Protocol Archive

This protocol describes the generation of DNAJC5 KO using CRISPR/Cas9 edition.

This protocol describes the in vitro depalmitoylation assay of DNAJC5.

This protocol describes membrane and cytosol fractionation of cells expressing different DNAJC5 isoforms.

Strep pull down assay for FIP200(NTD)-TSF WT or mutants were co-transfected with GST-ATG13(363-517) and/or ULK1(MIT)-MBP.

This protocol details a protocol for the trypsin digestion of PI3KC3-C1 and subsequent analysis of digested peptides using LC-MS/MS.

This protocol details plasmid construction in general terms for the insertion of genes into the pCAG mammalian expression vector.

Protocol for preparation of mitochondrial samples for immunoblot analysis.

This protocol details molecular dynamics simulations of PI3KC3-C1 on a lipid membrane.

Ion-pair reversed phase HPLC analysis of the nucleotide bound to PI3KC3-C1.

This protocol describes the denaturation of PI3KC3-C1, and subsequent analysis of eluted nucleotides by electrospray ionization mass spec.

This protocol details cryo-EM sample preparation for PI3KC3-C1~RAB1A complex.

This protocol details Cryo-EM grid preparation.

This protocol describes routine cell culture maintenance as described in Adriaenssens & Nguyen et al., 2023 (BioRxiv).

This protocol describes plasmid construction as described in Adriaenssens & Nguyen et al., 2023 (BioRxiv).

Protocol for performing an immunofluorescence assay with fixed HeLa cells.

Protocol for qRT-PCR sample preparation for analysis using a RotorGeneQ machine (Qiagen).

Protocol for analyzing oxygen consumption of isolated mitochondria using the Seahorse XFe96 analyzer.

Protocol for analysis of cellular ATP levels using the Promega Mitochondrial ToxGlo Kit.

Preparation of samples for measuring mitophagy levels using mtKeima reporter by fluorescence activated cell sorting (FACS).

Protocol for generating solubility calculations for mitochondrial proteins from starting 'soluble' and 'insoluble' fraction mass spectrometry data, using MaxQuant and Perseus software pipelines.