Control:Article Title: Ubiquitin is directly linked via an ester to protein-conjugated mono-ADP-ribose.
Article Snippet: .. Reagents and tools table Reagent/resource Reference or source Identifier or catalog number Experimental models HEK 293T (H. sapiens) ATCC CRL-3216 HEK 293 control and PARP1 KO (H. sapiens) Shrestha et al, 2016 https://doi.org/10.1074/ jbc.M116.726729 Prof. Michael Garabedian, NYU Langone, USA Recombinant DNA pET28b-DTX2389-622 (H. sapiens) This study N/A pET28a-UBE2D3 (H. sapiens) Gift from R. Klevit N/A pET17b-Ub (H. sapiens) Gift from D. Komander N/A pET21d-UBE1 (H. sapiens) Addgene #34965A pETM30-TssM and TssM* (B. pseudomallei) Szczesna et al, 2024 N/A pOPINS-USP21196-565 (H. sapiens) Ye et al, 2011 Addgene #61585 pOPINE-Cezanne129-438 (H. sapiens) Mevissen et al, 2016 N/A pOPINB-LotA-N1-300 (L. pneumophila) Warren et al, 2023 N/A pOPINK-OTUD2132-314 (H. sapiens) Mevissen et al, 2013 Addgene #61410 pOPINS-TRABID319-751 (D. melanogaster) Xia et al, 2022 [preprint] N/A OTUB1* (H. sapiens) Michel et al, 2015 Addgene #65441 AMSH* (H. sapiens) Michel et al, 2015 Addgene #66712 pOPINB-Otulin (H. sapiens) Keusekotten et al, 2013 Addgene #61464 pET28b-NUDT16 Javed et al, 2023 N/A pET28b-MD1 Javed et al, 2023 N/A pGEX-6p2-MD2 Javed et al, 2023 N/A pGEX-6p2-TARG1 Javed et al, 2023 N/A 10 The EMBO Journal © The Author(s) D ow nloaded from https://w w w .em bopress.org on M arch 1, 2025 from IP 2401:4900:1ce1:f8ae:54ac:d0c0:de67:d2a. .. Reagent/resource Reference or source Identifier or catalog number ChemiDoc MP imaging System Bio-Rad 12003154 AKTA Pure Cytiva Superdex75 Increase 10/ 300 GL Cytiva
Recombinant:Article Title: Ubiquitin is directly linked via an ester to protein-conjugated mono-ADP-ribose.
Article Snippet: .. Reagents and tools table Reagent/resource Reference or source Identifier or catalog number Experimental models HEK 293T (H. sapiens) ATCC CRL-3216 HEK 293 control and PARP1 KO (H. sapiens) Shrestha et al, 2016 https://doi.org/10.1074/ jbc.M116.726729 Prof. Michael Garabedian, NYU Langone, USA Recombinant DNA pET28b-DTX2389-622 (H. sapiens) This study N/A pET28a-UBE2D3 (H. sapiens) Gift from R. Klevit N/A pET17b-Ub (H. sapiens) Gift from D. Komander N/A pET21d-UBE1 (H. sapiens) Addgene #34965A pETM30-TssM and TssM* (B. pseudomallei) Szczesna et al, 2024 N/A pOPINS-USP21196-565 (H. sapiens) Ye et al, 2011 Addgene #61585 pOPINE-Cezanne129-438 (H. sapiens) Mevissen et al, 2016 N/A pOPINB-LotA-N1-300 (L. pneumophila) Warren et al, 2023 N/A pOPINK-OTUD2132-314 (H. sapiens) Mevissen et al, 2013 Addgene #61410 pOPINS-TRABID319-751 (D. melanogaster) Xia et al, 2022 [preprint] N/A OTUB1* (H. sapiens) Michel et al, 2015 Addgene #65441 AMSH* (H. sapiens) Michel et al, 2015 Addgene #66712 pOPINB-Otulin (H. sapiens) Keusekotten et al, 2013 Addgene #61464 pET28b-NUDT16 Javed et al, 2023 N/A pET28b-MD1 Javed et al, 2023 N/A pGEX-6p2-MD2 Javed et al, 2023 N/A pGEX-6p2-TARG1 Javed et al, 2023 N/A 10 The EMBO Journal © The Author(s) D ow nloaded from https://w w w .em bopress.org on M arch 1, 2025 from IP 2401:4900:1ce1:f8ae:54ac:d0c0:de67:d2a. .. Reagent/resource Reference or source Identifier or catalog number ChemiDoc MP imaging System Bio-Rad 12003154 AKTA Pure Cytiva Superdex75 Increase 10/ 300 GL Cytiva
Article Title: RNF114 and RNF166 exemplify reader-writer E3 ligases that extend K11 polyubiquitin onto sites of MARUbylation.
Article Snippet: .. Reagents and tools table Reagent/resource Reference or source Identifier or catalog number Experimental models HEK 293T ATCC CRL-3216 Recombinant DNA pET28b-DTX2389-622 (H. sapiens) Bejan et al, 2025 N/A pET28a-UBE2D3 (H. sapiens) Gift from R. Klevit N/A pET17b-Ub (H. sapiens) Gift from D. Komander N/A pET21d-UBE1 (H. sapiens) Berndsen & Wolberger, 2011 Addgene #34965A pETM30-TssM and TssM* (B. pseudomallei) Szczesna et al, 2024 N/A pOPINS-USP21196-565 (H. sapiens) Ye et al, 2011 Addgene #61585 pOPINE-Cezanne129-438 (H. sapiens) Mevissen et al, 2016 N/A pOPINB-LotA-N1-300 (L. pneumophila) Warren et al, 2023 N/A pOPINB-OTUB1* (H. sapiens) Michel et al, 2015 Addgene #65441 pOPINB-AMSH* (H. sapiens) Michel et al, 2015 Addgene #66712 Reagent/resource Reference or source Identifier or catalog number pOPINB-Otulin (H. sapiens) Keusekotten et al, 2013 Addgene #61464 HA-Ub Gift from A. Barnes pOPINB-RNF114 WT This study N/A pOPINB-RNF166 This study N/A pOPINS-3C-RNF138 This study N/A pEGFP-C1-WT-PARP7 Rodriguez et al, 2021 N/A GST-AF1521 Gift from M. Nielsen N/A Antibodies Mono-ADP-Ribose AbD33204 (1:250 = 2 μg/ml) Bio-Rad HCA354 GFP (1:2000) Proteintech pabg1 RNF114 (1:1000) Genetex GTX107046 DTX2 (1:500) Thermo Fisher Scientific PA5-60164 Tubulin (DM1A) (1:2000) Cell signaling technology 3873 HA-tag (C29F4) (1:1000) Cell signaling technology 3724 Peroxidase AffiniPureTM Goat Anti-Rabbit IgG (H + L) (1:10,000) Jackson ImmunoResearch 111-035-144 Goat anti-Mouse IgG (H + L) Secondary Antibody, HRP (1:5000) Invitrogen 62-6520 Oligonucleotides and other sequence-based reagents siRNA NT Horizon Discovery D-00181010-05 siRNA RNF114 Horizon Discovery L-00702400-0005 siRNA DTX2 Horizon Discovery L-00711400-0005 siRNA RNF166 Horizon Discovery L-00711900-0005 PCR primers This study (Table EV1) Chemicals, enzymes, and other reagents DMEM, high glucose Gibco 11965118 Fetal bovine serum Sigma-Aldrich F0926 GlutaMAXTM Supplement Gibco 35050061 Sodium pyruvate (100mM) Gibco 11360070 Basticidin S HCl Corning 30100RB Doxycycline hyclate Thermo Scientific chemicals 446060050 jetOPTIMIUS® DNA transfection reagent Polypolus-transfection 101000025 DharmaFECT 1 Transfection Reagent Horizon Discovery T-2001-02 Bovine serum albumin Sigma-Aldrich A9647 TCEP Thermo scientific 20490 cOmpleteTM, EDTA-free Protease inhibitor cocktail Roche 11873580001 BioRad Protein assay dye reagent concentrate Bio-Rad 5000006 12 The EMBO Journal © The Author(s) D ow nloaded from https://w w w .em bopress.org on O ctober 10, 2025 from IP 125.235.236.20. ..
Article Title: Mitochondrial membrane tension governs fission.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, peptides, and recombinant proteins Blebbistatin Sigma-Aldrich B0560 Nocodazole Sigma-Aldrich M1404 ML-7 hydrochlorine Santa Cruz Biotechnology 110448-33-4 Mito-FliptR Spirochrome SC023 TMRE ThermoFisher Scientific T669 MitoTracker Red CMXRos ThermoFisher Scientific M7512 FBS HyClone SV30160.03 Opti-MEM ThermoFisher Scientific 31985062 Lipofectamine 2000 ThermoFisher Scientific 11668030 DMEM ThermoFisher Scientific 31966021 Leibovitz medium ThermoFisher Scientific 21083027 PBS ThermoFisher Scientific 70013016 Glucose oxidase Sigma-Aldrich G7141 Catalase Sigma-Aldrich C1345 HEPES ThermoFisher Scientific 15630 Experimental models: Cell lines Cos 7 cell line HPA culture collections COS7-ECACC-87021302 Recombinant DNA Mito-GFP (Cox8 presequence) Gift from Hari Shroff N/A mCherry-Drp1 Friedman et al., 2011 Addgene #49152 MitoBFP Friedman et al., 2011 Addgene #49151 Dyn2-GFP Gift from Gia Voeltz N/A KDEL-RFP (adapted from KDEL-BFP) Friedman et al., 2011 Addgene #49150 Software and algorithms MATLAB MathWorks 2016b Fiji (ImageJ) (Schindelin et al., 2012), NIH https://imagej.net/Fiji Trainable Weka Segmentation Arganda-Carreras et al., 2017 3.2.33 Structured illumination microscopy simulator Alharbi, 2013 Alharbi, 2013 MitoWorks This study https://github.com/LEB-EPFL/MitoWorks ..
Article Title: VMHvll Cckar cells dynamically control female sexual behaviors over the reproductive cycle.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Guinea pig anti-Fos Synaptic Systems Cat# 226005; RRID: AB_2800522 Goat anti-Fos Santa Cruz Biotechnology Cat# sc-52-G; RRID: AB_2629503 Rabbit anti-Esr1 Millipore Cat# 06-935; RRID: AB_310305 Goat anti-Guinea pig Cyanine Cy 3 Jackson ImmunoResearch Cat# 706-165-148; RRID: AB_2340460 Donkey anti-Goat Alexa Fluor 488 Jackson ImmunoResearch Cat# 705-545-147; RRID: AB_2336933 Goat anti-Rabbit Cyanine Cy 5 Jackson ImmunoResearch Cat# 711-175-152; RRID: AB_2340607 Bacterial and virus strains AAV1-hSyn-DIO-hM4Di-mCherry Addgene; Krashes et al., 2011 Addgene# 44362-AAV1 AAV2-hSyn-DIO-hM3Dq-mCherry Addgene; Krashes et al., 2011 Addgene# 44361-AAV2 AAV2-hSyn-DIO-mCherry Addgene; Bryan Roth lab (unpublished) Addgene# 50459-AAV2 AAV1-hSyn1-SIO-stGtACR2-FusionRed Addgene; Mahn et al., 2018 Addgene# 105677-AAV1 AAV2-EF1a-DIO-ChR2-EYFP UNC Vector Core; Karl Deisseroth lab (unpublished) Cat# AV-2-AV4378p AAV2-CAG-Flex-GFP UNC Vector Core; Oh et al., 2014 Cat# AV-2-ALL854 AAV1-hSyn-Flex-GCaMP6s-WPRE.SV40 Addgene; Chen et al., 2013 Addgene# 100843-AAV1 Chemicals, peptides, and recombinant proteins Normal donkey serum Jackson ImmunoResearch Cat# 017-000-121; RRID: AB_2337258 Red Retrobeads Lumafluor, Inc N/A CNO Sigma Cat# 34233-69-7 Critical commercial assays Nanoliter injector World Precision Instruments Cat# Nanoliter 2000 Temperature Logger Star-Oddi DST nano-T Experimental models: Organisms/strains CckarCre knock-in mice This paper N/A C57BL/6 mice Charles River Strain Code 027 Esr1ZsGreen Yong Yu lab, Saito et al., 2016 N/A Ai9 mice Jackson Laboratory Strain# 007909 Ai6 mice Jackson Laboratory Strain# 007906 Software and algorithms MATLAB R2019b MathWorks https://www.mathworks.com/products/matlab.html; RRID: SCR_001622 Prism 9 GraphPad Software https://www.graphpad.com/scientific-software/prism/; RRID: SCR_002798 StreamPix 8 NorPix https://www.norpix.com/products/streampix/ streampix.php; RRID: SCR_015773 ImageJ NIH https://imagej.nih.gov/ij/index.html; RRID: SCR_003070 pCLAMP 11 Molecular Devices https://www.moleculardevices.com/; RRID: SCR_011323 Adobe Photoshop 2020 Adobe https://www.adobe.com/; RRID: SCR_014199 Adobe Illustrator 2020 Adobe https://www.adobe.com/; RRID: SCR_010279 Body tracking code David Anderson lab, Lin et al., 2011 https://github.com/pdollar/toolbox e1 Neuron 110, 3000–3017.e1–e8, September 21, 2022 ..
Sequencing:Article Title: RNF114 and RNF166 exemplify reader-writer E3 ligases that extend K11 polyubiquitin onto sites of MARUbylation.
Article Snippet: .. Reagents and tools table Reagent/resource Reference or source Identifier or catalog number Experimental models HEK 293T ATCC CRL-3216 Recombinant DNA pET28b-DTX2389-622 (H. sapiens) Bejan et al, 2025 N/A pET28a-UBE2D3 (H. sapiens) Gift from R. Klevit N/A pET17b-Ub (H. sapiens) Gift from D. Komander N/A pET21d-UBE1 (H. sapiens) Berndsen & Wolberger, 2011 Addgene #34965A pETM30-TssM and TssM* (B. pseudomallei) Szczesna et al, 2024 N/A pOPINS-USP21196-565 (H. sapiens) Ye et al, 2011 Addgene #61585 pOPINE-Cezanne129-438 (H. sapiens) Mevissen et al, 2016 N/A pOPINB-LotA-N1-300 (L. pneumophila) Warren et al, 2023 N/A pOPINB-OTUB1* (H. sapiens) Michel et al, 2015 Addgene #65441 pOPINB-AMSH* (H. sapiens) Michel et al, 2015 Addgene #66712 Reagent/resource Reference or source Identifier or catalog number pOPINB-Otulin (H. sapiens) Keusekotten et al, 2013 Addgene #61464 HA-Ub Gift from A. Barnes pOPINB-RNF114 WT This study N/A pOPINB-RNF166 This study N/A pOPINS-3C-RNF138 This study N/A pEGFP-C1-WT-PARP7 Rodriguez et al, 2021 N/A GST-AF1521 Gift from M. Nielsen N/A Antibodies Mono-ADP-Ribose AbD33204 (1:250 = 2 μg/ml) Bio-Rad HCA354 GFP (1:2000) Proteintech pabg1 RNF114 (1:1000) Genetex GTX107046 DTX2 (1:500) Thermo Fisher Scientific PA5-60164 Tubulin (DM1A) (1:2000) Cell signaling technology 3873 HA-tag (C29F4) (1:1000) Cell signaling technology 3724 Peroxidase AffiniPureTM Goat Anti-Rabbit IgG (H + L) (1:10,000) Jackson ImmunoResearch 111-035-144 Goat anti-Mouse IgG (H + L) Secondary Antibody, HRP (1:5000) Invitrogen 62-6520 Oligonucleotides and other sequence-based reagents siRNA NT Horizon Discovery D-00181010-05 siRNA RNF114 Horizon Discovery L-00702400-0005 siRNA DTX2 Horizon Discovery L-00711400-0005 siRNA RNF166 Horizon Discovery L-00711900-0005 PCR primers This study (Table EV1) Chemicals, enzymes, and other reagents DMEM, high glucose Gibco 11965118 Fetal bovine serum Sigma-Aldrich F0926 GlutaMAXTM Supplement Gibco 35050061 Sodium pyruvate (100mM) Gibco 11360070 Basticidin S HCl Corning 30100RB Doxycycline hyclate Thermo Scientific chemicals 446060050 jetOPTIMIUS® DNA transfection reagent Polypolus-transfection 101000025 DharmaFECT 1 Transfection Reagent Horizon Discovery T-2001-02 Bovine serum albumin Sigma-Aldrich A9647 TCEP Thermo scientific 20490 cOmpleteTM, EDTA-free Protease inhibitor cocktail Roche 11873580001 BioRad Protein assay dye reagent concentrate Bio-Rad 5000006 12 The EMBO Journal © The Author(s) D ow nloaded from https://w w w .em bopress.org on O ctober 10, 2025 from IP 125.235.236.20. ..
Polymerase Chain Reaction:Article Title: RNF114 and RNF166 exemplify reader-writer E3 ligases that extend K11 polyubiquitin onto sites of MARUbylation.
Article Snippet: .. Reagents and tools table Reagent/resource Reference or source Identifier or catalog number Experimental models HEK 293T ATCC CRL-3216 Recombinant DNA pET28b-DTX2389-622 (H. sapiens) Bejan et al, 2025 N/A pET28a-UBE2D3 (H. sapiens) Gift from R. Klevit N/A pET17b-Ub (H. sapiens) Gift from D. Komander N/A pET21d-UBE1 (H. sapiens) Berndsen & Wolberger, 2011 Addgene #34965A pETM30-TssM and TssM* (B. pseudomallei) Szczesna et al, 2024 N/A pOPINS-USP21196-565 (H. sapiens) Ye et al, 2011 Addgene #61585 pOPINE-Cezanne129-438 (H. sapiens) Mevissen et al, 2016 N/A pOPINB-LotA-N1-300 (L. pneumophila) Warren et al, 2023 N/A pOPINB-OTUB1* (H. sapiens) Michel et al, 2015 Addgene #65441 pOPINB-AMSH* (H. sapiens) Michel et al, 2015 Addgene #66712 Reagent/resource Reference or source Identifier or catalog number pOPINB-Otulin (H. sapiens) Keusekotten et al, 2013 Addgene #61464 HA-Ub Gift from A. Barnes pOPINB-RNF114 WT This study N/A pOPINB-RNF166 This study N/A pOPINS-3C-RNF138 This study N/A pEGFP-C1-WT-PARP7 Rodriguez et al, 2021 N/A GST-AF1521 Gift from M. Nielsen N/A Antibodies Mono-ADP-Ribose AbD33204 (1:250 = 2 μg/ml) Bio-Rad HCA354 GFP (1:2000) Proteintech pabg1 RNF114 (1:1000) Genetex GTX107046 DTX2 (1:500) Thermo Fisher Scientific PA5-60164 Tubulin (DM1A) (1:2000) Cell signaling technology 3873 HA-tag (C29F4) (1:1000) Cell signaling technology 3724 Peroxidase AffiniPureTM Goat Anti-Rabbit IgG (H + L) (1:10,000) Jackson ImmunoResearch 111-035-144 Goat anti-Mouse IgG (H + L) Secondary Antibody, HRP (1:5000) Invitrogen 62-6520 Oligonucleotides and other sequence-based reagents siRNA NT Horizon Discovery D-00181010-05 siRNA RNF114 Horizon Discovery L-00702400-0005 siRNA DTX2 Horizon Discovery L-00711400-0005 siRNA RNF166 Horizon Discovery L-00711900-0005 PCR primers This study (Table EV1) Chemicals, enzymes, and other reagents DMEM, high glucose Gibco 11965118 Fetal bovine serum Sigma-Aldrich F0926 GlutaMAXTM Supplement Gibco 35050061 Sodium pyruvate (100mM) Gibco 11360070 Basticidin S HCl Corning 30100RB Doxycycline hyclate Thermo Scientific chemicals 446060050 jetOPTIMIUS® DNA transfection reagent Polypolus-transfection 101000025 DharmaFECT 1 Transfection Reagent Horizon Discovery T-2001-02 Bovine serum albumin Sigma-Aldrich A9647 TCEP Thermo scientific 20490 cOmpleteTM, EDTA-free Protease inhibitor cocktail Roche 11873580001 BioRad Protein assay dye reagent concentrate Bio-Rad 5000006 12 The EMBO Journal © The Author(s) D ow nloaded from https://w w w .em bopress.org on O ctober 10, 2025 from IP 125.235.236.20. ..
Transfection:Article Title: RNF114 and RNF166 exemplify reader-writer E3 ligases that extend K11 polyubiquitin onto sites of MARUbylation.
Article Snippet: .. Reagents and tools table Reagent/resource Reference or source Identifier or catalog number Experimental models HEK 293T ATCC CRL-3216 Recombinant DNA pET28b-DTX2389-622 (H. sapiens) Bejan et al, 2025 N/A pET28a-UBE2D3 (H. sapiens) Gift from R. Klevit N/A pET17b-Ub (H. sapiens) Gift from D. Komander N/A pET21d-UBE1 (H. sapiens) Berndsen & Wolberger, 2011 Addgene #34965A pETM30-TssM and TssM* (B. pseudomallei) Szczesna et al, 2024 N/A pOPINS-USP21196-565 (H. sapiens) Ye et al, 2011 Addgene #61585 pOPINE-Cezanne129-438 (H. sapiens) Mevissen et al, 2016 N/A pOPINB-LotA-N1-300 (L. pneumophila) Warren et al, 2023 N/A pOPINB-OTUB1* (H. sapiens) Michel et al, 2015 Addgene #65441 pOPINB-AMSH* (H. sapiens) Michel et al, 2015 Addgene #66712 Reagent/resource Reference or source Identifier or catalog number pOPINB-Otulin (H. sapiens) Keusekotten et al, 2013 Addgene #61464 HA-Ub Gift from A. Barnes pOPINB-RNF114 WT This study N/A pOPINB-RNF166 This study N/A pOPINS-3C-RNF138 This study N/A pEGFP-C1-WT-PARP7 Rodriguez et al, 2021 N/A GST-AF1521 Gift from M. Nielsen N/A Antibodies Mono-ADP-Ribose AbD33204 (1:250 = 2 μg/ml) Bio-Rad HCA354 GFP (1:2000) Proteintech pabg1 RNF114 (1:1000) Genetex GTX107046 DTX2 (1:500) Thermo Fisher Scientific PA5-60164 Tubulin (DM1A) (1:2000) Cell signaling technology 3873 HA-tag (C29F4) (1:1000) Cell signaling technology 3724 Peroxidase AffiniPureTM Goat Anti-Rabbit IgG (H + L) (1:10,000) Jackson ImmunoResearch 111-035-144 Goat anti-Mouse IgG (H + L) Secondary Antibody, HRP (1:5000) Invitrogen 62-6520 Oligonucleotides and other sequence-based reagents siRNA NT Horizon Discovery D-00181010-05 siRNA RNF114 Horizon Discovery L-00702400-0005 siRNA DTX2 Horizon Discovery L-00711400-0005 siRNA RNF166 Horizon Discovery L-00711900-0005 PCR primers This study (Table EV1) Chemicals, enzymes, and other reagents DMEM, high glucose Gibco 11965118 Fetal bovine serum Sigma-Aldrich F0926 GlutaMAXTM Supplement Gibco 35050061 Sodium pyruvate (100mM) Gibco 11360070 Basticidin S HCl Corning 30100RB Doxycycline hyclate Thermo Scientific chemicals 446060050 jetOPTIMIUS® DNA transfection reagent Polypolus-transfection 101000025 DharmaFECT 1 Transfection Reagent Horizon Discovery T-2001-02 Bovine serum albumin Sigma-Aldrich A9647 TCEP Thermo scientific 20490 cOmpleteTM, EDTA-free Protease inhibitor cocktail Roche 11873580001 BioRad Protein assay dye reagent concentrate Bio-Rad 5000006 12 The EMBO Journal © The Author(s) D ow nloaded from https://w w w .em bopress.org on O ctober 10, 2025 from IP 125.235.236.20. ..
Protease Inhibitor:Article Title: RNF114 and RNF166 exemplify reader-writer E3 ligases that extend K11 polyubiquitin onto sites of MARUbylation.
Article Snippet: .. Reagents and tools table Reagent/resource Reference or source Identifier or catalog number Experimental models HEK 293T ATCC CRL-3216 Recombinant DNA pET28b-DTX2389-622 (H. sapiens) Bejan et al, 2025 N/A pET28a-UBE2D3 (H. sapiens) Gift from R. Klevit N/A pET17b-Ub (H. sapiens) Gift from D. Komander N/A pET21d-UBE1 (H. sapiens) Berndsen & Wolberger, 2011 Addgene #34965A pETM30-TssM and TssM* (B. pseudomallei) Szczesna et al, 2024 N/A pOPINS-USP21196-565 (H. sapiens) Ye et al, 2011 Addgene #61585 pOPINE-Cezanne129-438 (H. sapiens) Mevissen et al, 2016 N/A pOPINB-LotA-N1-300 (L. pneumophila) Warren et al, 2023 N/A pOPINB-OTUB1* (H. sapiens) Michel et al, 2015 Addgene #65441 pOPINB-AMSH* (H. sapiens) Michel et al, 2015 Addgene #66712 Reagent/resource Reference or source Identifier or catalog number pOPINB-Otulin (H. sapiens) Keusekotten et al, 2013 Addgene #61464 HA-Ub Gift from A. Barnes pOPINB-RNF114 WT This study N/A pOPINB-RNF166 This study N/A pOPINS-3C-RNF138 This study N/A pEGFP-C1-WT-PARP7 Rodriguez et al, 2021 N/A GST-AF1521 Gift from M. Nielsen N/A Antibodies Mono-ADP-Ribose AbD33204 (1:250 = 2 μg/ml) Bio-Rad HCA354 GFP (1:2000) Proteintech pabg1 RNF114 (1:1000) Genetex GTX107046 DTX2 (1:500) Thermo Fisher Scientific PA5-60164 Tubulin (DM1A) (1:2000) Cell signaling technology 3873 HA-tag (C29F4) (1:1000) Cell signaling technology 3724 Peroxidase AffiniPureTM Goat Anti-Rabbit IgG (H + L) (1:10,000) Jackson ImmunoResearch 111-035-144 Goat anti-Mouse IgG (H + L) Secondary Antibody, HRP (1:5000) Invitrogen 62-6520 Oligonucleotides and other sequence-based reagents siRNA NT Horizon Discovery D-00181010-05 siRNA RNF114 Horizon Discovery L-00702400-0005 siRNA DTX2 Horizon Discovery L-00711400-0005 siRNA RNF166 Horizon Discovery L-00711900-0005 PCR primers This study (Table EV1) Chemicals, enzymes, and other reagents DMEM, high glucose Gibco 11965118 Fetal bovine serum Sigma-Aldrich F0926 GlutaMAXTM Supplement Gibco 35050061 Sodium pyruvate (100mM) Gibco 11360070 Basticidin S HCl Corning 30100RB Doxycycline hyclate Thermo Scientific chemicals 446060050 jetOPTIMIUS® DNA transfection reagent Polypolus-transfection 101000025 DharmaFECT 1 Transfection Reagent Horizon Discovery T-2001-02 Bovine serum albumin Sigma-Aldrich A9647 TCEP Thermo scientific 20490 cOmpleteTM, EDTA-free Protease inhibitor cocktail Roche 11873580001 BioRad Protein assay dye reagent concentrate Bio-Rad 5000006 12 The EMBO Journal © The Author(s) D ow nloaded from https://w w w .em bopress.org on O ctober 10, 2025 from IP 125.235.236.20. ..
Real-time Polymerase Chain Reaction:Article Title: Transcriptional control of nucleus accumbens neuronal excitability by retinoid X receptor alpha tunes sensitivity to drug rewards.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies See Table S4 N/A N/A Anti-mouse peroxidase-conjugated secondary antibody Vector Laboratories Cat#PI-2000 Anti-rabbit peroxidase-conjugated secondary antibody Vector Laboratories Cat#PI-1000 Oligonucleotides See Table S5 for qPCR primers N/A N/A See method details for miRNA sequences N/A N/A FISH probe: Mm-Rxra ACD Bio Cat#63121 FISH probe: Mm-Drd1a-C2 ACD Bio Cat#406491-C2 FISH probe: Mm-Drd2-C3 ACD Bio Cat#406501-C3 Chemicals Cocaine HCl NIDA N/A Morphine SO4 NIDA N/A HX531 Tocris Cat#3912 PBS Thermo Fisher Scientific 14-190-144 DMSO Sigma D4540 CNO dihydrochloride Tocris Cat#6329 Experimental models: Organisms/strains Mouse: C57BL/6J The Jackson Laboratory Cat#000664 Mouse: Tg(Drd1-cre)FK150Gsat GENSAT MGI:3836633 Mouse: Tg(Drd2-cre)ER44Gsat GENSAT MGI:3836635 Mouse: Tg(Drd1-tdTomato)5Calak Shuen et al., 200869 MGI:4360387 Mouse: Rosa26fsTRAP The Jackson Laboratory IMSR_JAX:022367 Rat: SAS Sprague Dawley Charles River Cat#400 Viruses HSV-GFP Gene Delivery Core, MGH N/A HSV-RXRa-GFP Gene Delivery Core, MGH N/A AAV9-CAG-DIO-EGFP Viral Vector Core, Duke BK277 AAV9-CAG-DIO-EGFP-P2A-RXRa Viral Vector Core, Duke BK1432 AAV9-CMV-EYFP-miR-lacZ Viral Vector Core, Duke BK1202 AAV9-CMV-EYFP-miR-RXRa Viral Vector Core, Duke BK1149 AAV9-CMV-EGFP Wilson lab Addgene #105530 AAV9-CMV-EGFP-P2A-RXRa Viral Vector Core, Duke BK1418 AAV9-hSyn-DIO-hM3D(Gq)-mCherry Krashes et al., 2011 Addgene #44361 AAV9-hSyn-DIO-mCherry Roth lab Addgene #50459 Software and algorithms FastQC v0.11.9 Babraham Institute RRID:SCR_014583 Trimmomatic v0.27 Usadel lab RRID:SCR_011848 hisat2 v2.1.0 Kim lab RRID:SCR_015530 Picard v2.18.10 Broad Institute RRID:SCR_006525 subread v2.0.0 N/A RRID:SCR_009803 DESeq2 v1.34.0 Love et al.70 RRID:SCR_015687 (Continued on next page) e1 Neuron 111, 1453–1467.e1–e7, May 3, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER RRHO2 Cahill et al., 201871 github.com/RRHO2/RRHO2 PANTHER Mi et al, 201972 pantherdb.org ComDet v0.5.4 N/A github.com/ekatrukha/ComDet Axon pCLAMP 11 Software Suite Molecular Devices RRID:SCR_011323 R v4.0.2 R foundation RRID:SCR_001905 Image J v1.53c NIH RRID:SCR_003070 Deposited data Raw snRNAseq data N/A GEO: GSE198527
Fluorescence In Situ Hybridization:Article Title: Transcriptional control of nucleus accumbens neuronal excitability by retinoid X receptor alpha tunes sensitivity to drug rewards.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies See Table S4 N/A N/A Anti-mouse peroxidase-conjugated secondary antibody Vector Laboratories Cat#PI-2000 Anti-rabbit peroxidase-conjugated secondary antibody Vector Laboratories Cat#PI-1000 Oligonucleotides See Table S5 for qPCR primers N/A N/A See method details for miRNA sequences N/A N/A FISH probe: Mm-Rxra ACD Bio Cat#63121 FISH probe: Mm-Drd1a-C2 ACD Bio Cat#406491-C2 FISH probe: Mm-Drd2-C3 ACD Bio Cat#406501-C3 Chemicals Cocaine HCl NIDA N/A Morphine SO4 NIDA N/A HX531 Tocris Cat#3912 PBS Thermo Fisher Scientific 14-190-144 DMSO Sigma D4540 CNO dihydrochloride Tocris Cat#6329 Experimental models: Organisms/strains Mouse: C57BL/6J The Jackson Laboratory Cat#000664 Mouse: Tg(Drd1-cre)FK150Gsat GENSAT MGI:3836633 Mouse: Tg(Drd2-cre)ER44Gsat GENSAT MGI:3836635 Mouse: Tg(Drd1-tdTomato)5Calak Shuen et al., 200869 MGI:4360387 Mouse: Rosa26fsTRAP The Jackson Laboratory IMSR_JAX:022367 Rat: SAS Sprague Dawley Charles River Cat#400 Viruses HSV-GFP Gene Delivery Core, MGH N/A HSV-RXRa-GFP Gene Delivery Core, MGH N/A AAV9-CAG-DIO-EGFP Viral Vector Core, Duke BK277 AAV9-CAG-DIO-EGFP-P2A-RXRa Viral Vector Core, Duke BK1432 AAV9-CMV-EYFP-miR-lacZ Viral Vector Core, Duke BK1202 AAV9-CMV-EYFP-miR-RXRa Viral Vector Core, Duke BK1149 AAV9-CMV-EGFP Wilson lab Addgene #105530 AAV9-CMV-EGFP-P2A-RXRa Viral Vector Core, Duke BK1418 AAV9-hSyn-DIO-hM3D(Gq)-mCherry Krashes et al., 2011 Addgene #44361 AAV9-hSyn-DIO-mCherry Roth lab Addgene #50459 Software and algorithms FastQC v0.11.9 Babraham Institute RRID:SCR_014583 Trimmomatic v0.27 Usadel lab RRID:SCR_011848 hisat2 v2.1.0 Kim lab RRID:SCR_015530 Picard v2.18.10 Broad Institute RRID:SCR_006525 subread v2.0.0 N/A RRID:SCR_009803 DESeq2 v1.34.0 Love et al.70 RRID:SCR_015687 (Continued on next page) e1 Neuron 111, 1453–1467.e1–e7, May 3, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER RRHO2 Cahill et al., 201871 github.com/RRHO2/RRHO2 PANTHER Mi et al, 201972 pantherdb.org ComDet v0.5.4 N/A github.com/ekatrukha/ComDet Axon pCLAMP 11 Software Suite Molecular Devices RRID:SCR_011323 R v4.0.2 R foundation RRID:SCR_001905 Image J v1.53c NIH RRID:SCR_003070 Deposited data Raw snRNAseq data N/A GEO: GSE198527
Software:Article Title: Transcriptional control of nucleus accumbens neuronal excitability by retinoid X receptor alpha tunes sensitivity to drug rewards.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies See Table S4 N/A N/A Anti-mouse peroxidase-conjugated secondary antibody Vector Laboratories Cat#PI-2000 Anti-rabbit peroxidase-conjugated secondary antibody Vector Laboratories Cat#PI-1000 Oligonucleotides See Table S5 for qPCR primers N/A N/A See method details for miRNA sequences N/A N/A FISH probe: Mm-Rxra ACD Bio Cat#63121 FISH probe: Mm-Drd1a-C2 ACD Bio Cat#406491-C2 FISH probe: Mm-Drd2-C3 ACD Bio Cat#406501-C3 Chemicals Cocaine HCl NIDA N/A Morphine SO4 NIDA N/A HX531 Tocris Cat#3912 PBS Thermo Fisher Scientific 14-190-144 DMSO Sigma D4540 CNO dihydrochloride Tocris Cat#6329 Experimental models: Organisms/strains Mouse: C57BL/6J The Jackson Laboratory Cat#000664 Mouse: Tg(Drd1-cre)FK150Gsat GENSAT MGI:3836633 Mouse: Tg(Drd2-cre)ER44Gsat GENSAT MGI:3836635 Mouse: Tg(Drd1-tdTomato)5Calak Shuen et al., 200869 MGI:4360387 Mouse: Rosa26fsTRAP The Jackson Laboratory IMSR_JAX:022367 Rat: SAS Sprague Dawley Charles River Cat#400 Viruses HSV-GFP Gene Delivery Core, MGH N/A HSV-RXRa-GFP Gene Delivery Core, MGH N/A AAV9-CAG-DIO-EGFP Viral Vector Core, Duke BK277 AAV9-CAG-DIO-EGFP-P2A-RXRa Viral Vector Core, Duke BK1432 AAV9-CMV-EYFP-miR-lacZ Viral Vector Core, Duke BK1202 AAV9-CMV-EYFP-miR-RXRa Viral Vector Core, Duke BK1149 AAV9-CMV-EGFP Wilson lab Addgene #105530 AAV9-CMV-EGFP-P2A-RXRa Viral Vector Core, Duke BK1418 AAV9-hSyn-DIO-hM3D(Gq)-mCherry Krashes et al., 2011 Addgene #44361 AAV9-hSyn-DIO-mCherry Roth lab Addgene #50459 Software and algorithms FastQC v0.11.9 Babraham Institute RRID:SCR_014583 Trimmomatic v0.27 Usadel lab RRID:SCR_011848 hisat2 v2.1.0 Kim lab RRID:SCR_015530 Picard v2.18.10 Broad Institute RRID:SCR_006525 subread v2.0.0 N/A RRID:SCR_009803 DESeq2 v1.34.0 Love et al.70 RRID:SCR_015687 (Continued on next page) e1 Neuron 111, 1453–1467.e1–e7, May 3, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER RRHO2 Cahill et al., 201871 github.com/RRHO2/RRHO2 PANTHER Mi et al, 201972 pantherdb.org ComDet v0.5.4 N/A github.com/ekatrukha/ComDet Axon pCLAMP 11 Software Suite Molecular Devices RRID:SCR_011323 R v4.0.2 R foundation RRID:SCR_001905 Image J v1.53c NIH RRID:SCR_003070 Deposited data Raw snRNAseq data N/A GEO: GSE198527
Article Title: Mitochondrial membrane tension governs fission.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, peptides, and recombinant proteins Blebbistatin Sigma-Aldrich B0560 Nocodazole Sigma-Aldrich M1404 ML-7 hydrochlorine Santa Cruz Biotechnology 110448-33-4 Mito-FliptR Spirochrome SC023 TMRE ThermoFisher Scientific T669 MitoTracker Red CMXRos ThermoFisher Scientific M7512 FBS HyClone SV30160.03 Opti-MEM ThermoFisher Scientific 31985062 Lipofectamine 2000 ThermoFisher Scientific 11668030 DMEM ThermoFisher Scientific 31966021 Leibovitz medium ThermoFisher Scientific 21083027 PBS ThermoFisher Scientific 70013016 Glucose oxidase Sigma-Aldrich G7141 Catalase Sigma-Aldrich C1345 HEPES ThermoFisher Scientific 15630 Experimental models: Cell lines Cos 7 cell line HPA culture collections COS7-ECACC-87021302 Recombinant DNA Mito-GFP (Cox8 presequence) Gift from Hari Shroff N/A mCherry-Drp1 Friedman et al., 2011 Addgene #49152 MitoBFP Friedman et al., 2011 Addgene #49151 Dyn2-GFP Gift from Gia Voeltz N/A KDEL-RFP (adapted from KDEL-BFP) Friedman et al., 2011 Addgene #49150 Software and algorithms MATLAB MathWorks 2016b Fiji (ImageJ) (Schindelin et al., 2012), NIH https://imagej.net/Fiji Trainable Weka Segmentation Arganda-Carreras et al., 2017 3.2.33 Structured illumination microscopy simulator Alharbi, 2013 Alharbi, 2013 MitoWorks This study https://github.com/LEB-EPFL/MitoWorks ..
Article Title: VMHvll Cckar cells dynamically control female sexual behaviors over the reproductive cycle.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Guinea pig anti-Fos Synaptic Systems Cat# 226005; RRID: AB_2800522 Goat anti-Fos Santa Cruz Biotechnology Cat# sc-52-G; RRID: AB_2629503 Rabbit anti-Esr1 Millipore Cat# 06-935; RRID: AB_310305 Goat anti-Guinea pig Cyanine Cy 3 Jackson ImmunoResearch Cat# 706-165-148; RRID: AB_2340460 Donkey anti-Goat Alexa Fluor 488 Jackson ImmunoResearch Cat# 705-545-147; RRID: AB_2336933 Goat anti-Rabbit Cyanine Cy 5 Jackson ImmunoResearch Cat# 711-175-152; RRID: AB_2340607 Bacterial and virus strains AAV1-hSyn-DIO-hM4Di-mCherry Addgene; Krashes et al., 2011 Addgene# 44362-AAV1 AAV2-hSyn-DIO-hM3Dq-mCherry Addgene; Krashes et al., 2011 Addgene# 44361-AAV2 AAV2-hSyn-DIO-mCherry Addgene; Bryan Roth lab (unpublished) Addgene# 50459-AAV2 AAV1-hSyn1-SIO-stGtACR2-FusionRed Addgene; Mahn et al., 2018 Addgene# 105677-AAV1 AAV2-EF1a-DIO-ChR2-EYFP UNC Vector Core; Karl Deisseroth lab (unpublished) Cat# AV-2-AV4378p AAV2-CAG-Flex-GFP UNC Vector Core; Oh et al., 2014 Cat# AV-2-ALL854 AAV1-hSyn-Flex-GCaMP6s-WPRE.SV40 Addgene; Chen et al., 2013 Addgene# 100843-AAV1 Chemicals, peptides, and recombinant proteins Normal donkey serum Jackson ImmunoResearch Cat# 017-000-121; RRID: AB_2337258 Red Retrobeads Lumafluor, Inc N/A CNO Sigma Cat# 34233-69-7 Critical commercial assays Nanoliter injector World Precision Instruments Cat# Nanoliter 2000 Temperature Logger Star-Oddi DST nano-T Experimental models: Organisms/strains CckarCre knock-in mice This paper N/A C57BL/6 mice Charles River Strain Code 027 Esr1ZsGreen Yong Yu lab, Saito et al., 2016 N/A Ai9 mice Jackson Laboratory Strain# 007909 Ai6 mice Jackson Laboratory Strain# 007906 Software and algorithms MATLAB R2019b MathWorks https://www.mathworks.com/products/matlab.html; RRID: SCR_001622 Prism 9 GraphPad Software https://www.graphpad.com/scientific-software/prism/; RRID: SCR_002798 StreamPix 8 NorPix https://www.norpix.com/products/streampix/ streampix.php; RRID: SCR_015773 ImageJ NIH https://imagej.nih.gov/ij/index.html; RRID: SCR_003070 pCLAMP 11 Molecular Devices https://www.moleculardevices.com/; RRID: SCR_011323 Adobe Photoshop 2020 Adobe https://www.adobe.com/; RRID: SCR_014199 Adobe Illustrator 2020 Adobe https://www.adobe.com/; RRID: SCR_010279 Body tracking code David Anderson lab, Lin et al., 2011 https://github.com/pdollar/toolbox e1 Neuron 110, 3000–3017.e1–e8, September 21, 2022 ..
Article Title: Dynamin is primed at endocytic sites for ultrafast endocytosis.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER NaCl Sigma-Aldrich Cat# S7653 polyethylenimine Polysciences Cat# 23966-2 cOMPLETE protease inhibitor cocktail tablet Roche Cat# 11836153001 HEPES Merck Cat# 1.10110.0250 KCl Sigma-Aldrich Cat# P9333 Glucose Sigma-Aldrich Cat# 49159 MgCl2 Fluka Cat# 63020 NBQX Tocris Cat# 1044 Bicuculline Tocris Cat# 0130 Cationized ferritin Sigma-Aldrich Cat# F7879 Glutaraldehyde in anhydrous acetone EMS Cat# 16530 Osmium tetroxide EMS Cat# RT19132 Uranyl acetate EMS Cat# 22400 Acetone EMS Cat# RT10016 InFusion HD Cloning Kit Thermal Scientific Cat# 63649 Digitonin Sigma-Aldrich Cat# D141 1,6-Hexanediol Sigma-Aldrich Cat# 240117 2,5-Hexanediol Sigma-Aldrich Cat# H11904 1,4-Butanediol Sigma-Aldrich Cat# 493732 FK506 Tocris Cat# 3631 CHIR99021 Sigma-Aldrich Cat# SML 1046 ProLong Diamond Antifade Mountant Thermo Fisher Cat# P36971 Gold Seal Microscope Slides, 3’’31’’, 1mm thick Thermo Fisher Cat# 3010 JFX549 Luke Davis’s lab (Janelia Research Campus); (Grimm et al., 2016) N/A PA-JF646 Luke Davis’s lab (Janelia Research Campus) (Grimm et al., 2016) N/A Experimental models: Organisms/strains Dynamin-1, -3 DKO De Camilli’s Lab (Raimondi et al., 2011) N/A Dynamin-3 KO De Camilli’s Lab (Raimondi et al., 2011) N/A Recombinant DNA f(syn)NLS-RFP-P2A-hsDyn1xA This paper N/A f(syn)NLS-RFP-P2A-hsDyn1xA S774/778A This paper N/A f(syn)NLS-RFP-P2A-hsDyn1xA S774/778D This paper N/A f(syn)NLS-RFP-P2A-hsDyn1xB This paper N/A f(syn)NLS-RFP-P2A-hsDyn1xB S774/778A This paper N/A f(syn)NLS-RFP-P2A-hsDyn2 This paper N/A hDyn1-S774A-S778A in pcDNA3 Armbruster et al., 2013 N/A hDyn1-S774D-S778D in pcDNA3 Armbruster et al., 2013 N/A HA-hDyn2 in pcDNA3 Ferguson et al., 2007 N/A phsDyn1xA-EGFP-N1 Kong et al., 2018 Addgene #120313 phsDyn1xA S774/778A- EGFP-N1 This paper N/A phsDyn1xA S774/778D- EGFP-N1 This paper N/A phsDyn1xA I481D/H687D/L688S- EGFP-N1 This paper N/A (Continued on next page) Neuron 110, 2815–2835.e1–e13, September 7, 2022 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER phsDyn1xA-Halo This paper N/A pmCherry-Syb2 This paper N/A phsDyn1xA- EGFP-N1_P2A_mCherr-rtSyb2 This paper N/A phsDyn1xB- EGFP-N1 This paper N/A pDyn2-mCherry-N1 Taylor et al., 2011 Addgene #27689 pVAMP2(Syb2)-SNAP Martineau et al., 2017 Addgene #105288 pCAGGS-tdTomato This paper N/A pCMV-tdTomato Clontech Cat# 632534 pORANGE Willems et al., 2020 Addgene #131471 pORANGE-msDyn1xA-GFP This paper N/A pFUGW-mCherry This paper N/A pFUGW-mCherry_ORANGE_msDyn1xA-GFP This paper N/A pEGFP-N1 Clontech Cat# 6085-1 pmCherry-N1 Clontech Cat# 632523 pFUGW-spCas9 Willems et al., 2020 Addgene #131506 f(U6)scramble shRNA.hSyn-NLS-RFP-WPRE Watanabe et al., 2014 N/A f(U6)Syndapin 1-shRNA.hSyn-NLS-RFP-WPRE This paper N/A f(syn)NLS-RFP-P2A-Syndapin 1 This paper N/A f(syn)NLS-RFP-P2A-Syndapin 1 shRNA resistant This paper N/A f(syn)NLS-RFP-P2A-Syndapin 1 I122D/M123E shRNA resistant This paper N/A f(syn)NLS-RFP-P2A-Syndapin 1 P434L shRNA resistant This paper N/A pmCherry-N1_Syndapin 1 shRNA resistant This paper N/A pmCherry-N1_Syndapin 1 I122D/M123E shRNA resistant This paper N/A pmCherry-N1-Syndapin 1 P434L shRNA resistant This paper N/A pGex6T-Dyn1xA/Dyn1xA-S774/778D This paper N/A pGex6T-Syndapin1 This paper N/A pGex6T-Syndapin1 P434L This paper N/A pDyn1xA-PRM Anggono et al., 2006 N/A pDyn1xA-PRM S774/778A Anggono et al., 2006 N/A pDyn1xA-PRM S774/778E Anggono et al., 2006 N/A Software and algorithms SynapsEM Watanabe et al., 2020 https://github.com/shigekiwatanabe/ SynapsEM ImaegJ-Fiji Schindelin et al., 2012 https://imagej.net/Fiji Adobe Illustrator 2021 Adobe https://www.adobe.com/ Adobe Photoshop 2021 Adobe https://www.adobe.com/ Prism GraphPad (Prism 8) https://www.graphpad.com Excel Microsoft https://products.office.com/en-us/ explore-office-for-home MATLAB MathWorks https://www.mathworks.com/products/ matlab.html Microscopy Hitachi 7600 TEM Hitachi N/A LSM880 Carl Zeiss N/A (Continued on next page) e3 Neuron 110, 2815–2835.e1–e13, September 7, 2022 .. REAGENT or RESOURCE SOURCE IDENTIFIER Nikon Eclipse Ti2 Nikon N/A ORCA-Fusion BT Digital CMOS camera Hamamatsu N/A Ti:Sapphire laser head Mai Tai HP, Spectra-Physics N/A photonic crystal fiber Newport N/A acoustic optical tunable filter AA Opto-Electronic N/A 100-m long polarization-maintaining single-mode fiber OZ optics N/A vortex phase plate VPP-1, RPC photonics N/A avalanche photodiodes SPCM-AQR-14-FC Perkin Elmer N/A piezo-controlled stage Max311D Thorlabs N/A 405nm/250 mW laser RPMC Lasers Inc. N/A 488nm/300 mW laser MPB Communications N/A 560nm/500 mW laser MPB Communications N/A 642nm/500 mW laser MPB Communications N/A acoustic optical tunable filter AA Opto-Electronic N/A galvo mirrors Cambridge Technology 6215H CFI Apo LWD 25XW, 1.1 NA, 2 mm WD Nikon N/A Orca Flash 4.0 v3 Hamamatsu N/A Other Sapphire Disks, 6-nm Technotrade Cat# 616-100 AFS2 Leica microsystem N/A EM ICE Leica microsystem N/A
Microscopy:Article Title: Mitochondrial membrane tension governs fission.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, peptides, and recombinant proteins Blebbistatin Sigma-Aldrich B0560 Nocodazole Sigma-Aldrich M1404 ML-7 hydrochlorine Santa Cruz Biotechnology 110448-33-4 Mito-FliptR Spirochrome SC023 TMRE ThermoFisher Scientific T669 MitoTracker Red CMXRos ThermoFisher Scientific M7512 FBS HyClone SV30160.03 Opti-MEM ThermoFisher Scientific 31985062 Lipofectamine 2000 ThermoFisher Scientific 11668030 DMEM ThermoFisher Scientific 31966021 Leibovitz medium ThermoFisher Scientific 21083027 PBS ThermoFisher Scientific 70013016 Glucose oxidase Sigma-Aldrich G7141 Catalase Sigma-Aldrich C1345 HEPES ThermoFisher Scientific 15630 Experimental models: Cell lines Cos 7 cell line HPA culture collections COS7-ECACC-87021302 Recombinant DNA Mito-GFP (Cox8 presequence) Gift from Hari Shroff N/A mCherry-Drp1 Friedman et al., 2011 Addgene #49152 MitoBFP Friedman et al., 2011 Addgene #49151 Dyn2-GFP Gift from Gia Voeltz N/A KDEL-RFP (adapted from KDEL-BFP) Friedman et al., 2011 Addgene #49150 Software and algorithms MATLAB MathWorks 2016b Fiji (ImageJ) (Schindelin et al., 2012), NIH https://imagej.net/Fiji Trainable Weka Segmentation Arganda-Carreras et al., 2017 3.2.33 Structured illumination microscopy simulator Alharbi, 2013 Alharbi, 2013 MitoWorks This study https://github.com/LEB-EPFL/MitoWorks ..
Article Title: Dynamin is primed at endocytic sites for ultrafast endocytosis.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER NaCl Sigma-Aldrich Cat# S7653 polyethylenimine Polysciences Cat# 23966-2 cOMPLETE protease inhibitor cocktail tablet Roche Cat# 11836153001 HEPES Merck Cat# 1.10110.0250 KCl Sigma-Aldrich Cat# P9333 Glucose Sigma-Aldrich Cat# 49159 MgCl2 Fluka Cat# 63020 NBQX Tocris Cat# 1044 Bicuculline Tocris Cat# 0130 Cationized ferritin Sigma-Aldrich Cat# F7879 Glutaraldehyde in anhydrous acetone EMS Cat# 16530 Osmium tetroxide EMS Cat# RT19132 Uranyl acetate EMS Cat# 22400 Acetone EMS Cat# RT10016 InFusion HD Cloning Kit Thermal Scientific Cat# 63649 Digitonin Sigma-Aldrich Cat# D141 1,6-Hexanediol Sigma-Aldrich Cat# 240117 2,5-Hexanediol Sigma-Aldrich Cat# H11904 1,4-Butanediol Sigma-Aldrich Cat# 493732 FK506 Tocris Cat# 3631 CHIR99021 Sigma-Aldrich Cat# SML 1046 ProLong Diamond Antifade Mountant Thermo Fisher Cat# P36971 Gold Seal Microscope Slides, 3’’31’’, 1mm thick Thermo Fisher Cat# 3010 JFX549 Luke Davis’s lab (Janelia Research Campus); (Grimm et al., 2016) N/A PA-JF646 Luke Davis’s lab (Janelia Research Campus) (Grimm et al., 2016) N/A Experimental models: Organisms/strains Dynamin-1, -3 DKO De Camilli’s Lab (Raimondi et al., 2011) N/A Dynamin-3 KO De Camilli’s Lab (Raimondi et al., 2011) N/A Recombinant DNA f(syn)NLS-RFP-P2A-hsDyn1xA This paper N/A f(syn)NLS-RFP-P2A-hsDyn1xA S774/778A This paper N/A f(syn)NLS-RFP-P2A-hsDyn1xA S774/778D This paper N/A f(syn)NLS-RFP-P2A-hsDyn1xB This paper N/A f(syn)NLS-RFP-P2A-hsDyn1xB S774/778A This paper N/A f(syn)NLS-RFP-P2A-hsDyn2 This paper N/A hDyn1-S774A-S778A in pcDNA3 Armbruster et al., 2013 N/A hDyn1-S774D-S778D in pcDNA3 Armbruster et al., 2013 N/A HA-hDyn2 in pcDNA3 Ferguson et al., 2007 N/A phsDyn1xA-EGFP-N1 Kong et al., 2018 Addgene #120313 phsDyn1xA S774/778A- EGFP-N1 This paper N/A phsDyn1xA S774/778D- EGFP-N1 This paper N/A phsDyn1xA I481D/H687D/L688S- EGFP-N1 This paper N/A (Continued on next page) Neuron 110, 2815–2835.e1–e13, September 7, 2022 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER phsDyn1xA-Halo This paper N/A pmCherry-Syb2 This paper N/A phsDyn1xA- EGFP-N1_P2A_mCherr-rtSyb2 This paper N/A phsDyn1xB- EGFP-N1 This paper N/A pDyn2-mCherry-N1 Taylor et al., 2011 Addgene #27689 pVAMP2(Syb2)-SNAP Martineau et al., 2017 Addgene #105288 pCAGGS-tdTomato This paper N/A pCMV-tdTomato Clontech Cat# 632534 pORANGE Willems et al., 2020 Addgene #131471 pORANGE-msDyn1xA-GFP This paper N/A pFUGW-mCherry This paper N/A pFUGW-mCherry_ORANGE_msDyn1xA-GFP This paper N/A pEGFP-N1 Clontech Cat# 6085-1 pmCherry-N1 Clontech Cat# 632523 pFUGW-spCas9 Willems et al., 2020 Addgene #131506 f(U6)scramble shRNA.hSyn-NLS-RFP-WPRE Watanabe et al., 2014 N/A f(U6)Syndapin 1-shRNA.hSyn-NLS-RFP-WPRE This paper N/A f(syn)NLS-RFP-P2A-Syndapin 1 This paper N/A f(syn)NLS-RFP-P2A-Syndapin 1 shRNA resistant This paper N/A f(syn)NLS-RFP-P2A-Syndapin 1 I122D/M123E shRNA resistant This paper N/A f(syn)NLS-RFP-P2A-Syndapin 1 P434L shRNA resistant This paper N/A pmCherry-N1_Syndapin 1 shRNA resistant This paper N/A pmCherry-N1_Syndapin 1 I122D/M123E shRNA resistant This paper N/A pmCherry-N1-Syndapin 1 P434L shRNA resistant This paper N/A pGex6T-Dyn1xA/Dyn1xA-S774/778D This paper N/A pGex6T-Syndapin1 This paper N/A pGex6T-Syndapin1 P434L This paper N/A pDyn1xA-PRM Anggono et al., 2006 N/A pDyn1xA-PRM S774/778A Anggono et al., 2006 N/A pDyn1xA-PRM S774/778E Anggono et al., 2006 N/A Software and algorithms SynapsEM Watanabe et al., 2020 https://github.com/shigekiwatanabe/ SynapsEM ImaegJ-Fiji Schindelin et al., 2012 https://imagej.net/Fiji Adobe Illustrator 2021 Adobe https://www.adobe.com/ Adobe Photoshop 2021 Adobe https://www.adobe.com/ Prism GraphPad (Prism 8) https://www.graphpad.com Excel Microsoft https://products.office.com/en-us/ explore-office-for-home MATLAB MathWorks https://www.mathworks.com/products/ matlab.html Microscopy Hitachi 7600 TEM Hitachi N/A LSM880 Carl Zeiss N/A (Continued on next page) e3 Neuron 110, 2815–2835.e1–e13, September 7, 2022 .. REAGENT or RESOURCE SOURCE IDENTIFIER Nikon Eclipse Ti2 Nikon N/A ORCA-Fusion BT Digital CMOS camera Hamamatsu N/A Ti:Sapphire laser head Mai Tai HP, Spectra-Physics N/A photonic crystal fiber Newport N/A acoustic optical tunable filter AA Opto-Electronic N/A 100-m long polarization-maintaining single-mode fiber OZ optics N/A vortex phase plate VPP-1, RPC photonics N/A avalanche photodiodes SPCM-AQR-14-FC Perkin Elmer N/A piezo-controlled stage Max311D Thorlabs N/A 405nm/250 mW laser RPMC Lasers Inc. N/A 488nm/300 mW laser MPB Communications N/A 560nm/500 mW laser MPB Communications N/A 642nm/500 mW laser MPB Communications N/A acoustic optical tunable filter AA Opto-Electronic N/A galvo mirrors Cambridge Technology 6215H CFI Apo LWD 25XW, 1.1 NA, 2 mm WD Nikon N/A Orca Flash 4.0 v3 Hamamatsu N/A Other Sapphire Disks, 6-nm Technotrade Cat# 616-100 AFS2 Leica microsystem N/A EM ICE Leica microsystem N/A
Expressing:Article Title: Structural and functional analysis of the Mycobacterium tuberculosis MmpS5L5 efflux pump presages increased bedaquiline resistance
Article Snippet: .. pMEXC3GF ATc-inducible episomal expression construct with C-terminal GFP-FLAG tag This study pMEXC3GF Mtb MmpS5L5(∆CC) ATc-inducible episomal expression construct encoding MmpS5 and MmpL5 ∆CC (∆494–687) This study pET-His6-TEV-MmpL5(492–683) E. coli expression construct of E. coli codon-optimised MmpL5 coiled-coil domain This study pINIT-Cat FX cloning entry vector Geertsma and Dutzler, 2011 Addgene #46858 pMA-Int E. coli replicative vector which contains the mycophage L5 integrase gene required for attP/attB integration. .. Arnold et al. 2018 Addgene #110096 pINIT-Cat Mtb MmpS5L5 FX cloning entry vector containing SapIdomesticated Mtb MmpS5L5 operon This study pINIT-Cat Mtb MmpS4L4 FX cloning entry vector containing SapIdomesticated Mtb MmpS4L4 operon This study pFLAG-attP-Kan Single copy integrative vector, with L5 attP, but lacking L5 int.
Construct:Article Title: Structural and functional analysis of the Mycobacterium tuberculosis MmpS5L5 efflux pump presages increased bedaquiline resistance
Article Snippet: .. pMEXC3GF ATc-inducible episomal expression construct with C-terminal GFP-FLAG tag This study pMEXC3GF Mtb MmpS5L5(∆CC) ATc-inducible episomal expression construct encoding MmpS5 and MmpL5 ∆CC (∆494–687) This study pET-His6-TEV-MmpL5(492–683) E. coli expression construct of E. coli codon-optimised MmpL5 coiled-coil domain This study pINIT-Cat FX cloning entry vector Geertsma and Dutzler, 2011 Addgene #46858 pMA-Int E. coli replicative vector which contains the mycophage L5 integrase gene required for attP/attB integration. .. Arnold et al. 2018 Addgene #110096 pINIT-Cat Mtb MmpS5L5 FX cloning entry vector containing SapIdomesticated Mtb MmpS5L5 operon This study pINIT-Cat Mtb MmpS4L4 FX cloning entry vector containing SapIdomesticated Mtb MmpS4L4 operon This study pFLAG-attP-Kan Single copy integrative vector, with L5 attP, but lacking L5 int.
Cloning:Article Title: Structural and functional analysis of the Mycobacterium tuberculosis MmpS5L5 efflux pump presages increased bedaquiline resistance
Article Snippet: .. pMEXC3GF ATc-inducible episomal expression construct with C-terminal GFP-FLAG tag This study pMEXC3GF Mtb MmpS5L5(∆CC) ATc-inducible episomal expression construct encoding MmpS5 and MmpL5 ∆CC (∆494–687) This study pET-His6-TEV-MmpL5(492–683) E. coli expression construct of E. coli codon-optimised MmpL5 coiled-coil domain This study pINIT-Cat FX cloning entry vector Geertsma and Dutzler, 2011 Addgene #46858 pMA-Int E. coli replicative vector which contains the mycophage L5 integrase gene required for attP/attB integration. .. Arnold et al. 2018 Addgene #110096 pINIT-Cat Mtb MmpS5L5 FX cloning entry vector containing SapIdomesticated Mtb MmpS5L5 operon This study pINIT-Cat Mtb MmpS4L4 FX cloning entry vector containing SapIdomesticated Mtb MmpS4L4 operon This study pFLAG-attP-Kan Single copy integrative vector, with L5 attP, but lacking L5 int.
Virus:Article Title: VMHvll Cckar cells dynamically control female sexual behaviors over the reproductive cycle.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Guinea pig anti-Fos Synaptic Systems Cat# 226005; RRID: AB_2800522 Goat anti-Fos Santa Cruz Biotechnology Cat# sc-52-G; RRID: AB_2629503 Rabbit anti-Esr1 Millipore Cat# 06-935; RRID: AB_310305 Goat anti-Guinea pig Cyanine Cy 3 Jackson ImmunoResearch Cat# 706-165-148; RRID: AB_2340460 Donkey anti-Goat Alexa Fluor 488 Jackson ImmunoResearch Cat# 705-545-147; RRID: AB_2336933 Goat anti-Rabbit Cyanine Cy 5 Jackson ImmunoResearch Cat# 711-175-152; RRID: AB_2340607 Bacterial and virus strains AAV1-hSyn-DIO-hM4Di-mCherry Addgene; Krashes et al., 2011 Addgene# 44362-AAV1 AAV2-hSyn-DIO-hM3Dq-mCherry Addgene; Krashes et al., 2011 Addgene# 44361-AAV2 AAV2-hSyn-DIO-mCherry Addgene; Bryan Roth lab (unpublished) Addgene# 50459-AAV2 AAV1-hSyn1-SIO-stGtACR2-FusionRed Addgene; Mahn et al., 2018 Addgene# 105677-AAV1 AAV2-EF1a-DIO-ChR2-EYFP UNC Vector Core; Karl Deisseroth lab (unpublished) Cat# AV-2-AV4378p AAV2-CAG-Flex-GFP UNC Vector Core; Oh et al., 2014 Cat# AV-2-ALL854 AAV1-hSyn-Flex-GCaMP6s-WPRE.SV40 Addgene; Chen et al., 2013 Addgene# 100843-AAV1 Chemicals, peptides, and recombinant proteins Normal donkey serum Jackson ImmunoResearch Cat# 017-000-121; RRID: AB_2337258 Red Retrobeads Lumafluor, Inc N/A CNO Sigma Cat# 34233-69-7 Critical commercial assays Nanoliter injector World Precision Instruments Cat# Nanoliter 2000 Temperature Logger Star-Oddi DST nano-T Experimental models: Organisms/strains CckarCre knock-in mice This paper N/A C57BL/6 mice Charles River Strain Code 027 Esr1ZsGreen Yong Yu lab, Saito et al., 2016 N/A Ai9 mice Jackson Laboratory Strain# 007909 Ai6 mice Jackson Laboratory Strain# 007906 Software and algorithms MATLAB R2019b MathWorks https://www.mathworks.com/products/matlab.html; RRID: SCR_001622 Prism 9 GraphPad Software https://www.graphpad.com/scientific-software/prism/; RRID: SCR_002798 StreamPix 8 NorPix https://www.norpix.com/products/streampix/ streampix.php; RRID: SCR_015773 ImageJ NIH https://imagej.nih.gov/ij/index.html; RRID: SCR_003070 pCLAMP 11 Molecular Devices https://www.moleculardevices.com/; RRID: SCR_011323 Adobe Photoshop 2020 Adobe https://www.adobe.com/; RRID: SCR_014199 Adobe Illustrator 2020 Adobe https://www.adobe.com/; RRID: SCR_010279 Body tracking code David Anderson lab, Lin et al., 2011 https://github.com/pdollar/toolbox e1 Neuron 110, 3000–3017.e1–e8, September 21, 2022 ..
Knock-In:Article Title: VMHvll Cckar cells dynamically control female sexual behaviors over the reproductive cycle.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Guinea pig anti-Fos Synaptic Systems Cat# 226005; RRID: AB_2800522 Goat anti-Fos Santa Cruz Biotechnology Cat# sc-52-G; RRID: AB_2629503 Rabbit anti-Esr1 Millipore Cat# 06-935; RRID: AB_310305 Goat anti-Guinea pig Cyanine Cy 3 Jackson ImmunoResearch Cat# 706-165-148; RRID: AB_2340460 Donkey anti-Goat Alexa Fluor 488 Jackson ImmunoResearch Cat# 705-545-147; RRID: AB_2336933 Goat anti-Rabbit Cyanine Cy 5 Jackson ImmunoResearch Cat# 711-175-152; RRID: AB_2340607 Bacterial and virus strains AAV1-hSyn-DIO-hM4Di-mCherry Addgene; Krashes et al., 2011 Addgene# 44362-AAV1 AAV2-hSyn-DIO-hM3Dq-mCherry Addgene; Krashes et al., 2011 Addgene# 44361-AAV2 AAV2-hSyn-DIO-mCherry Addgene; Bryan Roth lab (unpublished) Addgene# 50459-AAV2 AAV1-hSyn1-SIO-stGtACR2-FusionRed Addgene; Mahn et al., 2018 Addgene# 105677-AAV1 AAV2-EF1a-DIO-ChR2-EYFP UNC Vector Core; Karl Deisseroth lab (unpublished) Cat# AV-2-AV4378p AAV2-CAG-Flex-GFP UNC Vector Core; Oh et al., 2014 Cat# AV-2-ALL854 AAV1-hSyn-Flex-GCaMP6s-WPRE.SV40 Addgene; Chen et al., 2013 Addgene# 100843-AAV1 Chemicals, peptides, and recombinant proteins Normal donkey serum Jackson ImmunoResearch Cat# 017-000-121; RRID: AB_2337258 Red Retrobeads Lumafluor, Inc N/A CNO Sigma Cat# 34233-69-7 Critical commercial assays Nanoliter injector World Precision Instruments Cat# Nanoliter 2000 Temperature Logger Star-Oddi DST nano-T Experimental models: Organisms/strains CckarCre knock-in mice This paper N/A C57BL/6 mice Charles River Strain Code 027 Esr1ZsGreen Yong Yu lab, Saito et al., 2016 N/A Ai9 mice Jackson Laboratory Strain# 007909 Ai6 mice Jackson Laboratory Strain# 007906 Software and algorithms MATLAB R2019b MathWorks https://www.mathworks.com/products/matlab.html; RRID: SCR_001622 Prism 9 GraphPad Software https://www.graphpad.com/scientific-software/prism/; RRID: SCR_002798 StreamPix 8 NorPix https://www.norpix.com/products/streampix/ streampix.php; RRID: SCR_015773 ImageJ NIH https://imagej.nih.gov/ij/index.html; RRID: SCR_003070 pCLAMP 11 Molecular Devices https://www.moleculardevices.com/; RRID: SCR_011323 Adobe Photoshop 2020 Adobe https://www.adobe.com/; RRID: SCR_014199 Adobe Illustrator 2020 Adobe https://www.adobe.com/; RRID: SCR_010279 Body tracking code David Anderson lab, Lin et al., 2011 https://github.com/pdollar/toolbox e1 Neuron 110, 3000–3017.e1–e8, September 21, 2022 ..
shRNA:Article Title: Dynamin is primed at endocytic sites for ultrafast endocytosis.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER NaCl Sigma-Aldrich Cat# S7653 polyethylenimine Polysciences Cat# 23966-2 cOMPLETE protease inhibitor cocktail tablet Roche Cat# 11836153001 HEPES Merck Cat# 1.10110.0250 KCl Sigma-Aldrich Cat# P9333 Glucose Sigma-Aldrich Cat# 49159 MgCl2 Fluka Cat# 63020 NBQX Tocris Cat# 1044 Bicuculline Tocris Cat# 0130 Cationized ferritin Sigma-Aldrich Cat# F7879 Glutaraldehyde in anhydrous acetone EMS Cat# 16530 Osmium tetroxide EMS Cat# RT19132 Uranyl acetate EMS Cat# 22400 Acetone EMS Cat# RT10016 InFusion HD Cloning Kit Thermal Scientific Cat# 63649 Digitonin Sigma-Aldrich Cat# D141 1,6-Hexanediol Sigma-Aldrich Cat# 240117 2,5-Hexanediol Sigma-Aldrich Cat# H11904 1,4-Butanediol Sigma-Aldrich Cat# 493732 FK506 Tocris Cat# 3631 CHIR99021 Sigma-Aldrich Cat# SML 1046 ProLong Diamond Antifade Mountant Thermo Fisher Cat# P36971 Gold Seal Microscope Slides, 3’’31’’, 1mm thick Thermo Fisher Cat# 3010 JFX549 Luke Davis’s lab (Janelia Research Campus); (Grimm et al., 2016) N/A PA-JF646 Luke Davis’s lab (Janelia Research Campus) (Grimm et al., 2016) N/A Experimental models: Organisms/strains Dynamin-1, -3 DKO De Camilli’s Lab (Raimondi et al., 2011) N/A Dynamin-3 KO De Camilli’s Lab (Raimondi et al., 2011) N/A Recombinant DNA f(syn)NLS-RFP-P2A-hsDyn1xA This paper N/A f(syn)NLS-RFP-P2A-hsDyn1xA S774/778A This paper N/A f(syn)NLS-RFP-P2A-hsDyn1xA S774/778D This paper N/A f(syn)NLS-RFP-P2A-hsDyn1xB This paper N/A f(syn)NLS-RFP-P2A-hsDyn1xB S774/778A This paper N/A f(syn)NLS-RFP-P2A-hsDyn2 This paper N/A hDyn1-S774A-S778A in pcDNA3 Armbruster et al., 2013 N/A hDyn1-S774D-S778D in pcDNA3 Armbruster et al., 2013 N/A HA-hDyn2 in pcDNA3 Ferguson et al., 2007 N/A phsDyn1xA-EGFP-N1 Kong et al., 2018 Addgene #120313 phsDyn1xA S774/778A- EGFP-N1 This paper N/A phsDyn1xA S774/778D- EGFP-N1 This paper N/A phsDyn1xA I481D/H687D/L688S- EGFP-N1 This paper N/A (Continued on next page) Neuron 110, 2815–2835.e1–e13, September 7, 2022 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER phsDyn1xA-Halo This paper N/A pmCherry-Syb2 This paper N/A phsDyn1xA- EGFP-N1_P2A_mCherr-rtSyb2 This paper N/A phsDyn1xB- EGFP-N1 This paper N/A pDyn2-mCherry-N1 Taylor et al., 2011 Addgene #27689 pVAMP2(Syb2)-SNAP Martineau et al., 2017 Addgene #105288 pCAGGS-tdTomato This paper N/A pCMV-tdTomato Clontech Cat# 632534 pORANGE Willems et al., 2020 Addgene #131471 pORANGE-msDyn1xA-GFP This paper N/A pFUGW-mCherry This paper N/A pFUGW-mCherry_ORANGE_msDyn1xA-GFP This paper N/A pEGFP-N1 Clontech Cat# 6085-1 pmCherry-N1 Clontech Cat# 632523 pFUGW-spCas9 Willems et al., 2020 Addgene #131506 f(U6)scramble shRNA.hSyn-NLS-RFP-WPRE Watanabe et al., 2014 N/A f(U6)Syndapin 1-shRNA.hSyn-NLS-RFP-WPRE This paper N/A f(syn)NLS-RFP-P2A-Syndapin 1 This paper N/A f(syn)NLS-RFP-P2A-Syndapin 1 shRNA resistant This paper N/A f(syn)NLS-RFP-P2A-Syndapin 1 I122D/M123E shRNA resistant This paper N/A f(syn)NLS-RFP-P2A-Syndapin 1 P434L shRNA resistant This paper N/A pmCherry-N1_Syndapin 1 shRNA resistant This paper N/A pmCherry-N1_Syndapin 1 I122D/M123E shRNA resistant This paper N/A pmCherry-N1-Syndapin 1 P434L shRNA resistant This paper N/A pGex6T-Dyn1xA/Dyn1xA-S774/778D This paper N/A pGex6T-Syndapin1 This paper N/A pGex6T-Syndapin1 P434L This paper N/A pDyn1xA-PRM Anggono et al., 2006 N/A pDyn1xA-PRM S774/778A Anggono et al., 2006 N/A pDyn1xA-PRM S774/778E Anggono et al., 2006 N/A Software and algorithms SynapsEM Watanabe et al., 2020 https://github.com/shigekiwatanabe/ SynapsEM ImaegJ-Fiji Schindelin et al., 2012 https://imagej.net/Fiji Adobe Illustrator 2021 Adobe https://www.adobe.com/ Adobe Photoshop 2021 Adobe https://www.adobe.com/ Prism GraphPad (Prism 8) https://www.graphpad.com Excel Microsoft https://products.office.com/en-us/ explore-office-for-home MATLAB MathWorks https://www.mathworks.com/products/ matlab.html Microscopy Hitachi 7600 TEM Hitachi N/A LSM880 Carl Zeiss N/A (Continued on next page) e3 Neuron 110, 2815–2835.e1–e13, September 7, 2022 .. REAGENT or RESOURCE SOURCE IDENTIFIER Nikon Eclipse Ti2 Nikon N/A ORCA-Fusion BT Digital CMOS camera Hamamatsu N/A Ti:Sapphire laser head Mai Tai HP, Spectra-Physics N/A photonic crystal fiber Newport N/A acoustic optical tunable filter AA Opto-Electronic N/A 100-m long polarization-maintaining single-mode fiber OZ optics N/A vortex phase plate VPP-1, RPC photonics N/A avalanche photodiodes SPCM-AQR-14-FC Perkin Elmer N/A piezo-controlled stage Max311D Thorlabs N/A 405nm/250 mW laser RPMC Lasers Inc. N/A 488nm/300 mW laser MPB Communications N/A 560nm/500 mW laser MPB Communications N/A 642nm/500 mW laser MPB Communications N/A acoustic optical tunable filter AA Opto-Electronic N/A galvo mirrors Cambridge Technology 6215H CFI Apo LWD 25XW, 1.1 NA, 2 mm WD Nikon N/A Orca Flash 4.0 v3 Hamamatsu N/A Other Sapphire Disks, 6-nm Technotrade Cat# 616-100 AFS2 Leica microsystem N/A EM ICE Leica microsystem N/A
Transmission Electron Microscopy:Article Title: Dynamin is primed at endocytic sites for ultrafast endocytosis.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER NaCl Sigma-Aldrich Cat# S7653 polyethylenimine Polysciences Cat# 23966-2 cOMPLETE protease inhibitor cocktail tablet Roche Cat# 11836153001 HEPES Merck Cat# 1.10110.0250 KCl Sigma-Aldrich Cat# P9333 Glucose Sigma-Aldrich Cat# 49159 MgCl2 Fluka Cat# 63020 NBQX Tocris Cat# 1044 Bicuculline Tocris Cat# 0130 Cationized ferritin Sigma-Aldrich Cat# F7879 Glutaraldehyde in anhydrous acetone EMS Cat# 16530 Osmium tetroxide EMS Cat# RT19132 Uranyl acetate EMS Cat# 22400 Acetone EMS Cat# RT10016 InFusion HD Cloning Kit Thermal Scientific Cat# 63649 Digitonin Sigma-Aldrich Cat# D141 1,6-Hexanediol Sigma-Aldrich Cat# 240117 2,5-Hexanediol Sigma-Aldrich Cat# H11904 1,4-Butanediol Sigma-Aldrich Cat# 493732 FK506 Tocris Cat# 3631 CHIR99021 Sigma-Aldrich Cat# SML 1046 ProLong Diamond Antifade Mountant Thermo Fisher Cat# P36971 Gold Seal Microscope Slides, 3’’31’’, 1mm thick Thermo Fisher Cat# 3010 JFX549 Luke Davis’s lab (Janelia Research Campus); (Grimm et al., 2016) N/A PA-JF646 Luke Davis’s lab (Janelia Research Campus) (Grimm et al., 2016) N/A Experimental models: Organisms/strains Dynamin-1, -3 DKO De Camilli’s Lab (Raimondi et al., 2011) N/A Dynamin-3 KO De Camilli’s Lab (Raimondi et al., 2011) N/A Recombinant DNA f(syn)NLS-RFP-P2A-hsDyn1xA This paper N/A f(syn)NLS-RFP-P2A-hsDyn1xA S774/778A This paper N/A f(syn)NLS-RFP-P2A-hsDyn1xA S774/778D This paper N/A f(syn)NLS-RFP-P2A-hsDyn1xB This paper N/A f(syn)NLS-RFP-P2A-hsDyn1xB S774/778A This paper N/A f(syn)NLS-RFP-P2A-hsDyn2 This paper N/A hDyn1-S774A-S778A in pcDNA3 Armbruster et al., 2013 N/A hDyn1-S774D-S778D in pcDNA3 Armbruster et al., 2013 N/A HA-hDyn2 in pcDNA3 Ferguson et al., 2007 N/A phsDyn1xA-EGFP-N1 Kong et al., 2018 Addgene #120313 phsDyn1xA S774/778A- EGFP-N1 This paper N/A phsDyn1xA S774/778D- EGFP-N1 This paper N/A phsDyn1xA I481D/H687D/L688S- EGFP-N1 This paper N/A (Continued on next page) Neuron 110, 2815–2835.e1–e13, September 7, 2022 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER phsDyn1xA-Halo This paper N/A pmCherry-Syb2 This paper N/A phsDyn1xA- EGFP-N1_P2A_mCherr-rtSyb2 This paper N/A phsDyn1xB- EGFP-N1 This paper N/A pDyn2-mCherry-N1 Taylor et al., 2011 Addgene #27689 pVAMP2(Syb2)-SNAP Martineau et al., 2017 Addgene #105288 pCAGGS-tdTomato This paper N/A pCMV-tdTomato Clontech Cat# 632534 pORANGE Willems et al., 2020 Addgene #131471 pORANGE-msDyn1xA-GFP This paper N/A pFUGW-mCherry This paper N/A pFUGW-mCherry_ORANGE_msDyn1xA-GFP This paper N/A pEGFP-N1 Clontech Cat# 6085-1 pmCherry-N1 Clontech Cat# 632523 pFUGW-spCas9 Willems et al., 2020 Addgene #131506 f(U6)scramble shRNA.hSyn-NLS-RFP-WPRE Watanabe et al., 2014 N/A f(U6)Syndapin 1-shRNA.hSyn-NLS-RFP-WPRE This paper N/A f(syn)NLS-RFP-P2A-Syndapin 1 This paper N/A f(syn)NLS-RFP-P2A-Syndapin 1 shRNA resistant This paper N/A f(syn)NLS-RFP-P2A-Syndapin 1 I122D/M123E shRNA resistant This paper N/A f(syn)NLS-RFP-P2A-Syndapin 1 P434L shRNA resistant This paper N/A pmCherry-N1_Syndapin 1 shRNA resistant This paper N/A pmCherry-N1_Syndapin 1 I122D/M123E shRNA resistant This paper N/A pmCherry-N1-Syndapin 1 P434L shRNA resistant This paper N/A pGex6T-Dyn1xA/Dyn1xA-S774/778D This paper N/A pGex6T-Syndapin1 This paper N/A pGex6T-Syndapin1 P434L This paper N/A pDyn1xA-PRM Anggono et al., 2006 N/A pDyn1xA-PRM S774/778A Anggono et al., 2006 N/A pDyn1xA-PRM S774/778E Anggono et al., 2006 N/A Software and algorithms SynapsEM Watanabe et al., 2020 https://github.com/shigekiwatanabe/ SynapsEM ImaegJ-Fiji Schindelin et al., 2012 https://imagej.net/Fiji Adobe Illustrator 2021 Adobe https://www.adobe.com/ Adobe Photoshop 2021 Adobe https://www.adobe.com/ Prism GraphPad (Prism 8) https://www.graphpad.com Excel Microsoft https://products.office.com/en-us/ explore-office-for-home MATLAB MathWorks https://www.mathworks.com/products/ matlab.html Microscopy Hitachi 7600 TEM Hitachi N/A LSM880 Carl Zeiss N/A (Continued on next page) e3 Neuron 110, 2815–2835.e1–e13, September 7, 2022 .. REAGENT or RESOURCE SOURCE IDENTIFIER Nikon Eclipse Ti2 Nikon N/A ORCA-Fusion BT Digital CMOS camera Hamamatsu N/A Ti:Sapphire laser head Mai Tai HP, Spectra-Physics N/A photonic crystal fiber Newport N/A acoustic optical tunable filter AA Opto-Electronic N/A 100-m long polarization-maintaining single-mode fiber OZ optics N/A vortex phase plate VPP-1, RPC photonics N/A avalanche photodiodes SPCM-AQR-14-FC Perkin Elmer N/A piezo-controlled stage Max311D Thorlabs N/A 405nm/250 mW laser RPMC Lasers Inc. N/A 488nm/300 mW laser MPB Communications N/A 560nm/500 mW laser MPB Communications N/A 642nm/500 mW laser MPB Communications N/A acoustic optical tunable filter AA Opto-Electronic N/A galvo mirrors Cambridge Technology 6215H CFI Apo LWD 25XW, 1.1 NA, 2 mm WD Nikon N/A Orca Flash 4.0 v3 Hamamatsu N/A Other Sapphire Disks, 6-nm Technotrade Cat# 616-100 AFS2 Leica microsystem N/A EM ICE Leica microsystem N/A
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