| Reagent/Resource | Reference or source | Identifier or catalog number |
|---|---|---|
| Experimental models | ||
|
HeLa WT (Homo sapiens) |
Prof Christian Behl | |
|
HeLa ATG5 KO (Homo sapiens) |
Prof Christian Behl | |
|
HeLa HA‐GABARAP (Homo sapiens) |
Prof Christian Behrends | |
|
MEF WT (Mus musculus) |
Prof Ivan Dikic | |
|
MEF FIP200 KO (Mus musculus) |
Prof Ivan Dikic | |
| Antibodies | ||
| Rabbit polyclonal anti‐MAP1LC3B (FlowCyt 4 μg; IF 1:200) | Novus | NB100‐2220 |
| Rabbit polyclonal anti‐MAP1LC3B‐AlexaFluor647 (FlowCyt 2 μg/4 μg) | Novus | NB100‐2220AF647 |
| Rabbit polyclonal anti‐MAP1LC3B (WB 1:500) | Sigma | L7543 |
| Mouse monoclonal [2G6] anti‐MAP1LC3B (IF 1:200) | Nanotools | 0260‐100/LC3‐2G6 |
| Mouse monoclonal [2G6] anti‐MAP1LC3B‐Fluorescein (FlowCyt 1 μg) | Enzo | BML‐PW1205‐0025 |
| Rabbit monoclonal [EPR4805] anti‐GABARAP+GABARAPL1+GABARAPL2 (FlowCyt 1 μg/4 μg; WB 1:500) | Abcam | ab109364 |
| Rabbit monoclonal [EPR4805] anti‐GABARAP+GABARAPL1+GABARAPL2‐APC (FlowCyt 2 μg) | Abcam | ab223949 |
| Rabbit polyclonal anti‐HA (FlowCyt 4 μg; IF 1:200) | Sigma | H6908 |
| Mouse monoclonal [6E2] anti‐HA (WB 1:500) | Cell Signaling | 2367 |
| Guinea pig polyclonal anti‐SQSTM1 (WB 1:500) | Progen | GP62‐C |
| Rabbit polyclonal anti‐ZFYVE1 (DFCP1) (WB 1:500) | ABclonal | A7527 |
| Mouse monoclonal [AP125] anti‐PLIN2 (WB 1:500) | Progen | 610102 |
| Rabbit polyclonal anti‐Sirt4 (WB 1:500) | Abcam | ab90485 |
| Mouse monoclonal [58K‐9] anti‐ 58K Golgi protein (FTCD) (WB 1:500) | Abcam | ab27043 |
| Mouse monoclonal [DM1A] anti‐Tubulin α (WB 1:500) | Sigma | T9026 |
| Mouse monoclonal [30F11] anti‐SOD1 (WB 1:500) | Leica Biosystems (Novocastra) | NCL‐SOD1 |
| Rabbit monoclonal [D5F5U] anti‐ATG5 (WB 1:500) | Cell Signaling | 12994 |
| Rabbit monoclonal [D10D11] anti‐FIP200 (WB 1:500) | Cell Signaling | 12436 |
| Mouse monoclonal [H4B4] anti‐LAMP2 (IF 1:200) | Abcam | ab25631 |
| Sheep polyclonal anti‐TGN46 (IF 1:200) | BioRad | AHP500 |
| Donkey polyclonal anti‐rabbit‐Cy3 (IF 1:200) | Jackson ImmunoResearch | 711‐165‐152 |
| Donkey polyclonal anti‐mouse‐Cy3 (IF 1:200) | Jackson ImmunoResearch | 715‐165‐151 |
| Donkey polyclonal anti‐sheep‐Cy3 (IF 1:200) | Jackson ImmunoResearch | 713‐165‐147 |
| Donkey polyclonal anti‐rabbit‐Cy5 (FlowCyt 3 μg/12 μg; IF 1:200) | Jackson ImmunoResearch | 711‐175‐152 |
| Donkey polyclonal anti‐mouse‐Cy5 (IF 1:200) | Jackson ImmunoResearch | 715‐175‐150 |
| Donkey polyclonal anti‐rabbit‐HRP (WB 1:7,000) | Jackson ImmunoResearch | 711‐035‐152 |
| Donkey polyclonal anti‐mouse‐HRP (WB 1:7,000) | Jackson ImmunoResearch | 715‐035‐151 |
| Donkey polyclonal anti‐guinea pig‐HRP (WB 1:7,000) | Jackson ImmunoResearch | 706‐035‐148 |
| Chemicals, enzymes, and other reagents | ||
| Acetonitrile | Carl Roth | AE70.1 |
| Antibiotic‐antimycotic solution | Sigma | A5955 |
| Bafilomycin A1 | Biozol | TRCB110000 |
| BODIPY FL C5‐shingomyelin | Fisher Scientific | 11510306 |
| BSA | Sigma | A7906 |
| CHAPS | Carl Roth | 1479 |
| Chloroacetamide | Sigma | 22790 |
| Chloroform | Carl Roth | 4432 |
| DAPI | Calbiochem | 382061 |
| DMEM | Thermo Fisher Scientific | 41965‐039 |
| DMSO | Carl Roth | A994.1 |
| EBSS | Sigma | E2888 |
| EDTA‐free protease inhibitor | Roche | 11873580001 |
| Empore SDB‐RPS | CDS Empore | 13‐110‐022 |
| FBS | Thermo Fisher Scientific | 10437‐028 |
| Formic acid solution | Merck | 1.11670.0250 |
| Isopropanol | Carl Roth | AE73.1 |
| LysC | Wako Chemicals | 4987481427648 |
| Methanol | VWR | 20903.368 |
| MG132 | Sigma | P0042 |
| Nonfat dried milk powder | AppliChem | A0830 |
| PBS | Sigma | D8537 |
| PMSF | Sigma | P7626 |
| Proteinase K | Roche | 03115887001 |
| ROTI Histofix (PFA), 4% | Carl Roth | P087 |
| Sodium deoxycholate | Applichem | A1531 |
| Sodium pyruvate | Thermo Fisher Scientific | 11360070 |
| TCEP | Sigma | 646547 |
| TFA | Sigma | 302031 |
| TRIS | Carl Roth | 4855 |
| Trypsin | Promega | V5113 |
| Trypsin/EDTA | Thermo Fisher Scientific | 15400054 |
| Tween20 | Carl Roth | 9127 |
| Urea | VWR | 28877.235 |
| Software | ||
| Aida Image Analyzer 4.26 | Raytest | |
| CorelDraw 2022 | Corel Corporation | |
| Cytoscape 3.8.2 | Cytoscape Consortium | |
| Excel 2016 | Microsoft | |
| FIJI ImageJ 1.53c | GNU General Public License | Nature Methods, 9(7), 676–682 |
| FlowJo 10.6.1 | BD Biosciences | |
| GIMP 2.8 | GNU General Public License | |
| GraphPad Prism 6.0 | GraphPad Software | |
| MaxQuant 1.6.17 | Max Planck Institute of Biochemistry | |
| Multiquant 3.0.3 | AB Sciex | |
| SigmaStat 4.0 | Systat Software | |
| Other | ||
| AF7000 widefield microscope | Leica | |
| Amersham Imager 600 | GE Healthcare Life Science | |
| Amicon Ultra‐15 filters | Merck | UFC901024 |
| BCA Protein‐Assay‐Kit | Thermo Fisher Scientific | J63283.QA |
| EASY‐nCL 1200 | Thermo Fisher Scientific | |
| FACSAria III SORP | BD Biosciences | |
| LSM710 laser scanning microscope | Zeiss | |
| LSRFortessa SORP | BD Biosciences | |
| NuPage Bis‐Tris gels | Thermo Fisher Scientific | NP0335 |
| Optima MAX‐XP Ultracentrifuge; TLA120.2 and TLA110 rotor | Beckman Coulter | |
| Precellys 24 | Bertin Technologies | |
| QExactive HF mass spectrometer | Thermo Fisher Scientific | |
| QTRAP 55500 mass spectrometer | AB Sciex | |
| ReproSil‐Pur Fused‐silica column C18 | Dr. Maisch | |
| TEM900 transmission electron microscope (2K CCD camera) |
Zeiss (TRS Tröndle) |
|
| Trans‐Blot Turbo RTA mini nitrocellulose transfer kit | BioRad | 170‐4270 |
| UP50H ultrasonic processor | Hielscher | |
| Venor GeM Mycoplasma PCR detection kit | Minerva Biolabs | 11‐1050 |
| Vivaspin 2 filters | VWR | 512‐3760 |
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