KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Rabbit monoclonal MultiMab Malonyl-Lysine antibody | Cell Signaling Technologies | Cat# 14942 |
| Anti-FLAG (DYKDDDDK) Tag Antibody (HRP-linked) | Cell Signaling Technologies | Cat# 2044 |
| Anti-rabbit IgG antibody (HRP-linked) | Cell Signaling Technologies | Cat # 7074 |
| Bacterial and Virus Strains | ||
| n/a | ||
| Biological Samples | ||
| Cell pellets from HeLa S3 epithelial suspension cell line | Cell Culture Company | Cat # HA48 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| NHS-Activated Sepharose 4 Fast Flow resin | GE Healthcare | Cat# 71-5000-14 AD |
| Amine-functionalized Lys-CoA-Ahx | Montgomery et al,, 2016 | n/a |
| U-13C6-glucose | Cambridge Isotope Laboratories | Cat# CLM-1396 |
| U-13C2-acetate | Cambridge Isotope Laboratories | Cat# CLM-440 |
| acetyl-CoA | Sigma-Aldrich | Cat# A2056 |
| coenzyme A | Sigma-Aldrich | Cat# |
| butyryl-CoA | Sigma-Aldrich | Cat# B1508 |
| crotonyl-CoA | Sigma-Aldrich | Cat# 28007 |
| palmitoyl-CoA | Sigma-Aldrich | Cat# P9716 |
| acetic-CoA | This study | n/a |
| Critical Commercial Assays | ||
| Anti-FLAG IP kit | Sigma-Aldrich | Cat# FLAGIPT1-1KT |
| TRIzol reagent | ThermoFisher Scientific | Cat#15596026 |
| oligo-(dT)25 Dynabeads | ThermoFisher Scientific | Cat# 61005 |
| Qubit Broad Sensitivity Protein Assay Kit | ThermoFisher Scientific | Cat# Q33211 |
| Deposited Data | ||
| Proteomic datasets for CATNIP (Lys-CoA) pulldowns and competitions | ProteomeXchange Consortium; PRIDE | PXD013157 |
| Experimental Models: Cell Lines | ||
| HeLa S3 cells | ATCC | CCL-2.2 |
| HEK-293T cells | ATCC | CRL-3216 |
| LN229 ACLY knockout cells | Zhao et al. 2016 | n/a |
| LN229 ACLY wild-type cells | Zhao et al. 2016 | n/a |
| Experimental Models: Organisms/Strains | ||
| Oligonucleotides | ||
| Recombinant DNA | ||
| Software and Algorithms | ||
| DTASelect v.1.9/ CONTRAST for protein detection | Tabb et al.,2002 | |
| NSAF7 | Zhang, et al., 2010 | |
| QSPEC/QPROT for the statistical analysis of protein differentiation | Choi, et al., 2015 | http://http//sourceforge.net/p/qprot/ |
| tSNE and k-means algorithms for proteins separation and clustering | Van der Maaten, et al., 2008 | R source |
| TDA software for the topological analysis | Lum et al., 2013. | https://platform.ayasdi.com/workbench (AYASDI Inc., Menlo Park CA) |
| DAVID gene ontology for functional enrichment | DAVID tool | http://david.abcc.ncifcrf.gov/ |
| ConsensusPathDB | http://cpdb.molgen.mpg.de/CPDB/rlFrame | |
| Other | ||