Key Resources Table
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Rabbit α calnexin | Abcam | Cat#ab22595; RRID: AB_2069006 |
| Rabbit α emerin | Proteintech | Cat#10351; RRID: AB_2100056 |
| Mouse α tubulin DM1A | Millipore Sigma | Cat#05-829; RRID: AB_310035 |
| Mouse α FLAG | Sigma | Cat#F3165; RRID: AB_259529 |
| Rabbit α HA | Cell Signaling Technologies | Cat#3724; RRID: AB_1549585 |
| Rhodamine RedX Donkey α mouse IgG | Jackson Immuno | Cat#715-295-150; RRID: AB_2340831 |
| FITC Goat α mouse IgG | Jackson Immuno | Cat#115-095-146; RRID: AB_2338599 |
| FITC Goat α rabbit IgG | Jackson Immuno | Cat#111-095-003; RRID: AB_2337972 |
| FITC Donkey α Goat IgG | Jackson Immuno | Cat#705-095-147; RRID: AB_2340401 |
| Rhodamine RedX goat α rabbit IgG | Jackson Immuno | Cat#111-295-003; RRID: AB_2338022 |
| Alexa Fluor 488 Donkey α mouse IgG | Jackson Immuno | Cat#715-545-150; RRID: AB_2340846 |
| Alexa Fluor 647 goat α mouse IgG | Jackson Immuno | Cat#115-605-003; RRID: AB_2338902 |
| Alexa Fluor 647 donkey α rabbit IgG | Jackson Immuno | Cat#711-605-152; RRID: AB_2492288 |
| Rabbit α lipin-1 | Millipore Sigma | Cat#ABS400 (discontinued) |
| Rabbit α lipin-1 | Proteintech | Cat# 27026-1-AP; RRID: AB_2880727 |
| Rabbit α Phospho-p70 S6 Kinase (Thr389) (108D2) | Cell Signaling Technology | Cat#9234; RRID: AB_2269803 |
| Rabbit α p70 S6 kinase | Cell Signaling Technology | Cat#9202; RRID: AB_331676 |
| Rabbit α Phospho 4E-BP1 (Ser65) | Cell Signaling Technology | Cat#9451; RRID: AB_330947 |
| Rabbit α 4E-BP1 | Cell Signaling Technology | Cat#9452; RRID: AB_331692 |
| Rabbit α NRF2 | Abcam | Cat#ab62352; RRID: AB_944418 |
| Goat α mouse IgG-HRP | Thermo Fisher | Cat#31430; RRID: AB_228307 |
| Goat α rabbit IgG-HRP | Thermo Fisher | Cat#31460; RRID: AB_228341 |
| Mouse α cyclin A2 | Proteintech | Cat#66391; RRID: AB_2881767 |
| Mouse α BrdU | Santa Cruz | Cat#sc-32323; RRID: AB_626766 |
| Mouse α cyclin B1 (GNS1) | Santa Cruz | Cat#sc-245; RRID: AB_627338 |
| Mouse α cyclin E1 (HE12) | Cell Signaling Technology | Cat#4129; RRID: AB_2071200 |
| Chemicals, peptides, and recombinant proteins | ||
| Torin 1 | ApexBio | Cat#A8312 |
| Cycloheximide | Cell Signaling | Cat#2112 |
| MG132 z-Leu-Leu-Leu-Al | Fisher Scientific | Cat#AAJ63250LB0 |
| Nocodazole | Sigma | Cat#M1404 |
| RO-3306 | EMD Millipore | Cat#217699 |
| TOFA | Cayman Chemicals | Cat#10005263 |
| NMS-P715 | EMD Millipore | Cat#475949 |
| SiR-DNA | Cytoskeleton, Inc. | Cat#CY-SC007 |
| ER Tracker Green | Invitrogen | Cat#E34251 |
| Puromycin HCl | Thermo Fisher | Cat#A1113803 |
| G418 | EMD Millipore | Cat#345810 |
| Blasticidin | Sigma | Cat#R21001 |
| Palmitic acid | Sigma | Cat#P0500 |
| Oleic acid | Sigma | Cat#O1008 |
| Linoleic acid | Sigma | Cat#L5900 |
| 1,2-C14-acetic acid sodium salt | Perkin-Elmer | Cat#NEC553 |
| ProMag™ 3 Series - Streptavadin beads | Bangslabs | Cat#PMS3N |
| 1,2-Dioleoyl-sn-glycerol | Avanti Polar Lipids | Cat#800811 |
| 1,2-Dioleoyl-sn-glycero-3-phosphate | Avanti Polar Lipids | Cat#840875 |
| Triton X-100 | Sigma-Aldrich | Cat# T9284 |
| [γ-32P] ATP (6000 Ci/mmol, 150 mCi/mL) | Perkin-Elmer | Cat# NEG035C005MC |
| Escherichia coli DAG kinase, 1 mg/mL, 2 U/mg | Sigma-Aldrich | Cat# D3065 |
| 5’ethynyl-2’-deoxyuridine (EdU) | Lumiprobe | Cat#10540 |
| Sulfo-Cyanine 5 Azide | Lumiprobe | Cat#A3330 |
| Bromodeoxyuridine (BrdU) | BioLegend | Cat#423401 |
| Sodium tetraborate decahydrate | Sigma | Cat#S9640 |
| RNAse A | Sigma | Cat#AB12023-00100 |
| Propidium Iodide | BioLegend | Cat#421301 |
| Thymidine | Sigma | T1895 |
| 2’ deoxycytidine | Sigma | D3897 |
| Critical commercial assays | ||
| Zymopure II plasmid Midi prep kit | Zymogen | Cat#D4200 |
| Pierce BCA Protein Assay kit | Thermo Scientific | Cat#23225 |
| Experimental models: Cell lines | ||
| U2OS | Slack lab (Harvard Medical School) | N/A |
| RPE-1 | Breslow lab (Yale University) | N/A |
| HEK293 | Breslow lab (Yale University) | N/A |
| U2OS GFP-Sec61β | Rapoport lab (Harvard Medical School) | N/A |
| U2OS GFP-Sec61β H2B-mCherry | This study | N/A |
| U2OS CTDNEP1KO | This study | N/A |
| U2OS CTDNEP1KO CTDNEP1-HAstable | This study | N/A |
| U2OS CTDNEP1KO CTDNEP1-HAstable PD (D67E D69T) | This study | N/A |
| Oligonucleotides | ||
| siRNA targeting sequence: CTDNEP1 custom single siRNA FWD, no modifications: AGGCAGAUCCGCACGGUAA | Dharmacon | N/A |
| siRNA targeting sequence: Lipin 1 custom single siRNA, no modifications: GAAUGGAAUGCCAGCUGAA | (Brohée, 2015) (Sołtysik et al., 2021), Dharmacon | N/A |
| siRNA targeting sequence: CTDNEP1 SMARTpool siRNA | Dharmacon | Cat#M-017869-00-0005 |
| siRNA targeting sequence: siGENOME Non-targeting siRNA Pool #2 | Dharmacon | Cat#D-001206-14-05 |
| Silencer Negative control siRNA #1 | Invitrogen | Cat#AM4611 |
| Silencer Select negative control siRNA #1 | Life Technologies | Cat#4390843 |
| qPCR primer: Hs GAPDH forward: GTCTCCTCTGACTTCAACAGCG | (Nabokina et al., 2014) | N/A |
| qPCR primer: Hs GAPDH reverse: ACCACCCTGTTGCTGTAGCCAA | (Nabokina et al., 2014) | N/A |
| qPCR primer: Hs CTDNEP1 forward: CATTTACCTTCTGCGGAGGC | This study | N/A |
| qPCR primer: Hs CTDNEP1 reverse: CACCTGGGCTAGCCGATTC | This study | N/A |
| qPCR primer: Hs ACACA forward: TCACACCTGAAGACCTTAAAGCC | (Shimizu et al., 2017) | N/A |
| qPCR primer: Hs ACACA reverse: AGCCCACACTGCTTGTACTG | (Shimizu et al., 2017) | N/A |
| qPCR primer: Hs FDPS forward: TGTGACCGGCAAAATTGGC | (Shimizu et al., 2017) | N/A |
| qPCR primer: Hs FDPS reverse: GCCCGTTGCAGACACTGAA | (Shimizu et al., 2017) | N/A |
| qPCR primer: Hs SCD forward: TCTAGCTCCTATACCACCACCA | (Shimizu et al., 2017) | N/A |
| qPCR primer: Hs SCD reverse: TCGTCTCCAACTTATCTCCTCC | (Shimizu et al., 2017) | N/A |
| qPCR primer: Hs HMGCR forward: GGACCCCTTTGCTTAGATGAAA | (Bertolio et al., 2019) | N/A |
| qPCR primer: Hs HMGCR reverse: CCACCAAGACCTATTGCTCTG | (Bertolio et al., 2019) | N/A |
| qPCR primer: Hs FASN forward: CATCCAGATAGGCCTCATAGA | (Bertolio et al., 2019) | N/A |
| qPCR primer: Hs FASN reverse: CTCCATGAAGTAGGAGTGGAA | (Bertolio et al., 2019) | N/A |
| qPCR primer: Hs 36B4 forward: AACATGCTCAACATCTCCCC | (Neuhaus et al., 2011) | N/A |
| qPCR primer: Hs 36B4 reverse: CCGACTCCTCCGACTCTTC | (Neuhaus et al., 2011) | N/A |
| Recombinant DNA | ||
| pSPCas9(BB)-2A-Puro (PX459) v2.0 | (Ran et al., 2013) | Cat#62988; RRID: Addgene_62988 |
| pH2B_mCherry_IRES_puro2 | (Steigemann et al., 2009) | Cat#21045; RRID: Addgene_21045 |
| GFP-KDEL | This study | N/A |
| pRK5 FLAG-lipin1β (Mm) | (Peterson et al., 2011) | RRID: Addgene_32005 |
| pRK5 FLAG-lipin1β 19xA | (Peterson et al., 2011) | RRID: Addgene_32007 |
| pRK5 FLAG-lipin1β 19xA PAP dead (D712E, D714E) | This study | N/A |
| Human lipin 1β-GFP | (Sołtysik et al., 2021) | N/A |
| pcDNA CTDNEP1-HA | This study | N/A |
| pcDNA CTDNEP1 D67E-HA | This study | N/A |
| pcDNA CTDNEP1 D67ED69T-HA | This study | N/A |
| FLAG-CNEP1R1 | This study | N/A |
| pMRX CTDNEP1 D67E-HA | This study | N/A |
| pMRX CTDNEP1 D67ED69T-HA | This study | N/A |
| pMRX_EGFP_Blast | H. Arai lab (University of Tokyo) | N/A |
| Software and algorithms | ||
| FIJI | (Schindelin et al., 2012) | https://imagej.net/Fiji |
| GraphPad Prism 8/9 | GraphPad Software | https://www.graphpad.com/scientific-software/prism/ |
| MATLAB | MathWorks | https://www.mathworks.com/products/matlab.html |
| PIVlab | (Thielicke, 2014; Thielicke and Stamhuis, 2014) | https://www.mathworks.com/matlabcentral/fileexchan |
| FlowJo 10 | FlowJo, LLC | https://www.flowjo.com/solutions/flowjo |
| Image Lab Software | Bio-Rad | https://www.bio-rad.com/en-us/product/image-lab-software |
| ImageJ Filename_Randomizer | Tiago Ferreira (EMBL) | https://imagej.nih.gov/ij/macros/Filename_Randomizer.txt |