Reagents and tools table
| Reagent/resource . | Reference or source . | Identifier or catalog number . |
|---|---|---|
| Experimental models | ||
| Cell lines | ||
| D. melanogaster: S2 cells | Life Technologies | Cat# R69007, RRID:CVCL_Z232 |
| Human: HeLa cells | ATCC | Cat# CCL-2, RRID:CVCL_0030 |
| Human: HeLa PCNT KO cells | Watanabe et al. (2020) | ODCL0025 |
| Human: U2-OS cells | ATCC | Cat# HTB-96, RRID:CVCL_0042 |
| Organisms/strains | ||
| D. melanogaster: Asl RNAi/P{TRiP.HMS01453}attP2 | BDSC | BDSC ID: 35039, RRID: BDSC_35039 |
| D. melanogaster: Asl-GFP & H2A-RFP; CmbΔ/P{His2Av-mRFP1}; P{UAS.asl-asl-GFP.B}; CmbΔ/Tmb6 SbTb | This study | N/A |
| D. melanogaster: Asl-GFP & H2A-RFP/P{His2Av-mRFP1}; P{UAS.asl-asl-GFP.B} | This study | N/A |
| D. melanogaster: Asl-GFP/P{UAS.asl-asl-GFP.B} | Blachon et al. (2008) | FlyBase ID: FBtp0040947 |
| D. melanogaster: Bam-GAL4 & Nanos-GAL4/P{GAL4-nos.NGT}40; P{bam-GAL4:VP16} | Dobbelaere et al. (2023) | N/A |
| D. melanogaster: Cmb OE/P{UAS-cmb.RA} | Fagan et al. (2014) | FlyBase ID: FBtp0095481 |
| D. melanogaster: Cmb RNAi 1/P{KK103563}VIE-260B | VDRC | VDRC ID: 109767, RRID: Flybase_FBst0481420 |
| D. melanogaster: Cmb RNAi 2/P{GD7077}v18666 | VDRC | VDRC ID: 18666, RRID: Flybase_FBst0453208 |
| D. melanogaster: Cmb-GFP rescue/PBac{fTRG01063.sfGFP-TVPTBF}VK00002; CmbΔ | This study | N/A |
| D. melanogaster: Cmb-GFP/PBac{fTRG01063.sfGFP-TVPTBF}VK00002 | VDRC | VDRC ID: 318739, RRID: Flybase_FBst0491914 |
| D. melanogaster: CmbΔ/CmbΔ/Tm6 SbTb | Fagan et al. (2014) | FlyBase ID: FBal0298847 |
| D. melanogaster: Cnn RNAi/P{GD1726}v44526 | VDRC | VDRC ID: 44526, RRID: Flybase_FBst0465625 |
| D. melanogaster: Control RNAi/P{TRiP.HMS00045}attP2 | BDSC | BDSC ID: 33644, RRID: BDSC_33644 |
| D. melanogaster: Deficiency 1/w[1118]; Df(3L)BSC614/TM6C, cu[1] Sb[1] | BDSC | BDSC ID: 25689, RRID: BDSC_25689 |
| D. melanogaster: Deficiency 2/w[1118]; Df(3L)BSC737/TM6C, Sb[1] cu[1] | BDSC | BDSC ID: 26835, RRID: BDSC_26835 |
| D. melanogaster: Elav-GAL4/P{GawB}elav[C155] | BDSC | BDSC ID: 458, RRID: BDSC_458 |
| D. melanogaster: Frtz RNAi/P{GD9437}v40088 | VDRC | VDRC ID: 40088, RRID: Flybase_FBst0463379 |
| D. melanogaster: GFP nanobody–TurboID/P{egg-TurboID.vhhGFP.3xHA} | This study | N/A |
| D. melanogaster: H2A-RFP/P{His2Av-mRFP1} P{UAS.asl-asl-GFP.B} | Pandey et al. (2005) | FlyBase ID: FBtp0056035 |
| D. melanogaster: In RNAi/P{GD10892}v27252 | VDRC | VDRC ID: 27252, RRID: Flybase_FBst0456836 |
| D. melanogaster: Plp RNAi/P{GD9625}v20667 | VDRC | VDRC ID: 20667 |
| D. melanogaster: Pnr-GAL4/P{GawB}pnr[MD237] | Calleja et al. (2000) | FlyBase ID: FBti0004011 |
| D. melanogaster: RFP-Cnn; CmbΔ/P{Ubi-p63E-cnn.RFP}; CmbΔ/Tmb6 SbTb | This study | N/A |
| D. melanogaster: RFP-Cnn/P{Ubi-p63E-cnn.RFP} | Conduit et al. (2010) | FlyBase ID: FBtp0056991 |
| D. melanogaster: Sas-4 RNAi/P{GD6852}v17975 | VDRC | VDRC ID: 17975, RRID: Flybase_FBst0452943 |
| D. melanogaster: Spd-2 RNAi/P{KK110116}VIE-260B | VDRC | VDRC ID: 101882, RRID: Flybase_FBst0473755 |
| D. melanogaster: Wild-type/w[1118] | BDSC | BDSC ID: 6326, RRID: BDSC_6326 |
| Recombinant DNA | ||
| Blasticidin selection vector: pCoBlast | Thermo Fisher Scientific | Cat# K515001 |
| GST expression vector: pGEX-6P-1 Cmb (aa1-150) | This study | N/A |
| BioID control vector: pMt-myc-BirA* | This study | N/A |
| BioID SAS-4 vector: pMt-Sas-4-myc-BirA* | This study | N/A |
| S2 cell expression vector: pMt-V5-6xHis B | Invitrogen | Cat# V412020 |
| CMB-GFP vector: pMt-V5-6xHis-Cmb-GFP | This study | N/A |
| TurboID CMB vector: pMt-V5-TurboID-Cmb | This study | N/A |
| TurboID control vector: pMt-V5-TurboID-GW | Norbert Perrimon | N/A |
| Indirect TurboID fly expression vector: pUASz-TurboID-vhhGFP-3xHA | This study | N/A |
| Indirect TurboID expression vector (+NLS): pUASz-TurboID-vhhGFP-3xHA-NLS | Baumgartner et al. (2022) | N/A |
| Gateway vector: pDONR/Zeo | Thermo Fisher Scientific | Cat# 12535035 |
| BioID source vector: pcDNA3.1 myc-BirA* | Kyle Roux | N/A |
| CMB-GFP vector: pcDNA3.1 Cmb-GFP | This study | N/A |
| PCM1 GFP vector: pEGFP-N-PCM1-GFP | This study | N/A |
| Antibodies | ||
| Donkey anti-goat IgG (H + L) Cy2-conjugated antibody | Jackson ImmunoResearch | Cat# 705-225-147, RRID: AB_2307341 |
| Donkey anti-mouse IgG (H + L) Cy2-conjugated antibody | Jackson ImmunoResearch | Cat# 715-225-150, RRID: AB_2340826 |
| Donkey anti-mouse IgG (H + L) Cy3-conjugated antibody | Jackson ImmunoResearch | Cat# 715-165-150, RRID: AB_2340813 |
| Donkey anti-mouse IgG (H + L) Cy5-conjugated antibody | Jackson ImmunoResearch | Cat# 715-175-150, RRID: AB_2340819 |
| Donkey anti-rabbit IgG (H + L) Cy2-conjugated antibody | Jackson ImmunoResearch | Cat# 711-225-152, RRID: AB_2340612 |
| Donkey anti-rabbit IgG (H + L) Cy3-conjugated antibody | Jackson ImmunoResearch | Cat# 711-165-152, RRID:AB_2307443 |
| Donkey anti-rabbit IgG (H + L) Cy5-conjugated antibody | Jackson ImmunoResearch | Cat# 711-175-152, RRID:AB_2340607 |
| Goat polyclonal anti-GFP antibody | Dammermann et al. (2004) | N/A |
| Mouse monoclonal anti-dmNompC antibody | Liang et al. (2011) | N/A |
| Mouse monoclonal anti-gamma tubulin antibody | Sigma-Aldrich | Cat# T6557, RRID: AB_477584 |
| Mouse monoclonal anti-hsPCM1 antibody | Santa Cruz Biotechnology | Cat# sc-398365, RRID: AB_2827155 |
| Mouse monoclonal anti-puromycin | Merck Millipore | Cat# MABE343, RRID: AB_2566826 |
| Rabbit polyclonal anti-dmANA1 antibody | Conduit et al. (2010) | N/A |
| Rabbit polyclonal anti-dmANA2 antibody | Cabral et al. (2019) | N/A |
| Rabbit polyclonal anti-dmCEP97-N-ter antibody | Dobbelaere et al. (2020) | N/A |
| Rabbit polyclonal anti-dmCMB antibody | This study | N/A |
| Rabbit polyclonal anti-dmCNN antibody | Dobbelaere et al. (2008) | N/A |
| Rabbit polyclonal anti-dmCP110 antibody | Franz et al. (2013) | N/A |
| Rabbit polyclonal anti-dmSAS-4 antibody | Basto et al. (2006) | N/A |
| Rabbit polyclonal anti-dmSPD-2 antibody | Cabral et al. (2019) | N/A |
| Rabbit polyclonal anti-hsCDK5RAP2 antibody | Merck Millipore | Cat# 06-1398, RRID: AB_11203651 |
| Rabbit polyclonal anti-hsCEP131/AZI1 antibody | Abcam | Cat# ab84864, RRID: AB_1859791 |
| Rabbit polyclonal anti-hsCEP290 antibody | Novus Biologicals | Cat# NB100-86991, RRID: AB_1201171 |
| Rabbit polyclonal anti-hsMIB1 antibody | Sigma-Aldrich | Cat# M5948; RRID: AB_1841007 |
| Rabbit polyclonal anti-hsOFD1 antibody | Sigma-Aldrich | Cat# HPA031103, RRID: AB_10602188 |
| Rabbit polyclonal anti-hsPCM1 antibody | Dammermann and Merdes (2002) | N/A |
| Rabbit polyclonal anti-hsPCNT antibody | Abcam | Cat# ab4448, RRID: AB_304461 |
| Oligonucleotides and other sequence-based reagents | ||
| siRNA targeting sequence: PCM-1 #1: 5′-GGGCUCUAAACGUGCCUCC-3′ | Dammermann and Merdes (2002) | N/A |
| siRNA targeting sequence: PCM-1 #2: 5′-UCAGCUUCGUGAUUCUCAG-3′ | Dammermann and Merdes (2002) | N/A |
| RNA FISH probes: see Table S3 | Sigma-Aldrich/Biosearch Technologies | N/A |
| smiFISH secondary probe: 5′-CACTGAGTCCAGCTCGAAACTTAGGAGG-3′ | Biosearch Technologies | N/A |
| Chemicals, enzymes, and other reagents | ||
| Agar 100 resin | Agar Scientific | Cat# AGR1031; CAS: 25038–04-4 |
| UltraPure BSA, Nonacetylated | Invitrogen | Cat# AM2618 |
| Cycloheximide | Sigma-Aldrich | Cat# C1988; CAS: 66-81-9 |
| 25% glutaraldehyde, EM grade | Agar Scientific | Cat# AGR1020; CAS: 111-30-8 |
| Hoechst 33258 | Thermo Fisher Scientific | Cat# H1398; CAS: 23491–45-4 |
| Lysyl endopeptidase (LysC) | FUJIFILM Wako Chemicals | Cat# 129-02541 |
| Osmium tetroxide 4% solution | Electron Microscopy Sciences | Cat# 19170; CAS: 20816–12-0 |
| Paraformaldehyde | Roth | Cat# O335.1; CAS: 30525-89-4 |
| 32% paraformaldehyde, EM grade | Electron Microscopy Sciences | Cat# 15714 |
| Phalloidin/Alexa Fluor 568 | Thermo Fisher Scientific | Cat# A12380 |
| Pierce Streptavidin Magnetic Beads | Thermo Scientific Pierce | Cat# 88817 |
| Polyethylenimine | Polysciences | Cat# 23966; CAS: 26913-06-4 |
| Puromycin dihydrochloride | Sigma-Aldrich | Cat# P8833 |
| Reynolds’ lead citrate | Delta Microscopies | Cat# 11300; CAS: 512–26-5 |
| Trypsin Gold Mass Spec Grade | Promega | Cat# V5280 |
| Uranyl acetate | Science Services | Cat# E22400; CAS: 541–09-3 |
| Vanadyl ribonucleoside complexes solution | Sigma-Aldrich | Cat# 94742 |
| Vectashield Plus | Vector Laboratories | Cat# H-1900 |
| Critical commercial assays | ||
| Duolink In Situ Detection Reagents Red | Sigma-Aldrich | Cat# DUO92008 |
| Duolink In Situ PLA Probe Anti-Mouse MINUS | Sigma-Aldrich | Cat# DUO92004 |
| Duolink In Situ PLA Probe Anti-Rabbit PLUS | Sigma-Aldrich | Cat# DUO92002 |
| Duolink In Situ Wash Buffers, Fluorescence | Sigma-Aldrich | Cat# DUO82049 |
| Lipofectamine RNAiMAX | Invitrogen | Cat# 13778100 |
| TransIT Insect Transfection reagent | Mirus Bio | Cat# MIR 6104 |
| Software | ||
| Fiji v 2.0.0 | NIH | https://imagej.net/software/fiji/ |
| FragPipe v 20.0 | University of Michigan Medical School | https://github.com/Nesvilab/FragPipe |
| GraphPad Prism 10 | GraphPad | https://www.graphpad.com/scientific-software/prism |
| HMMER v 3.4 | Eddy (2011) | https://hmmer.org/ |
| Ilastik v 1.4.0 | Berg et al. (2019) | https://www.ilastik.org |
| IonQuant v 1.9.8 | Yu et al. (2021) | https://github.com/Nesvilab/IonQuant |
| Jalview v 2.11.1.4 | Waterhouse et al. (2009) | https://www.jalview.org/ |
| MAFFT v 7 | Katoh et al. (2019) | https://mafft.cbrc.jp/alignment/server/ |
| MATLAB v R2023a | MathWorks | https://www.mathworks.com |
| MSFragger v 3.8 | Kong et al. (2017) | https://github.com/Nesvilab/MSFragger |
| MsReport v 0.0.23 | Max Perutz Labs Mass Spectrometry Facility | N/A |
| NCBI BLAST+ v 2.13.0 | Altschul et al. (1997) | https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ |
| Philosopher v 5.0.0 | da Veiga Leprevost et al. (2020) | https://github.com/Nesvilab/philosopher |
| Reagent/resource . | Reference or source . | Identifier or catalog number . |
|---|---|---|
| Experimental models | ||
| Cell lines | ||
| D. melanogaster: S2 cells | Life Technologies | Cat# R69007, RRID:CVCL_Z232 |
| Human: HeLa cells | ATCC | Cat# CCL-2, RRID:CVCL_0030 |
| Human: HeLa PCNT KO cells | Watanabe et al. (2020) | ODCL0025 |
| Human: U2-OS cells | ATCC | Cat# HTB-96, RRID:CVCL_0042 |
| Organisms/strains | ||
| D. melanogaster: Asl RNAi/P{TRiP.HMS01453}attP2 | BDSC | BDSC ID: 35039, RRID: BDSC_35039 |
| D. melanogaster: Asl-GFP & H2A-RFP; CmbΔ/P{His2Av-mRFP1}; P{UAS.asl-asl-GFP.B}; CmbΔ/Tmb6 SbTb | This study | N/A |
| D. melanogaster: Asl-GFP & H2A-RFP/P{His2Av-mRFP1}; P{UAS.asl-asl-GFP.B} | This study | N/A |
| D. melanogaster: Asl-GFP/P{UAS.asl-asl-GFP.B} | Blachon et al. (2008) | FlyBase ID: FBtp0040947 |
| D. melanogaster: Bam-GAL4 & Nanos-GAL4/P{GAL4-nos.NGT}40; P{bam-GAL4:VP16} | Dobbelaere et al. (2023) | N/A |
| D. melanogaster: Cmb OE/P{UAS-cmb.RA} | Fagan et al. (2014) | FlyBase ID: FBtp0095481 |
| D. melanogaster: Cmb RNAi 1/P{KK103563}VIE-260B | VDRC | VDRC ID: 109767, RRID: Flybase_FBst0481420 |
| D. melanogaster: Cmb RNAi 2/P{GD7077}v18666 | VDRC | VDRC ID: 18666, RRID: Flybase_FBst0453208 |
| D. melanogaster: Cmb-GFP rescue/PBac{fTRG01063.sfGFP-TVPTBF}VK00002; CmbΔ | This study | N/A |
| D. melanogaster: Cmb-GFP/PBac{fTRG01063.sfGFP-TVPTBF}VK00002 | VDRC | VDRC ID: 318739, RRID: Flybase_FBst0491914 |
| D. melanogaster: CmbΔ/CmbΔ/Tm6 SbTb | Fagan et al. (2014) | FlyBase ID: FBal0298847 |
| D. melanogaster: Cnn RNAi/P{GD1726}v44526 | VDRC | VDRC ID: 44526, RRID: Flybase_FBst0465625 |
| D. melanogaster: Control RNAi/P{TRiP.HMS00045}attP2 | BDSC | BDSC ID: 33644, RRID: BDSC_33644 |
| D. melanogaster: Deficiency 1/w[1118]; Df(3L)BSC614/TM6C, cu[1] Sb[1] | BDSC | BDSC ID: 25689, RRID: BDSC_25689 |
| D. melanogaster: Deficiency 2/w[1118]; Df(3L)BSC737/TM6C, Sb[1] cu[1] | BDSC | BDSC ID: 26835, RRID: BDSC_26835 |
| D. melanogaster: Elav-GAL4/P{GawB}elav[C155] | BDSC | BDSC ID: 458, RRID: BDSC_458 |
| D. melanogaster: Frtz RNAi/P{GD9437}v40088 | VDRC | VDRC ID: 40088, RRID: Flybase_FBst0463379 |
| D. melanogaster: GFP nanobody–TurboID/P{egg-TurboID.vhhGFP.3xHA} | This study | N/A |
| D. melanogaster: H2A-RFP/P{His2Av-mRFP1} P{UAS.asl-asl-GFP.B} | Pandey et al. (2005) | FlyBase ID: FBtp0056035 |
| D. melanogaster: In RNAi/P{GD10892}v27252 | VDRC | VDRC ID: 27252, RRID: Flybase_FBst0456836 |
| D. melanogaster: Plp RNAi/P{GD9625}v20667 | VDRC | VDRC ID: 20667 |
| D. melanogaster: Pnr-GAL4/P{GawB}pnr[MD237] | Calleja et al. (2000) | FlyBase ID: FBti0004011 |
| D. melanogaster: RFP-Cnn; CmbΔ/P{Ubi-p63E-cnn.RFP}; CmbΔ/Tmb6 SbTb | This study | N/A |
| D. melanogaster: RFP-Cnn/P{Ubi-p63E-cnn.RFP} | Conduit et al. (2010) | FlyBase ID: FBtp0056991 |
| D. melanogaster: Sas-4 RNAi/P{GD6852}v17975 | VDRC | VDRC ID: 17975, RRID: Flybase_FBst0452943 |
| D. melanogaster: Spd-2 RNAi/P{KK110116}VIE-260B | VDRC | VDRC ID: 101882, RRID: Flybase_FBst0473755 |
| D. melanogaster: Wild-type/w[1118] | BDSC | BDSC ID: 6326, RRID: BDSC_6326 |
| Recombinant DNA | ||
| Blasticidin selection vector: pCoBlast | Thermo Fisher Scientific | Cat# K515001 |
| GST expression vector: pGEX-6P-1 Cmb (aa1-150) | This study | N/A |
| BioID control vector: pMt-myc-BirA* | This study | N/A |
| BioID SAS-4 vector: pMt-Sas-4-myc-BirA* | This study | N/A |
| S2 cell expression vector: pMt-V5-6xHis B | Invitrogen | Cat# V412020 |
| CMB-GFP vector: pMt-V5-6xHis-Cmb-GFP | This study | N/A |
| TurboID CMB vector: pMt-V5-TurboID-Cmb | This study | N/A |
| TurboID control vector: pMt-V5-TurboID-GW | Norbert Perrimon | N/A |
| Indirect TurboID fly expression vector: pUASz-TurboID-vhhGFP-3xHA | This study | N/A |
| Indirect TurboID expression vector (+NLS): pUASz-TurboID-vhhGFP-3xHA-NLS | Baumgartner et al. (2022) | N/A |
| Gateway vector: pDONR/Zeo | Thermo Fisher Scientific | Cat# 12535035 |
| BioID source vector: pcDNA3.1 myc-BirA* | Kyle Roux | N/A |
| CMB-GFP vector: pcDNA3.1 Cmb-GFP | This study | N/A |
| PCM1 GFP vector: pEGFP-N-PCM1-GFP | This study | N/A |
| Antibodies | ||
| Donkey anti-goat IgG (H + L) Cy2-conjugated antibody | Jackson ImmunoResearch | Cat# 705-225-147, RRID: AB_2307341 |
| Donkey anti-mouse IgG (H + L) Cy2-conjugated antibody | Jackson ImmunoResearch | Cat# 715-225-150, RRID: AB_2340826 |
| Donkey anti-mouse IgG (H + L) Cy3-conjugated antibody | Jackson ImmunoResearch | Cat# 715-165-150, RRID: AB_2340813 |
| Donkey anti-mouse IgG (H + L) Cy5-conjugated antibody | Jackson ImmunoResearch | Cat# 715-175-150, RRID: AB_2340819 |
| Donkey anti-rabbit IgG (H + L) Cy2-conjugated antibody | Jackson ImmunoResearch | Cat# 711-225-152, RRID: AB_2340612 |
| Donkey anti-rabbit IgG (H + L) Cy3-conjugated antibody | Jackson ImmunoResearch | Cat# 711-165-152, RRID:AB_2307443 |
| Donkey anti-rabbit IgG (H + L) Cy5-conjugated antibody | Jackson ImmunoResearch | Cat# 711-175-152, RRID:AB_2340607 |
| Goat polyclonal anti-GFP antibody | Dammermann et al. (2004) | N/A |
| Mouse monoclonal anti-dmNompC antibody | Liang et al. (2011) | N/A |
| Mouse monoclonal anti-gamma tubulin antibody | Sigma-Aldrich | Cat# T6557, RRID: AB_477584 |
| Mouse monoclonal anti-hsPCM1 antibody | Santa Cruz Biotechnology | Cat# sc-398365, RRID: AB_2827155 |
| Mouse monoclonal anti-puromycin | Merck Millipore | Cat# MABE343, RRID: AB_2566826 |
| Rabbit polyclonal anti-dmANA1 antibody | Conduit et al. (2010) | N/A |
| Rabbit polyclonal anti-dmANA2 antibody | Cabral et al. (2019) | N/A |
| Rabbit polyclonal anti-dmCEP97-N-ter antibody | Dobbelaere et al. (2020) | N/A |
| Rabbit polyclonal anti-dmCMB antibody | This study | N/A |
| Rabbit polyclonal anti-dmCNN antibody | Dobbelaere et al. (2008) | N/A |
| Rabbit polyclonal anti-dmCP110 antibody | Franz et al. (2013) | N/A |
| Rabbit polyclonal anti-dmSAS-4 antibody | Basto et al. (2006) | N/A |
| Rabbit polyclonal anti-dmSPD-2 antibody | Cabral et al. (2019) | N/A |
| Rabbit polyclonal anti-hsCDK5RAP2 antibody | Merck Millipore | Cat# 06-1398, RRID: AB_11203651 |
| Rabbit polyclonal anti-hsCEP131/AZI1 antibody | Abcam | Cat# ab84864, RRID: AB_1859791 |
| Rabbit polyclonal anti-hsCEP290 antibody | Novus Biologicals | Cat# NB100-86991, RRID: AB_1201171 |
| Rabbit polyclonal anti-hsMIB1 antibody | Sigma-Aldrich | Cat# M5948; RRID: AB_1841007 |
| Rabbit polyclonal anti-hsOFD1 antibody | Sigma-Aldrich | Cat# HPA031103, RRID: AB_10602188 |
| Rabbit polyclonal anti-hsPCM1 antibody | Dammermann and Merdes (2002) | N/A |
| Rabbit polyclonal anti-hsPCNT antibody | Abcam | Cat# ab4448, RRID: AB_304461 |
| Oligonucleotides and other sequence-based reagents | ||
| siRNA targeting sequence: PCM-1 #1: 5′-GGGCUCUAAACGUGCCUCC-3′ | Dammermann and Merdes (2002) | N/A |
| siRNA targeting sequence: PCM-1 #2: 5′-UCAGCUUCGUGAUUCUCAG-3′ | Dammermann and Merdes (2002) | N/A |
| RNA FISH probes: see Table S3 | Sigma-Aldrich/Biosearch Technologies | N/A |
| smiFISH secondary probe: 5′-CACTGAGTCCAGCTCGAAACTTAGGAGG-3′ | Biosearch Technologies | N/A |
| Chemicals, enzymes, and other reagents | ||
| Agar 100 resin | Agar Scientific | Cat# AGR1031; CAS: 25038–04-4 |
| UltraPure BSA, Nonacetylated | Invitrogen | Cat# AM2618 |
| Cycloheximide | Sigma-Aldrich | Cat# C1988; CAS: 66-81-9 |
| 25% glutaraldehyde, EM grade | Agar Scientific | Cat# AGR1020; CAS: 111-30-8 |
| Hoechst 33258 | Thermo Fisher Scientific | Cat# H1398; CAS: 23491–45-4 |
| Lysyl endopeptidase (LysC) | FUJIFILM Wako Chemicals | Cat# 129-02541 |
| Osmium tetroxide 4% solution | Electron Microscopy Sciences | Cat# 19170; CAS: 20816–12-0 |
| Paraformaldehyde | Roth | Cat# O335.1; CAS: 30525-89-4 |
| 32% paraformaldehyde, EM grade | Electron Microscopy Sciences | Cat# 15714 |
| Phalloidin/Alexa Fluor 568 | Thermo Fisher Scientific | Cat# A12380 |
| Pierce Streptavidin Magnetic Beads | Thermo Scientific Pierce | Cat# 88817 |
| Polyethylenimine | Polysciences | Cat# 23966; CAS: 26913-06-4 |
| Puromycin dihydrochloride | Sigma-Aldrich | Cat# P8833 |
| Reynolds’ lead citrate | Delta Microscopies | Cat# 11300; CAS: 512–26-5 |
| Trypsin Gold Mass Spec Grade | Promega | Cat# V5280 |
| Uranyl acetate | Science Services | Cat# E22400; CAS: 541–09-3 |
| Vanadyl ribonucleoside complexes solution | Sigma-Aldrich | Cat# 94742 |
| Vectashield Plus | Vector Laboratories | Cat# H-1900 |
| Critical commercial assays | ||
| Duolink In Situ Detection Reagents Red | Sigma-Aldrich | Cat# DUO92008 |
| Duolink In Situ PLA Probe Anti-Mouse MINUS | Sigma-Aldrich | Cat# DUO92004 |
| Duolink In Situ PLA Probe Anti-Rabbit PLUS | Sigma-Aldrich | Cat# DUO92002 |
| Duolink In Situ Wash Buffers, Fluorescence | Sigma-Aldrich | Cat# DUO82049 |
| Lipofectamine RNAiMAX | Invitrogen | Cat# 13778100 |
| TransIT Insect Transfection reagent | Mirus Bio | Cat# MIR 6104 |
| Software | ||
| Fiji v 2.0.0 | NIH | https://imagej.net/software/fiji/ |
| FragPipe v 20.0 | University of Michigan Medical School | https://github.com/Nesvilab/FragPipe |
| GraphPad Prism 10 | GraphPad | https://www.graphpad.com/scientific-software/prism |
| HMMER v 3.4 | Eddy (2011) | https://hmmer.org/ |
| Ilastik v 1.4.0 | Berg et al. (2019) | https://www.ilastik.org |
| IonQuant v 1.9.8 | Yu et al. (2021) | https://github.com/Nesvilab/IonQuant |
| Jalview v 2.11.1.4 | Waterhouse et al. (2009) | https://www.jalview.org/ |
| MAFFT v 7 | Katoh et al. (2019) | https://mafft.cbrc.jp/alignment/server/ |
| MATLAB v R2023a | MathWorks | https://www.mathworks.com |
| MSFragger v 3.8 | Kong et al. (2017) | https://github.com/Nesvilab/MSFragger |
| MsReport v 0.0.23 | Max Perutz Labs Mass Spectrometry Facility | N/A |
| NCBI BLAST+ v 2.13.0 | Altschul et al. (1997) | https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ |
| Philosopher v 5.0.0 | da Veiga Leprevost et al. (2020) | https://github.com/Nesvilab/philosopher |