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. Author manuscript; available in PMC: 2023 Mar 2.
Published in final edited form as: Neuron. 2022 Jan 21;110(5):824–840.e10. doi: 10.1016/j.neuron.2021.12.031

KEY RESOURCES TABLE

REAGENT or RESOURCE SOURCE IDENTIFIER
Chemicals
Cold Water Fish Skin Gelatin Aurion SKU#900.033
Anhydrous Acetone (glass distilled) Electron Microscopy Sciences (EMS) Cat#10015;
CAS: 67–64-1
Bovine Serum Albumin EMS Cat#25554
EMBed-812 Embedding Kit EMS Cat#14120
Glutaraldehyde (10% in acetone) EMS Cat#16530
Lead Nitrate EMS Cat#17900;
CAS: 10099–74-8
Lowicryl HM20 EMS Cat#14340
Osmium Tetroxide EMS Cat#19100;
CAS: 20816–12-0
Sodium Citrate EMS Cat#21140;
CAS: 6132–04-3
Tannic Acid EMS Cat#21700;
CAS: 1401–55-4
Uranyl acetate EMS Cat#22400;
CAS: 541–09-3
Ammonium chloride Millipore Cat#1011450500; CAS: 12125–02-9
1-Hexadecene Sigma-Aldrich SKU#H2131;
CAS: 629–73-2
4-Hydroxytamoxifen Sigma-Aldrich SKU#H6278;
CAS: 68392–35-8
Glycine powder Sigma-Aldrich SKU#G7126;
CAS: 56–40-6
Levamisole Hydrochloride Sigma-Aldrich SKU#PHR1798;
CAS: 16595–80-5
EZ-Link™ Sulfo-NHS-LC-Biotin Thermo Scientific Cat#21335
NeutrAvidin Agarose Resin Thermo Scientific Cat#29200
PierceTM BCA Protein Assay Kit Thermo Scientific Cat#23225
Protein A Gold 10 nm University Medical Center Utrecht Order: PAG 10 nm/S
Toluidine Blue Ward’s Science Item#470302–956;
CAS: 92–31-9
Experimental Models: Organisms/Strains
C. elegans: olaIs34 [DACR808 (pttx-3::atg-9::gfp) (10 ng/μl) + DACR18 (pttx-3:mCh:rab-3) (30 ng/μl)] III This paper DCR4755
C. elegans: olaex2264 [DACR1821 (punc-14::atg-9::GFP)(5ng/μl)] (Stavoe et al., 2016) DCR4535
C. elegans: olaex2264 This paper DCR4535
C. elegans: unc-26(e205);olaex2264 This paper DCR5952
C. elegans: unc-101(m1) I Caenorhabditis Genetics Center DR1
C. elegans: unc-101(m1);olaIs34 This paper DCR8064
C. elegans: dpy-23(e840) X Caenorhabditis Genetics Center CB840
C. elegans: dpy-23(e840);olaIs34 This paper DCR8633
C. elegans: apb-3(ok429) I Caenorhabditis Genetics Center RB662
C. elegans: apb-3(ok429);olaIs34 This paper DGR7823
C. elegans: olaex4060 [DAGR922 (pttx-3::atg-9::mCh) (20ng/μl) + DAGR2716 (pttx-3::sng-1::gfp) (15ng/μl)] This paper DGR6797
C. elegans: apb-3(ok429);olaex4060 This paper DGR8584
C. elegans: apm-3(gk771233) X Caenorhabditis Genetics Center VG40707
C. elegans: apm-3(gk771233);olaIs34 This paper DGR8058
C. elegans: apd-3(gk805642) II Caenorhabditis Genetics Center VG40775
C. elegans: apd-3(gk805642);olaIs34 This paper DGR8135
C. elegans: olaEx4710 [DAGR941 (pttx-3::aman-2::gfp) (0.5ng/μl) + DAGR922 (pttx-3::atg-9::mCh) (20ng/μl)] This paper DGR8018
C. elegans: olaEx4966 [DAGR808 (pttx-3::atg-9::gfp) (10ng/μl) + DAGR3393 (pttx-3::tgn-38::mCh) (20ng/μl)] This paper DGR8582
C. elegans: olaEx4805 [DGR930 (pttx-3::sp12::GFP) (5ng/μl) + DAGR922 (pttx-3::atg-9::mCh) (20ng/μl)] This paper DGR7899
C. elegans: olaEx5178 [DAGR1617 (pttx-3::tomm-20::gfp) (30 ng/μl) + DAGR18 (pttx-3::atg-9::mCh) (30 ng/μl)] This paper DGR8567
C. elegans: unc-26(s1710) IV Caenorhabditis Genetics Center EG3027
C. elegans: unc-26(e205) IV Caenorhabditis Genetics Center GB205
C. elegans: unc-26(e205);olaIs34 This paper DGR5578
C. elegans: unc-26(s1710);olaIs34 This paper DGR6121
C. elegans: unc-26(pek228[unc-26_R216Q]) IV This paper BJH728
C. elegans: unc-57(ok310) I Kang Shen Laboratory (Stanford University, California) (Li et al., 2016; Schuske et al., 2003) EG2710
C. elegans: unc-57(ok310);olaIs34 This paper DGR5599
C. elegans: unc-11(e47) I Caenorhabditis Genetics Center GB47
C. elegans: unc-11(e47);olaIs34 This paper DGR5893
C. elegans: dyn-1(ky51) X Caenorhabditis Genetics Center GX51
C. elegans: dyn-1(ky51);olaIs34 This paper DGR5953
C. elegans: unc-18(e81) X Caenorhabditis Genetics Center GB81
C. elegans: unc-18(e81);olaIs34 This paper DGR8033
C. elegans: unc-18(e81);unc-26(s 1710);olaIs34 This paper DGR8387
C. elegans: unc-13(s69) I Erik Jorgensen Laboratory (University of Utah, Salt Lake City, Utah) (Richmond etal., 1999) BG168
C. elegans: unc-13(s69);olaIs34 This paper DGR5598
C. elegans: unc-13(s69);unc-26(e205);olaIs34 This paper DGR6406
C. elegans: unc-26(s 1710);olaex3465;olaIs34 This paper DGR7497
C. elegans: olaIs17 [pmod-1::GCaMP6s;pttx-3::mCherry;punc-
122:dsRed]		 (Hawk etal., 2018) DGR3056
C. elegans: xuIs230 (pttx-3s::NpHR::yfp;pttx-3s::DsRed;punc-122::yfp);unc-26(s1710);olaIs34 This paper DCR8661
C. elegans: olaEx4099 [DACR2739 (pttx-3::sng-1::bfp) (30ng/|μl)];olaIs34 This paper DCR6894
C. elegans: olaEx4099 [DACR2739 (pttx-3::sng-1::bfp) (30ng/μl)];unc-26(s1710);olaIs34 This paper DCR6877
C. elegans: olaEx4020 [DACR2739 (pttx-3::sng-1::bfp) (30ng/μl) + DACR808 (pttx-3::atg-9::gfp) (10ng/μl)] This paper DCR6710
C. elegans: unc-26(s1710);olaex4020 This paper DCR6838
C. elegans: olaEx3462 [DACR4860 (pttx-3::unc-26) (5ng/μl)];unc-26(e205);olaIs34 This paper DCR5950
C. elegans: unc-26(s1710);olaEx1360 [DACR922 (pttx-3::mCh::atg-9) (30 ng/μl)];olaIs44 [DACR1321 (pttx-3::gfp::lgg-1) (15ng/μl)] This paper DCR7339
C. elegans: unc-26(s1710);olaex4290 [DACR2877 (pttx-3::bfp::chc-1) (5ng/μl)];olaIs34 This paper DCR7332
C. elegans: epg-9(bp320);olaex4290;olaIs34 This paper DCR8924
C. elegans: pfk-1.1(gk922689) X Caenorhabditis Genetics Center VC41001
C. elegans: pfk-1.1(gk922689);olaIs34 This paper DCR6129
C. elegans: pfk-1.1(gk922689);unc-13(s69);olaIs34 This paper DCR8873
C. elegans: unc-51(e369) V Caenorhabditis Genetics Center CB369
C. elegans: unc-51(e69);olaIs34 This paper DCR7527
C. elegans: epg-9(bp320) IV Caenorhabditis Genetics Center HZ1692
C. elegans: epg-9(bp320);olaIs34 This paper DCR7047
C. elegans: epg-9(bp320);unc-13(s69);olaIs34 This paper DCR8869
C. elegans: epg-8(bp251) I Caenorhabditis Genetics Center HZ1691
C. elegans: epg-8(bp251);olaIs34 This paper DCR7048
C. elegans: atg-13(bp414) III Caenorhabditis Genetics Center HZ1688
C. elegans: olaIs33 [DACR808 (pttx-3::atg-9::gfp) (10 ng/μl) + DACR18 (pttx-3::mCh::rab-3) (30 ng/μl)] This paper DCR4654
C. elegans: atg-13(bp414);olaIs33 This paper DCR7479
C. elegans: olaEx4718 [DACR3209 (pttx-3::atg-9(ΔAP)::gfp) (10ng/μl)] This paper DCR7770
C. elegans: olaEx4719 [DACR3209 (pttx-3::atg-9(ΔAP)::gfp) (10ng/μl)] This paper DCR7771
C. elegans: olaIs35 (pttx-3::egfp::lgg-1;pttx-3::mCh) (Stavoe et al., 2016) DCR4750
C. elegans: unc-13(e450);olaIs35 (Hill et al., 2019) DCR5581
C. elegans: atg-9(wy56);olaIs35 (Stavoe et al., 2016) DCR4851
C. elegans: unc-26(s1710);olaIs35 This paper DCR6122
C. elegans: unc-26(s1710);atg-9(wy56);olaIs35 This paper DCR8128
C. elegans: atg-9(ΔAP);olaIs35 This paper DCR8868
C. elegans: unc-26(R216Q) IV This paper DGR7333
C. elegans: unc-26(R216Q);olaIs34 This paper DGR7337
C. elegans: sac-2/W09C5.7(gk346019) I Caenorhabditis Genetics Center VG20557
C. elegans: sac-2/W09C5.7(gk927434) I Caenorhabditis Genetics Center VG41013
C. elegans: sac-2/W09C5.7(gk346019);olaIs34 This paper DGR6730
C. elegans: sac-2/W09C5.7(gk927434);olaIs34 This paper DGR6731
C. elegans: unc-26(s1710);sac-2(gk346019);olaIs34 This paper DGR7077
C. elegans: unc-26(s1710); sac-2(gk927434);olaIs34 This paper DGR7062
C. elegans: unc-26(R216Q); sac-2(gk346019);olaIs34 This paper DGR8871
C. elegans: olaex4504 [DAGR3699 (pttx-3:gfp:chc-1) (5ng/μl)] This paper DGR7480
C. elegans: unc-26(R216Q);olaex4504 This paper DGR7748
C. elegans: olaex4016 [DAGR2716 (pttx-3::sng-1::gfp) (15ng/μl) + DAGR922 (pttx-3::atg-9::mCh) (20ng/μl)] This paper DGR6704
C. elegans: unc-26(R216Q);olaex4016 This paper DGR7769
C. elegans: unc-26(R216Q);olaex4290;olaIs34 This paper DGR8586
Recombinant DNA
Plasmid: pttx-3::atg-9::gfp (Liang et al., 2012) DAGR808
Plasmid: pttx-3::atg-9::mCh This paper DAGR922
Plasmid: pttx-3::sng-1::bfp This paper DAGR2739
Plasmid: pttx-3::mCh::rab-3 (Colon-Ramos et al., 2007) DAGR18
Plasmid: punc-14::atg-9::gfp (Stavoe et al., 2016) DAGR1821
Plasmid: pttx-3::unc-26 This paper DAGR4860
Plasmid: pttx-3::sng-1::gfp This paper DAGR2716
Plasmid: pttx-3::sng-1::bfp This paper DAGR2739
Plasmid: pttx-3::aman-2::gfp This paper DAGR941
Plasmid: pttx-3::tgn-38::mCh This paper DAGR3393
Plasmid: pttx-3::sp12::gfp (Hill etal., 2019) DGR930
Plasmid: pttx-3::tomm-20::gfp (Hill etal., 2019) DAGR1617
Plasmid: pttx-3::gfp::lgg-1 (Stavoe et al., 2016) DAGR1321
Plasmid: pttx-3::bfp::chc-1 This paper DAGR2877
Plasmid: pttx-3:gfp:chc-1 This paper DAGR3699
Antibodies
Rabbit polyclonal anti-GFP Abcam Cat#ab6556; RRID: AB_305564
Rabbit monoclonal anti-ATG9A Abcam Cat#ab108338; RRID: AB_10863880
Mouse monoclonal anti-Bin1 (Amphiphysin2) Upstate/Millipore Cat#05–449; RRID: AB_309738
Guinea Pig polyclonal anti-VGAT Gaibiochem Cat#676780; RRID: AB_212625
Mouse monoclonal anti-Transferrin Receptor Invitrogen/Thermo Fisher Cat#13–6800; RRID: AB_86623
Mouse monoclonal anti-Dynamin BD Transduction Laboratories/BD Biosciences Cat#610246; RRID: AB_397641
Rabbit polyclonal anti-beta-Tubulin Invitrogen/Thermo Fisher Cat#PA1–21153; RRID: AB_561870
Software and Algorithms
Voiocity Improvision by Perkin Elmer N/A
Fiji (Schindelin et al., 2012) https://imagej.net/Fiji/Downioads
Prism Graphpad Software Inc https://www.graphpad.com/
Adobe Illustrator Adobe https://www.adobe.com/products/iiiustrator.html
Adobe Photoshop Adobe https://www.adobe.com/products/photoshop.html
MATLAB MathWorks https://www.mathworks.com/products/matiab.html
TrakEM2 (Cardona et al., 2012) https://imagej.net/TrakEM2
ApE M. Wayne Davis https://jorgensen.bioiogy.utah.edu/wayned/ape/
Deposited Data
Hippocampal Neuron Culture Protocol Protocols.io, ASAP Collaborative Research Network https://dx.doi.org/10.17504/protocols.io.b2deqa3e
Immunofluorescence Protocol Protocols.io, ASAP Collaborative Research Network https://dx.doi.org/10.17504/protocols.io.b2c7qazn
Dynamin Conditional Knockout Protocol Protocols.io, ASAP Collaborative Research Network https://dx.doi.org/10.17504/protocols.io.b2ddqa26
Surface Protein Biotinylation Protocol Protocols.io, ASAP Collaborative Research Network https://doi.org/10.17504/protocols.io.b2c8qazw
Code to Quantify Expressivity of ATG-9::GFP Subsynaptic Foci at the Presynaptic Region GitHub https://github.com/yangsisi76/Quantify-distribution-of-cell-structures.
Other
Sample transfer box Custom, Yale machine shop N/A
Diamond sectioning knife (Ultra 45°,4mm) Diatome N/A
Diamond trimming knife (45°) Diatome N/A
Aclar sheets 200 um (7.8mil) EMS Cat#50425
Chang embedding mold EMS Cat#70910
Nickel slot grids EMS Cat#FCF2010-Ni
Field Electron and Ion Company (FEI) Tecnai Biotwin FEI N/A
Flow-through rings Leica Microsystems Cat#16707157
Leica EM AFS2 Leica Microsystems N/A
Leica EM HPM 100 Leica Microsystems N/A
Leica EM UG7 Leica Microsystems N/A
Leica plastic capsules (D5 x H15) Leica Microsystems Cat#16702738
Universal container for plastic capsules Leica Microsystems Cat#16702735
UltraView VoX spinning disc confocal microscope with a 60x CFI Plan Apo VC, NA 1.4, oil objective on a NikonTi-E stand PerkinElmer N/A
Specimen Carrier Type A Technotrade International Part# 241
Specimen Carrier Type B Technotrade International Part# 242
Talos L120G Thermo Fisher N/A
Gene Frame Adhesive Frames Thermo Scientific Cat#AB-0576