal | LI-COR Biosciences | Cat # 926–68073; RRID:AB_10954442 | WB (1:10,000) |
| Antibody | Anti-Mouse IgG Light Chain-AlexaFluor680, Goat Polyclonal | Jackson ImmunoResearch Labs | Cat # 115-625-174; RRID:AB_2338937 | WB (1:20,000) |
| Sequence-based reagent | ON-TARGET plus SMARTpool Mouse Wipi2 siRNA | Dharmacon | Cat # L-057690–01 | Proprietary sequence |
| Sequence-based reagent | ON-TARGET plus non-targeting siRNA | Dharmacon | Cat # D-001810–01 | Proprietary sequence |
| Chemical compound, drug | SNAP-Cell 647-SiR | New England Biolabs | Cat # S9102S | |
| Chemical compound, drug | SNAP-Cell TMR-Star | New England Biolabs | Cat # S9105S | |
| Chemical compound, drug | SNAP-Cell 430 | New England Biolabs | Cat # S9109S | |
| Chemical compound, drug | HaloTag TMR | Promega | Cat # G8251 | |
| Chemical compound, drug | silicon-rhodamine-Halo | K. Johnsson, École Polytechnique Federale de Lausanne | ||
| Chemical compound, drug | JF646-Halo | Luke Lavis, Janelia Farms (HHMI) | ||
| Chemical compound, drug | α-Bungarotoxin-tetramethylrhodamine | Sigma | T0195 | |
| Software, algorithm | Volocity | PerkinElmer | ||
| Software, algorithm | FIJI | PMID: 22743772 | ||
| Software, algorithm | Prism 6, Prism 8 | GraphPad | ||
| Software, algorithm | Adobe Illustrator CS4 | Adobe Systems |