Fluorescence:Article Title: Deciphering the nanoscale architecture of presynaptic actin using a micropatterned presynapse-on-glass model
Article Snippet: Primary antibodies used are chicken anti-map2 (1:1,000, ab5392, RRID:AB_2138153; Abcam), mouse anti-ß2-spectrin (1:100, clone 42/aa 2101-2189, #612563, RRID:AB_399854; BD Bioscience), guinea pig anti-synaptophysin (1:400, 101 004, RRID:AB_1210382; Synaptic Systems), mouse anti-synaptotag-min1 (1:600, clone 604.2/aa 1-12, 105 311, RRID:AB_993036; Synaptic Systems), rabbit anti-adducin alpha (1:100, ab40760, RRID:AB_722627; Abcam), mouse anti-bassoon (1:200, clone SAP7F407, ab82958, RRID:AB_1860018; Abcam), rabbit anti-GFP (1:750, ab290, RRID:AB_303395; Abcam), mouse anti-GFP (1:750, clone 9F9.F9, ab1218, RRID:AB_298911; Abcam), rabbit anti-munc13-1 (1:500, 126 103, RRID:AB_887733; Synaptic Systems).
Article Title: Rapid Aging in the Perforant Path Projections to the Rodent Dentate Gyrus
Article Snippet: Primary antisera included rabbit anti-phosphorylated FAK (1:1000; catalog #ab39967, Abcam), anti-GluN2A (1:25,000; catalog #AB1555, EMD-Millipore), and anti-TrkB (1:2000; catalog #07–225, EMD-Millipore); guinea pig anti-synaptophysin (1:2500; catalog #101004, SySy Systems); and mouse anti-PSD-95 (1:1000; catalog #MA1-045, Thermo Fisher Scientific).
Article Title: Disrupted presynaptic nectin1-based neuronal adhesion in the entorhinal-hippocampal circuit contributes to early-life stress-induced memory deficits
Article Snippet: Primary rabbit anti-nectin1 (1:1000, sc-28639, Santa Cruz Biotechnology, Santa Cruz, CA, USA), rabbit anti-nectin3 (1:1000, ab63931, Abcam, Cambridge, UK), and guinea pig anti-synaptophysin (1:500, 101004, Synaptic Systems, Göttingen, Germany) antibodies were used.
Article Title: Rapid Aging in the Perforant Path Projections to the Rodent Dentate Gyrus
Article Snippet: Primary antisera included rabbit antiphosphorylated FAK (1:1000; catalog #ab39967, Abcam), anti-GluN2A (1:25,000; catalog #AB1555, EMD-Millipore), and anti-TrkB (1:2000; catalog #07–225, EMD-Millipore); guinea pig anti-synaptophysin (1:2500; catalog #101004, SySy Systems); and mouse anti-PSD-95 (1:1000; catalog #MA1-045, Thermo Fisher Scientific).
Article Title: KIF21B binds Myosin Va for Spine Entry and regulates Actin Dynamics to control Homeostatic Synaptic Downscaling
Article Snippet: Rabbit anti-KIF21B (1:1,000; Sigma-Aldrich, Taufkirchen, Germany), Mouse anti-Homer1 (1:1,000; Synaptic Systems, Göttingen, Germany), mouse anti-GluA2 extracellular (1:1,000; Millipore, Darmstadt, Germany), rabbit anti-MyoVa (1:1,000; Sigma-Aldrich, Taufkirchen, Germany), rabbit anti-MyoVI (1:1,000; Sigma-Aldrich, Taufkirchen, Germany), mouse anti-PSD95 (1:100; Thermo Fisher Scientific, Dreieich, Germany), goat anti-Shank1-3 (1:1,000; Abcam, Cambridge, UK), guinea pig anti-Synaptophysin (1:1,000; Synaptic Systems, Göttingen, Germany), rabbit anti-KIF21A (1:1,000; Dianova, Hamburg, Germany).
Article Title: N-glycoproteomics of brain synapses and synaptic vesicles.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies SV2 mAb DSHB SV2 (RRID:AB_2315387) Syt1 mAb DSHB mAb 48 (RRID:AB_2199314) Guinea pig anti-synaptophysin Synaptic Systems 104 211 (RRID:AB_1210382) Goat anti-mouse HRP-conjugated secondary Ab Bio-Rad 1706516 Goat anti-guinea pig HRP-conjugated secondary Ab Thermo Fisher A18769 Chemicals, peptides, and recombinant proteins Protein G Sepharose fast flow Cytiva 17061801 Dynabeads M-270 epoxy Thermo Fisher 14302D cOmplete mini, EDTA-free Sigma (Roche) 04693159001 Dynabeads M-270 carboxylic acid Thermo Fisher 14305D Trypsin Promega V5111 SOLA SAX 10 mg cartridge Thermo Fisher 60109–003 PNGase F NEB P0708 Procainamide Sigma SML2088 Sodium cyanoborohydride, 5 M in 1 M NaOH Sigma 296945 OASIS HLB 30 mg cartridge Waters WAT094225 a(1–2,3,6) mannosidase NEB P0768 a(1–3,4) fucosidase NEB P0769 a(1–2) fucosidase NEB P0724 a(1–2,4,6) fucosidase O NEB P0749 b(1–3,4) galactosidase NEB P0746 b-GlcNAcase S NEB P0744 Deposited data LC-MS raw data deposited at MassIVE This paper https://doi.org/10.25345/C5TB0Z526 Experimental models: Organisms/strains Mouse: C57B6/J Jackson Laboratory 000664 (RRID:IMSR_JAX:000664) Software and algorithms FragPipe Nesvizhskii Lab v. 17.1 Agilent ChemStation Agilent LTS 01.11 R/Rstudio CRAN/Posit v. 2021.09.0 R scripts used in this paper This paper https://doi.org/10.5281/zenodo.7659070 The Gene Ontology resource Geneontology.org v. 2023-01-01 Prism GraphPad v. 9.3.1
Article Title: High-Content Screening of Synaptic Density Modulators in Primary Neuronal Cultures.
Article Snippet: See the T erm s and C onditions (https://onlinelibrary.w iley.com /term s-and-conditions) on W iley O nline L ibrary for rules of use; O A articles are governed by the applicable C reative C om m ons L icense 2.5% (w/v) bovine serum albumin (BSA) in DPBS with 0.1% (v/v) Triton X-100 Primary antibodies: Chicken anti-Homer1 (Synaptic Systems, cat. no. 160006) Guinea pig anti-Synaptophysin (Synaptic Systems, cat. no. 101004) Mouse anti-MAP2 (Synaptic Systems, cat. no. 188011) 1× DPBS Secondary antibodies: Donkey anti-chicken Alexa 488 (Jackson ImmunoResearch, cat. no. 703-545-155) Goat anti-guinea pig Alexa 555 (Life Technologies, cat. no. A21435) Donkey anti-mouse Alexa 647 (Jackson ImmunoResearch, cat. no. 715-605-151) 16-channel pipet (Finnpipette F1; Thermo Scientific, cat. no. 4661090N) Aluminum sealing tape (Dutscher, cat. no. 106570, or similar) PlateHUB rotating plate-storage carousel (Agilent, model G5500-23447) Plate washer associated with liquid handler (BioTek, model EL406) Wash_Primary.pro and Wash_Secondary.pro programs (see Supporting Information) VWorks automation control software (Agilent) Aspirate.LHC and Aspirate-Dispense.LHC subroutines (see Supporting Information) Direct Drive Robot (Agilent) NOTE: Use sterile pipet tips with filters (Finntip 50; Thermo Scientific, cat. no. 94052060).
Cell Culture:Article Title: Deciphering the nanoscale architecture of presynaptic actin using a micropatterned presynapse-on-glass model
Article Snippet: Primary antibodies used are chicken anti-map2 (1:1,000, ab5392, RRID:AB_2138153; Abcam), mouse anti-ß2-spectrin (1:100, clone 42/aa 2101-2189, #612563, RRID:AB_399854; BD Bioscience), guinea pig anti-synaptophysin (1:400, 101 004, RRID:AB_1210382; Synaptic Systems), mouse anti-synaptotag-min1 (1:600, clone 604.2/aa 1-12, 105 311, RRID:AB_993036; Synaptic Systems), rabbit anti-adducin alpha (1:100, ab40760, RRID:AB_722627; Abcam), mouse anti-bassoon (1:200, clone SAP7F407, ab82958, RRID:AB_1860018; Abcam), rabbit anti-GFP (1:750, ab290, RRID:AB_303395; Abcam), mouse anti-GFP (1:750, clone 9F9.F9, ab1218, RRID:AB_298911; Abcam), rabbit anti-munc13-1 (1:500, 126 103, RRID:AB_887733; Synaptic Systems).
Article Title: Rapid Aging in the Perforant Path Projections to the Rodent Dentate Gyrus
Article Snippet: Primary antisera included rabbit anti-phosphorylated FAK (1:1000; catalog #ab39967, Abcam), anti-GluN2A (1:25,000; catalog #AB1555, EMD-Millipore), and anti-TrkB (1:2000; catalog #07–225, EMD-Millipore); guinea pig anti-synaptophysin (1:2500; catalog #101004, SySy Systems); and mouse anti-PSD-95 (1:1000; catalog #MA1-045, Thermo Fisher Scientific).
Article Title: Disrupted presynaptic nectin1-based neuronal adhesion in the entorhinal-hippocampal circuit contributes to early-life stress-induced memory deficits
Article Snippet: Primary rabbit anti-nectin1 (1:1000, sc-28639, Santa Cruz Biotechnology, Santa Cruz, CA, USA), rabbit anti-nectin3 (1:1000, ab63931, Abcam, Cambridge, UK), and guinea pig anti-synaptophysin (1:500, 101004, Synaptic Systems, Göttingen, Germany) antibodies were used.
Article Title: Rapid Aging in the Perforant Path Projections to the Rodent Dentate Gyrus
Article Snippet: Primary antisera included rabbit antiphosphorylated FAK (1:1000; catalog #ab39967, Abcam), anti-GluN2A (1:25,000; catalog #AB1555, EMD-Millipore), and anti-TrkB (1:2000; catalog #07–225, EMD-Millipore); guinea pig anti-synaptophysin (1:2500; catalog #101004, SySy Systems); and mouse anti-PSD-95 (1:1000; catalog #MA1-045, Thermo Fisher Scientific).
Article Title: KIF21B binds Myosin Va for Spine Entry and regulates Actin Dynamics to control Homeostatic Synaptic Downscaling
Article Snippet: Rabbit anti-KIF21B (1:1,000; Sigma-Aldrich, Taufkirchen, Germany), Mouse anti-Homer1 (1:1,000; Synaptic Systems, Göttingen, Germany), mouse anti-GluA2 extracellular (1:1,000; Millipore, Darmstadt, Germany), rabbit anti-MyoVa (1:1,000; Sigma-Aldrich, Taufkirchen, Germany), rabbit anti-MyoVI (1:1,000; Sigma-Aldrich, Taufkirchen, Germany), mouse anti-PSD95 (1:100; Thermo Fisher Scientific, Dreieich, Germany), goat anti-Shank1-3 (1:1,000; Abcam, Cambridge, UK), guinea pig anti-Synaptophysin (1:1,000; Synaptic Systems, Göttingen, Germany), rabbit anti-KIF21A (1:1,000; Dianova, Hamburg, Germany).
Article Title: N-glycoproteomics of brain synapses and synaptic vesicles.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies SV2 mAb DSHB SV2 (RRID:AB_2315387) Syt1 mAb DSHB mAb 48 (RRID:AB_2199314) Guinea pig anti-synaptophysin Synaptic Systems 104 211 (RRID:AB_1210382) Goat anti-mouse HRP-conjugated secondary Ab Bio-Rad 1706516 Goat anti-guinea pig HRP-conjugated secondary Ab Thermo Fisher A18769 Chemicals, peptides, and recombinant proteins Protein G Sepharose fast flow Cytiva 17061801 Dynabeads M-270 epoxy Thermo Fisher 14302D cOmplete mini, EDTA-free Sigma (Roche) 04693159001 Dynabeads M-270 carboxylic acid Thermo Fisher 14305D Trypsin Promega V5111 SOLA SAX 10 mg cartridge Thermo Fisher 60109–003 PNGase F NEB P0708 Procainamide Sigma SML2088 Sodium cyanoborohydride, 5 M in 1 M NaOH Sigma 296945 OASIS HLB 30 mg cartridge Waters WAT094225 a(1–2,3,6) mannosidase NEB P0768 a(1–3,4) fucosidase NEB P0769 a(1–2) fucosidase NEB P0724 a(1–2,4,6) fucosidase O NEB P0749 b(1–3,4) galactosidase NEB P0746 b-GlcNAcase S NEB P0744 Deposited data LC-MS raw data deposited at MassIVE This paper https://doi.org/10.25345/C5TB0Z526 Experimental models: Organisms/strains Mouse: C57B6/J Jackson Laboratory 000664 (RRID:IMSR_JAX:000664) Software and algorithms FragPipe Nesvizhskii Lab v. 17.1 Agilent ChemStation Agilent LTS 01.11 R/Rstudio CRAN/Posit v. 2021.09.0 R scripts used in this paper This paper https://doi.org/10.5281/zenodo.7659070 The Gene Ontology resource Geneontology.org v. 2023-01-01 Prism GraphPad v. 9.3.1
Article Title: High-Content Screening of Synaptic Density Modulators in Primary Neuronal Cultures.
Article Snippet: See the T erm s and C onditions (https://onlinelibrary.w iley.com /term s-and-conditions) on W iley O nline L ibrary for rules of use; O A articles are governed by the applicable C reative C om m ons L icense 2.5% (w/v) bovine serum albumin (BSA) in DPBS with 0.1% (v/v) Triton X-100 Primary antibodies: Chicken anti-Homer1 (Synaptic Systems, cat. no. 160006) Guinea pig anti-Synaptophysin (Synaptic Systems, cat. no. 101004) Mouse anti-MAP2 (Synaptic Systems, cat. no. 188011) 1× DPBS Secondary antibodies: Donkey anti-chicken Alexa 488 (Jackson ImmunoResearch, cat. no. 703-545-155) Goat anti-guinea pig Alexa 555 (Life Technologies, cat. no. A21435) Donkey anti-mouse Alexa 647 (Jackson ImmunoResearch, cat. no. 715-605-151) 16-channel pipet (Finnpipette F1; Thermo Scientific, cat. no. 4661090N) Aluminum sealing tape (Dutscher, cat. no. 106570, or similar) PlateHUB rotating plate-storage carousel (Agilent, model G5500-23447) Plate washer associated with liquid handler (BioTek, model EL406) Wash_Primary.pro and Wash_Secondary.pro programs (see Supporting Information) VWorks automation control software (Agilent) Aspirate.LHC and Aspirate-Dispense.LHC subroutines (see Supporting Information) Direct Drive Robot (Agilent) NOTE: Use sterile pipet tips with filters (Finntip 50; Thermo Scientific, cat. no. 94052060).
Labeling:Article Title: Deciphering the nanoscale architecture of presynaptic actin using a micropatterned presynapse-on-glass model
Article Snippet: Primary antibodies used are chicken anti-map2 (1:1,000, ab5392, RRID:AB_2138153; Abcam), mouse anti-ß2-spectrin (1:100, clone 42/aa 2101-2189, #612563, RRID:AB_399854; BD Bioscience), guinea pig anti-synaptophysin (1:400, 101 004, RRID:AB_1210382; Synaptic Systems), mouse anti-synaptotag-min1 (1:600, clone 604.2/aa 1-12, 105 311, RRID:AB_993036; Synaptic Systems), rabbit anti-adducin alpha (1:100, ab40760, RRID:AB_722627; Abcam), mouse anti-bassoon (1:200, clone SAP7F407, ab82958, RRID:AB_1860018; Abcam), rabbit anti-GFP (1:750, ab290, RRID:AB_303395; Abcam), mouse anti-GFP (1:750, clone 9F9.F9, ab1218, RRID:AB_298911; Abcam), rabbit anti-munc13-1 (1:500, 126 103, RRID:AB_887733; Synaptic Systems).
Article Title: Rapid Aging in the Perforant Path Projections to the Rodent Dentate Gyrus
Article Snippet: Primary antisera included rabbit anti-phosphorylated FAK (1:1000; catalog #ab39967, Abcam), anti-GluN2A (1:25,000; catalog #AB1555, EMD-Millipore), and anti-TrkB (1:2000; catalog #07–225, EMD-Millipore); guinea pig anti-synaptophysin (1:2500; catalog #101004, SySy Systems); and mouse anti-PSD-95 (1:1000; catalog #MA1-045, Thermo Fisher Scientific).
Article Title: Disrupted presynaptic nectin1-based neuronal adhesion in the entorhinal-hippocampal circuit contributes to early-life stress-induced memory deficits
Article Snippet: Primary rabbit anti-nectin1 (1:1000, sc-28639, Santa Cruz Biotechnology, Santa Cruz, CA, USA), rabbit anti-nectin3 (1:1000, ab63931, Abcam, Cambridge, UK), and guinea pig anti-synaptophysin (1:500, 101004, Synaptic Systems, Göttingen, Germany) antibodies were used.
Article Title: Rapid Aging in the Perforant Path Projections to the Rodent Dentate Gyrus
Article Snippet: Primary antisera included rabbit antiphosphorylated FAK (1:1000; catalog #ab39967, Abcam), anti-GluN2A (1:25,000; catalog #AB1555, EMD-Millipore), and anti-TrkB (1:2000; catalog #07–225, EMD-Millipore); guinea pig anti-synaptophysin (1:2500; catalog #101004, SySy Systems); and mouse anti-PSD-95 (1:1000; catalog #MA1-045, Thermo Fisher Scientific).
Article Title: KIF21B binds Myosin Va for Spine Entry and regulates Actin Dynamics to control Homeostatic Synaptic Downscaling
Article Snippet: Rabbit anti-KIF21B (1:1,000; Sigma-Aldrich, Taufkirchen, Germany), Mouse anti-Homer1 (1:1,000; Synaptic Systems, Göttingen, Germany), mouse anti-GluA2 extracellular (1:1,000; Millipore, Darmstadt, Germany), rabbit anti-MyoVa (1:1,000; Sigma-Aldrich, Taufkirchen, Germany), rabbit anti-MyoVI (1:1,000; Sigma-Aldrich, Taufkirchen, Germany), mouse anti-PSD95 (1:100; Thermo Fisher Scientific, Dreieich, Germany), goat anti-Shank1-3 (1:1,000; Abcam, Cambridge, UK), guinea pig anti-Synaptophysin (1:1,000; Synaptic Systems, Göttingen, Germany), rabbit anti-KIF21A (1:1,000; Dianova, Hamburg, Germany).
Article Title: N-glycoproteomics of brain synapses and synaptic vesicles.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies SV2 mAb DSHB SV2 (RRID:AB_2315387) Syt1 mAb DSHB mAb 48 (RRID:AB_2199314) Guinea pig anti-synaptophysin Synaptic Systems 104 211 (RRID:AB_1210382) Goat anti-mouse HRP-conjugated secondary Ab Bio-Rad 1706516 Goat anti-guinea pig HRP-conjugated secondary Ab Thermo Fisher A18769 Chemicals, peptides, and recombinant proteins Protein G Sepharose fast flow Cytiva 17061801 Dynabeads M-270 epoxy Thermo Fisher 14302D cOmplete mini, EDTA-free Sigma (Roche) 04693159001 Dynabeads M-270 carboxylic acid Thermo Fisher 14305D Trypsin Promega V5111 SOLA SAX 10 mg cartridge Thermo Fisher 60109–003 PNGase F NEB P0708 Procainamide Sigma SML2088 Sodium cyanoborohydride, 5 M in 1 M NaOH Sigma 296945 OASIS HLB 30 mg cartridge Waters WAT094225 a(1–2,3,6) mannosidase NEB P0768 a(1–3,4) fucosidase NEB P0769 a(1–2) fucosidase NEB P0724 a(1–2,4,6) fucosidase O NEB P0749 b(1–3,4) galactosidase NEB P0746 b-GlcNAcase S NEB P0744 Deposited data LC-MS raw data deposited at MassIVE This paper https://doi.org/10.25345/C5TB0Z526 Experimental models: Organisms/strains Mouse: C57B6/J Jackson Laboratory 000664 (RRID:IMSR_JAX:000664) Software and algorithms FragPipe Nesvizhskii Lab v. 17.1 Agilent ChemStation Agilent LTS 01.11 R/Rstudio CRAN/Posit v. 2021.09.0 R scripts used in this paper This paper https://doi.org/10.5281/zenodo.7659070 The Gene Ontology resource Geneontology.org v. 2023-01-01 Prism GraphPad v. 9.3.1
Article Title: High-Content Screening of Synaptic Density Modulators in Primary Neuronal Cultures.
Article Snippet: See the T erm s and C onditions (https://onlinelibrary.w iley.com /term s-and-conditions) on W iley O nline L ibrary for rules of use; O A articles are governed by the applicable C reative C om m ons L icense 2.5% (w/v) bovine serum albumin (BSA) in DPBS with 0.1% (v/v) Triton X-100 Primary antibodies: Chicken anti-Homer1 (Synaptic Systems, cat. no. 160006) Guinea pig anti-Synaptophysin (Synaptic Systems, cat. no. 101004) Mouse anti-MAP2 (Synaptic Systems, cat. no. 188011) 1× DPBS Secondary antibodies: Donkey anti-chicken Alexa 488 (Jackson ImmunoResearch, cat. no. 703-545-155) Goat anti-guinea pig Alexa 555 (Life Technologies, cat. no. A21435) Donkey anti-mouse Alexa 647 (Jackson ImmunoResearch, cat. no. 715-605-151) 16-channel pipet (Finnpipette F1; Thermo Scientific, cat. no. 4661090N) Aluminum sealing tape (Dutscher, cat. no. 106570, or similar) PlateHUB rotating plate-storage carousel (Agilent, model G5500-23447) Plate washer associated with liquid handler (BioTek, model EL406) Wash_Primary.pro and Wash_Secondary.pro programs (see Supporting Information) VWorks automation control software (Agilent) Aspirate.LHC and Aspirate-Dispense.LHC subroutines (see Supporting Information) Direct Drive Robot (Agilent) NOTE: Use sterile pipet tips with filters (Finntip 50; Thermo Scientific, cat. no. 94052060).
Isolation:Article Title: Deciphering the nanoscale architecture of presynaptic actin using a micropatterned presynapse-on-glass model
Article Snippet: Primary antibodies used are chicken anti-map2 (1:1,000, ab5392, RRID:AB_2138153; Abcam), mouse anti-ß2-spectrin (1:100, clone 42/aa 2101-2189, #612563, RRID:AB_399854; BD Bioscience), guinea pig anti-synaptophysin (1:400, 101 004, RRID:AB_1210382; Synaptic Systems), mouse anti-synaptotag-min1 (1:600, clone 604.2/aa 1-12, 105 311, RRID:AB_993036; Synaptic Systems), rabbit anti-adducin alpha (1:100, ab40760, RRID:AB_722627; Abcam), mouse anti-bassoon (1:200, clone SAP7F407, ab82958, RRID:AB_1860018; Abcam), rabbit anti-GFP (1:750, ab290, RRID:AB_303395; Abcam), mouse anti-GFP (1:750, clone 9F9.F9, ab1218, RRID:AB_298911; Abcam), rabbit anti-munc13-1 (1:500, 126 103, RRID:AB_887733; Synaptic Systems).
Article Title: Rapid Aging in the Perforant Path Projections to the Rodent Dentate Gyrus
Article Snippet: Primary antisera included rabbit anti-phosphorylated FAK (1:1000; catalog #ab39967, Abcam), anti-GluN2A (1:25,000; catalog #AB1555, EMD-Millipore), and anti-TrkB (1:2000; catalog #07–225, EMD-Millipore); guinea pig anti-synaptophysin (1:2500; catalog #101004, SySy Systems); and mouse anti-PSD-95 (1:1000; catalog #MA1-045, Thermo Fisher Scientific).
Article Title: Disrupted presynaptic nectin1-based neuronal adhesion in the entorhinal-hippocampal circuit contributes to early-life stress-induced memory deficits
Article Snippet: Primary rabbit anti-nectin1 (1:1000, sc-28639, Santa Cruz Biotechnology, Santa Cruz, CA, USA), rabbit anti-nectin3 (1:1000, ab63931, Abcam, Cambridge, UK), and guinea pig anti-synaptophysin (1:500, 101004, Synaptic Systems, Göttingen, Germany) antibodies were used.
Article Title: Rapid Aging in the Perforant Path Projections to the Rodent Dentate Gyrus
Article Snippet: Primary antisera included rabbit antiphosphorylated FAK (1:1000; catalog #ab39967, Abcam), anti-GluN2A (1:25,000; catalog #AB1555, EMD-Millipore), and anti-TrkB (1:2000; catalog #07–225, EMD-Millipore); guinea pig anti-synaptophysin (1:2500; catalog #101004, SySy Systems); and mouse anti-PSD-95 (1:1000; catalog #MA1-045, Thermo Fisher Scientific).
Article Title: KIF21B binds Myosin Va for Spine Entry and regulates Actin Dynamics to control Homeostatic Synaptic Downscaling
Article Snippet: Rabbit anti-KIF21B (1:1,000; Sigma-Aldrich, Taufkirchen, Germany), Mouse anti-Homer1 (1:1,000; Synaptic Systems, Göttingen, Germany), mouse anti-GluA2 extracellular (1:1,000; Millipore, Darmstadt, Germany), rabbit anti-MyoVa (1:1,000; Sigma-Aldrich, Taufkirchen, Germany), rabbit anti-MyoVI (1:1,000; Sigma-Aldrich, Taufkirchen, Germany), mouse anti-PSD95 (1:100; Thermo Fisher Scientific, Dreieich, Germany), goat anti-Shank1-3 (1:1,000; Abcam, Cambridge, UK), guinea pig anti-Synaptophysin (1:1,000; Synaptic Systems, Göttingen, Germany), rabbit anti-KIF21A (1:1,000; Dianova, Hamburg, Germany).
Article Title: N-glycoproteomics of brain synapses and synaptic vesicles.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies SV2 mAb DSHB SV2 (RRID:AB_2315387) Syt1 mAb DSHB mAb 48 (RRID:AB_2199314) Guinea pig anti-synaptophysin Synaptic Systems 104 211 (RRID:AB_1210382) Goat anti-mouse HRP-conjugated secondary Ab Bio-Rad 1706516 Goat anti-guinea pig HRP-conjugated secondary Ab Thermo Fisher A18769 Chemicals, peptides, and recombinant proteins Protein G Sepharose fast flow Cytiva 17061801 Dynabeads M-270 epoxy Thermo Fisher 14302D cOmplete mini, EDTA-free Sigma (Roche) 04693159001 Dynabeads M-270 carboxylic acid Thermo Fisher 14305D Trypsin Promega V5111 SOLA SAX 10 mg cartridge Thermo Fisher 60109–003 PNGase F NEB P0708 Procainamide Sigma SML2088 Sodium cyanoborohydride, 5 M in 1 M NaOH Sigma 296945 OASIS HLB 30 mg cartridge Waters WAT094225 a(1–2,3,6) mannosidase NEB P0768 a(1–3,4) fucosidase NEB P0769 a(1–2) fucosidase NEB P0724 a(1–2,4,6) fucosidase O NEB P0749 b(1–3,4) galactosidase NEB P0746 b-GlcNAcase S NEB P0744 Deposited data LC-MS raw data deposited at MassIVE This paper https://doi.org/10.25345/C5TB0Z526 Experimental models: Organisms/strains Mouse: C57B6/J Jackson Laboratory 000664 (RRID:IMSR_JAX:000664) Software and algorithms FragPipe Nesvizhskii Lab v. 17.1 Agilent ChemStation Agilent LTS 01.11 R/Rstudio CRAN/Posit v. 2021.09.0 R scripts used in this paper This paper https://doi.org/10.5281/zenodo.7659070 The Gene Ontology resource Geneontology.org v. 2023-01-01 Prism GraphPad v. 9.3.1
Article Title: High-Content Screening of Synaptic Density Modulators in Primary Neuronal Cultures.
Article Snippet: See the T erm s and C onditions (https://onlinelibrary.w iley.com /term s-and-conditions) on W iley O nline L ibrary for rules of use; O A articles are governed by the applicable C reative C om m ons L icense 2.5% (w/v) bovine serum albumin (BSA) in DPBS with 0.1% (v/v) Triton X-100 Primary antibodies: Chicken anti-Homer1 (Synaptic Systems, cat. no. 160006) Guinea pig anti-Synaptophysin (Synaptic Systems, cat. no. 101004) Mouse anti-MAP2 (Synaptic Systems, cat. no. 188011) 1× DPBS Secondary antibodies: Donkey anti-chicken Alexa 488 (Jackson ImmunoResearch, cat. no. 703-545-155) Goat anti-guinea pig Alexa 555 (Life Technologies, cat. no. A21435) Donkey anti-mouse Alexa 647 (Jackson ImmunoResearch, cat. no. 715-605-151) 16-channel pipet (Finnpipette F1; Thermo Scientific, cat. no. 4661090N) Aluminum sealing tape (Dutscher, cat. no. 106570, or similar) PlateHUB rotating plate-storage carousel (Agilent, model G5500-23447) Plate washer associated with liquid handler (BioTek, model EL406) Wash_Primary.pro and Wash_Secondary.pro programs (see Supporting Information) VWorks automation control software (Agilent) Aspirate.LHC and Aspirate-Dispense.LHC subroutines (see Supporting Information) Direct Drive Robot (Agilent) NOTE: Use sterile pipet tips with filters (Finntip 50; Thermo Scientific, cat. no. 94052060).
Staining:Article Title: Deciphering the nanoscale architecture of presynaptic actin using a micropatterned presynapse-on-glass model
Article Snippet: Primary antibodies used are chicken anti-map2 (1:1,000, ab5392, RRID:AB_2138153; Abcam), mouse anti-ß2-spectrin (1:100, clone 42/aa 2101-2189, #612563, RRID:AB_399854; BD Bioscience), guinea pig anti-synaptophysin (1:400, 101 004, RRID:AB_1210382; Synaptic Systems), mouse anti-synaptotag-min1 (1:600, clone 604.2/aa 1-12, 105 311, RRID:AB_993036; Synaptic Systems), rabbit anti-adducin alpha (1:100, ab40760, RRID:AB_722627; Abcam), mouse anti-bassoon (1:200, clone SAP7F407, ab82958, RRID:AB_1860018; Abcam), rabbit anti-GFP (1:750, ab290, RRID:AB_303395; Abcam), mouse anti-GFP (1:750, clone 9F9.F9, ab1218, RRID:AB_298911; Abcam), rabbit anti-munc13-1 (1:500, 126 103, RRID:AB_887733; Synaptic Systems).
Article Title: Rapid Aging in the Perforant Path Projections to the Rodent Dentate Gyrus
Article Snippet: Primary antisera included rabbit anti-phosphorylated FAK (1:1000; catalog #ab39967, Abcam), anti-GluN2A (1:25,000; catalog #AB1555, EMD-Millipore), and anti-TrkB (1:2000; catalog #07–225, EMD-Millipore); guinea pig anti-synaptophysin (1:2500; catalog #101004, SySy Systems); and mouse anti-PSD-95 (1:1000; catalog #MA1-045, Thermo Fisher Scientific).
Article Title: Disrupted presynaptic nectin1-based neuronal adhesion in the entorhinal-hippocampal circuit contributes to early-life stress-induced memory deficits
Article Snippet: Primary rabbit anti-nectin1 (1:1000, sc-28639, Santa Cruz Biotechnology, Santa Cruz, CA, USA), rabbit anti-nectin3 (1:1000, ab63931, Abcam, Cambridge, UK), and guinea pig anti-synaptophysin (1:500, 101004, Synaptic Systems, Göttingen, Germany) antibodies were used.
Article Title: Rapid Aging in the Perforant Path Projections to the Rodent Dentate Gyrus
Article Snippet: Primary antisera included rabbit antiphosphorylated FAK (1:1000; catalog #ab39967, Abcam), anti-GluN2A (1:25,000; catalog #AB1555, EMD-Millipore), and anti-TrkB (1:2000; catalog #07–225, EMD-Millipore); guinea pig anti-synaptophysin (1:2500; catalog #101004, SySy Systems); and mouse anti-PSD-95 (1:1000; catalog #MA1-045, Thermo Fisher Scientific).
Article Title: KIF21B binds Myosin Va for Spine Entry and regulates Actin Dynamics to control Homeostatic Synaptic Downscaling
Article Snippet: Rabbit anti-KIF21B (1:1,000; Sigma-Aldrich, Taufkirchen, Germany), Mouse anti-Homer1 (1:1,000; Synaptic Systems, Göttingen, Germany), mouse anti-GluA2 extracellular (1:1,000; Millipore, Darmstadt, Germany), rabbit anti-MyoVa (1:1,000; Sigma-Aldrich, Taufkirchen, Germany), rabbit anti-MyoVI (1:1,000; Sigma-Aldrich, Taufkirchen, Germany), mouse anti-PSD95 (1:100; Thermo Fisher Scientific, Dreieich, Germany), goat anti-Shank1-3 (1:1,000; Abcam, Cambridge, UK), guinea pig anti-Synaptophysin (1:1,000; Synaptic Systems, Göttingen, Germany), rabbit anti-KIF21A (1:1,000; Dianova, Hamburg, Germany).
Article Title: N-glycoproteomics of brain synapses and synaptic vesicles.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies SV2 mAb DSHB SV2 (RRID:AB_2315387) Syt1 mAb DSHB mAb 48 (RRID:AB_2199314) Guinea pig anti-synaptophysin Synaptic Systems 104 211 (RRID:AB_1210382) Goat anti-mouse HRP-conjugated secondary Ab Bio-Rad 1706516 Goat anti-guinea pig HRP-conjugated secondary Ab Thermo Fisher A18769 Chemicals, peptides, and recombinant proteins Protein G Sepharose fast flow Cytiva 17061801 Dynabeads M-270 epoxy Thermo Fisher 14302D cOmplete mini, EDTA-free Sigma (Roche) 04693159001 Dynabeads M-270 carboxylic acid Thermo Fisher 14305D Trypsin Promega V5111 SOLA SAX 10 mg cartridge Thermo Fisher 60109–003 PNGase F NEB P0708 Procainamide Sigma SML2088 Sodium cyanoborohydride, 5 M in 1 M NaOH Sigma 296945 OASIS HLB 30 mg cartridge Waters WAT094225 a(1–2,3,6) mannosidase NEB P0768 a(1–3,4) fucosidase NEB P0769 a(1–2) fucosidase NEB P0724 a(1–2,4,6) fucosidase O NEB P0749 b(1–3,4) galactosidase NEB P0746 b-GlcNAcase S NEB P0744 Deposited data LC-MS raw data deposited at MassIVE This paper https://doi.org/10.25345/C5TB0Z526 Experimental models: Organisms/strains Mouse: C57B6/J Jackson Laboratory 000664 (RRID:IMSR_JAX:000664) Software and algorithms FragPipe Nesvizhskii Lab v. 17.1 Agilent ChemStation Agilent LTS 01.11 R/Rstudio CRAN/Posit v. 2021.09.0 R scripts used in this paper This paper https://doi.org/10.5281/zenodo.7659070 The Gene Ontology resource Geneontology.org v. 2023-01-01 Prism GraphPad v. 9.3.1
Article Title: High-Content Screening of Synaptic Density Modulators in Primary Neuronal Cultures.
Article Snippet: See the T erm s and C onditions (https://onlinelibrary.w iley.com /term s-and-conditions) on W iley O nline L ibrary for rules of use; O A articles are governed by the applicable C reative C om m ons L icense 2.5% (w/v) bovine serum albumin (BSA) in DPBS with 0.1% (v/v) Triton X-100 Primary antibodies: Chicken anti-Homer1 (Synaptic Systems, cat. no. 160006) Guinea pig anti-Synaptophysin (Synaptic Systems, cat. no. 101004) Mouse anti-MAP2 (Synaptic Systems, cat. no. 188011) 1× DPBS Secondary antibodies: Donkey anti-chicken Alexa 488 (Jackson ImmunoResearch, cat. no. 703-545-155) Goat anti-guinea pig Alexa 555 (Life Technologies, cat. no. A21435) Donkey anti-mouse Alexa 647 (Jackson ImmunoResearch, cat. no. 715-605-151) 16-channel pipet (Finnpipette F1; Thermo Scientific, cat. no. 4661090N) Aluminum sealing tape (Dutscher, cat. no. 106570, or similar) PlateHUB rotating plate-storage carousel (Agilent, model G5500-23447) Plate washer associated with liquid handler (BioTek, model EL406) Wash_Primary.pro and Wash_Secondary.pro programs (see Supporting Information) VWorks automation control software (Agilent) Aspirate.LHC and Aspirate-Dispense.LHC subroutines (see Supporting Information) Direct Drive Robot (Agilent) NOTE: Use sterile pipet tips with filters (Finntip 50; Thermo Scientific, cat. no. 94052060).
Software:Article Title: Deciphering the nanoscale architecture of presynaptic actin using a micropatterned presynapse-on-glass model
Article Snippet: Primary antibodies used are chicken anti-map2 (1:1,000, ab5392, RRID:AB_2138153; Abcam), mouse anti-ß2-spectrin (1:100, clone 42/aa 2101-2189, #612563, RRID:AB_399854; BD Bioscience), guinea pig anti-synaptophysin (1:400, 101 004, RRID:AB_1210382; Synaptic Systems), mouse anti-synaptotag-min1 (1:600, clone 604.2/aa 1-12, 105 311, RRID:AB_993036; Synaptic Systems), rabbit anti-adducin alpha (1:100, ab40760, RRID:AB_722627; Abcam), mouse anti-bassoon (1:200, clone SAP7F407, ab82958, RRID:AB_1860018; Abcam), rabbit anti-GFP (1:750, ab290, RRID:AB_303395; Abcam), mouse anti-GFP (1:750, clone 9F9.F9, ab1218, RRID:AB_298911; Abcam), rabbit anti-munc13-1 (1:500, 126 103, RRID:AB_887733; Synaptic Systems).
Article Title: Rapid Aging in the Perforant Path Projections to the Rodent Dentate Gyrus
Article Snippet: Primary antisera included rabbit anti-phosphorylated FAK (1:1000; catalog #ab39967, Abcam), anti-GluN2A (1:25,000; catalog #AB1555, EMD-Millipore), and anti-TrkB (1:2000; catalog #07–225, EMD-Millipore); guinea pig anti-synaptophysin (1:2500; catalog #101004, SySy Systems); and mouse anti-PSD-95 (1:1000; catalog #MA1-045, Thermo Fisher Scientific).
Article Title: Disrupted presynaptic nectin1-based neuronal adhesion in the entorhinal-hippocampal circuit contributes to early-life stress-induced memory deficits
Article Snippet: Primary rabbit anti-nectin1 (1:1000, sc-28639, Santa Cruz Biotechnology, Santa Cruz, CA, USA), rabbit anti-nectin3 (1:1000, ab63931, Abcam, Cambridge, UK), and guinea pig anti-synaptophysin (1:500, 101004, Synaptic Systems, Göttingen, Germany) antibodies were used.
Article Title: Rapid Aging in the Perforant Path Projections to the Rodent Dentate Gyrus
Article Snippet: Primary antisera included rabbit antiphosphorylated FAK (1:1000; catalog #ab39967, Abcam), anti-GluN2A (1:25,000; catalog #AB1555, EMD-Millipore), and anti-TrkB (1:2000; catalog #07–225, EMD-Millipore); guinea pig anti-synaptophysin (1:2500; catalog #101004, SySy Systems); and mouse anti-PSD-95 (1:1000; catalog #MA1-045, Thermo Fisher Scientific).
Article Title: KIF21B binds Myosin Va for Spine Entry and regulates Actin Dynamics to control Homeostatic Synaptic Downscaling
Article Snippet: Rabbit anti-KIF21B (1:1,000; Sigma-Aldrich, Taufkirchen, Germany), Mouse anti-Homer1 (1:1,000; Synaptic Systems, Göttingen, Germany), mouse anti-GluA2 extracellular (1:1,000; Millipore, Darmstadt, Germany), rabbit anti-MyoVa (1:1,000; Sigma-Aldrich, Taufkirchen, Germany), rabbit anti-MyoVI (1:1,000; Sigma-Aldrich, Taufkirchen, Germany), mouse anti-PSD95 (1:100; Thermo Fisher Scientific, Dreieich, Germany), goat anti-Shank1-3 (1:1,000; Abcam, Cambridge, UK), guinea pig anti-Synaptophysin (1:1,000; Synaptic Systems, Göttingen, Germany), rabbit anti-KIF21A (1:1,000; Dianova, Hamburg, Germany).
Article Title: N-glycoproteomics of brain synapses and synaptic vesicles.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies SV2 mAb DSHB SV2 (RRID:AB_2315387) Syt1 mAb DSHB mAb 48 (RRID:AB_2199314) Guinea pig anti-synaptophysin Synaptic Systems 104 211 (RRID:AB_1210382) Goat anti-mouse HRP-conjugated secondary Ab Bio-Rad 1706516 Goat anti-guinea pig HRP-conjugated secondary Ab Thermo Fisher A18769 Chemicals, peptides, and recombinant proteins Protein G Sepharose fast flow Cytiva 17061801 Dynabeads M-270 epoxy Thermo Fisher 14302D cOmplete mini, EDTA-free Sigma (Roche) 04693159001 Dynabeads M-270 carboxylic acid Thermo Fisher 14305D Trypsin Promega V5111 SOLA SAX 10 mg cartridge Thermo Fisher 60109–003 PNGase F NEB P0708 Procainamide Sigma SML2088 Sodium cyanoborohydride, 5 M in 1 M NaOH Sigma 296945 OASIS HLB 30 mg cartridge Waters WAT094225 a(1–2,3,6) mannosidase NEB P0768 a(1–3,4) fucosidase NEB P0769 a(1–2) fucosidase NEB P0724 a(1–2,4,6) fucosidase O NEB P0749 b(1–3,4) galactosidase NEB P0746 b-GlcNAcase S NEB P0744 Deposited data LC-MS raw data deposited at MassIVE This paper https://doi.org/10.25345/C5TB0Z526 Experimental models: Organisms/strains Mouse: C57B6/J Jackson Laboratory 000664 (RRID:IMSR_JAX:000664) Software and algorithms FragPipe Nesvizhskii Lab v. 17.1 Agilent ChemStation Agilent LTS 01.11 R/Rstudio CRAN/Posit v. 2021.09.0 R scripts used in this paper This paper https://doi.org/10.5281/zenodo.7659070 The Gene Ontology resource Geneontology.org v. 2023-01-01 Prism GraphPad v. 9.3.1
Article Title: High-Content Screening of Synaptic Density Modulators in Primary Neuronal Cultures.
Article Snippet: See the T erm s and C onditions (https://onlinelibrary.w iley.com /term s-and-conditions) on W iley O nline L ibrary for rules of use; O A articles are governed by the applicable C reative C om m ons L icense 2.5% (w/v) bovine serum albumin (BSA) in DPBS with 0.1% (v/v) Triton X-100 Primary antibodies: Chicken anti-Homer1 (Synaptic Systems, cat. no. 160006) Guinea pig anti-Synaptophysin (Synaptic Systems, cat. no. 101004) Mouse anti-MAP2 (Synaptic Systems, cat. no. 188011) 1× DPBS Secondary antibodies: Donkey anti-chicken Alexa 488 (Jackson ImmunoResearch, cat. no. 703-545-155) Goat anti-guinea pig Alexa 555 (Life Technologies, cat. no. A21435) Donkey anti-mouse Alexa 647 (Jackson ImmunoResearch, cat. no. 715-605-151) 16-channel pipet (Finnpipette F1; Thermo Scientific, cat. no. 4661090N) Aluminum sealing tape (Dutscher, cat. no. 106570, or similar) PlateHUB rotating plate-storage carousel (Agilent, model G5500-23447) Plate washer associated with liquid handler (BioTek, model EL406) Wash_Primary.pro and Wash_Secondary.pro programs (see Supporting Information) VWorks automation control software (Agilent) Aspirate.LHC and Aspirate-Dispense.LHC subroutines (see Supporting Information) Direct Drive Robot (Agilent) NOTE: Use sterile pipet tips with filters (Finntip 50; Thermo Scientific, cat. no. 94052060).
Sterility:Article Title: Deciphering the nanoscale architecture of presynaptic actin using a micropatterned presynapse-on-glass model
Article Snippet: Primary antibodies used are chicken anti-map2 (1:1,000, ab5392, RRID:AB_2138153; Abcam), mouse anti-ß2-spectrin (1:100, clone 42/aa 2101-2189, #612563, RRID:AB_399854; BD Bioscience), guinea pig anti-synaptophysin (1:400, 101 004, RRID:AB_1210382; Synaptic Systems), mouse anti-synaptotag-min1 (1:600, clone 604.2/aa 1-12, 105 311, RRID:AB_993036; Synaptic Systems), rabbit anti-adducin alpha (1:100, ab40760, RRID:AB_722627; Abcam), mouse anti-bassoon (1:200, clone SAP7F407, ab82958, RRID:AB_1860018; Abcam), rabbit anti-GFP (1:750, ab290, RRID:AB_303395; Abcam), mouse anti-GFP (1:750, clone 9F9.F9, ab1218, RRID:AB_298911; Abcam), rabbit anti-munc13-1 (1:500, 126 103, RRID:AB_887733; Synaptic Systems).
Article Title: Rapid Aging in the Perforant Path Projections to the Rodent Dentate Gyrus
Article Snippet: Primary antisera included rabbit anti-phosphorylated FAK (1:1000; catalog #ab39967, Abcam), anti-GluN2A (1:25,000; catalog #AB1555, EMD-Millipore), and anti-TrkB (1:2000; catalog #07–225, EMD-Millipore); guinea pig anti-synaptophysin (1:2500; catalog #101004, SySy Systems); and mouse anti-PSD-95 (1:1000; catalog #MA1-045, Thermo Fisher Scientific).
Article Title: Disrupted presynaptic nectin1-based neuronal adhesion in the entorhinal-hippocampal circuit contributes to early-life stress-induced memory deficits
Article Snippet: Primary rabbit anti-nectin1 (1:1000, sc-28639, Santa Cruz Biotechnology, Santa Cruz, CA, USA), rabbit anti-nectin3 (1:1000, ab63931, Abcam, Cambridge, UK), and guinea pig anti-synaptophysin (1:500, 101004, Synaptic Systems, Göttingen, Germany) antibodies were used.
Article Title: Rapid Aging in the Perforant Path Projections to the Rodent Dentate Gyrus
Article Snippet: Primary antisera included rabbit antiphosphorylated FAK (1:1000; catalog #ab39967, Abcam), anti-GluN2A (1:25,000; catalog #AB1555, EMD-Millipore), and anti-TrkB (1:2000; catalog #07–225, EMD-Millipore); guinea pig anti-synaptophysin (1:2500; catalog #101004, SySy Systems); and mouse anti-PSD-95 (1:1000; catalog #MA1-045, Thermo Fisher Scientific).
Article Title: KIF21B binds Myosin Va for Spine Entry and regulates Actin Dynamics to control Homeostatic Synaptic Downscaling
Article Snippet: Rabbit anti-KIF21B (1:1,000; Sigma-Aldrich, Taufkirchen, Germany), Mouse anti-Homer1 (1:1,000; Synaptic Systems, Göttingen, Germany), mouse anti-GluA2 extracellular (1:1,000; Millipore, Darmstadt, Germany), rabbit anti-MyoVa (1:1,000; Sigma-Aldrich, Taufkirchen, Germany), rabbit anti-MyoVI (1:1,000; Sigma-Aldrich, Taufkirchen, Germany), mouse anti-PSD95 (1:100; Thermo Fisher Scientific, Dreieich, Germany), goat anti-Shank1-3 (1:1,000; Abcam, Cambridge, UK), guinea pig anti-Synaptophysin (1:1,000; Synaptic Systems, Göttingen, Germany), rabbit anti-KIF21A (1:1,000; Dianova, Hamburg, Germany).
Article Title: N-glycoproteomics of brain synapses and synaptic vesicles.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies SV2 mAb DSHB SV2 (RRID:AB_2315387) Syt1 mAb DSHB mAb 48 (RRID:AB_2199314) Guinea pig anti-synaptophysin Synaptic Systems 104 211 (RRID:AB_1210382) Goat anti-mouse HRP-conjugated secondary Ab Bio-Rad 1706516 Goat anti-guinea pig HRP-conjugated secondary Ab Thermo Fisher A18769 Chemicals, peptides, and recombinant proteins Protein G Sepharose fast flow Cytiva 17061801 Dynabeads M-270 epoxy Thermo Fisher 14302D cOmplete mini, EDTA-free Sigma (Roche) 04693159001 Dynabeads M-270 carboxylic acid Thermo Fisher 14305D Trypsin Promega V5111 SOLA SAX 10 mg cartridge Thermo Fisher 60109–003 PNGase F NEB P0708 Procainamide Sigma SML2088 Sodium cyanoborohydride, 5 M in 1 M NaOH Sigma 296945 OASIS HLB 30 mg cartridge Waters WAT094225 a(1–2,3,6) mannosidase NEB P0768 a(1–3,4) fucosidase NEB P0769 a(1–2) fucosidase NEB P0724 a(1–2,4,6) fucosidase O NEB P0749 b(1–3,4) galactosidase NEB P0746 b-GlcNAcase S NEB P0744 Deposited data LC-MS raw data deposited at MassIVE This paper https://doi.org/10.25345/C5TB0Z526 Experimental models: Organisms/strains Mouse: C57B6/J Jackson Laboratory 000664 (RRID:IMSR_JAX:000664) Software and algorithms FragPipe Nesvizhskii Lab v. 17.1 Agilent ChemStation Agilent LTS 01.11 R/Rstudio CRAN/Posit v. 2021.09.0 R scripts used in this paper This paper https://doi.org/10.5281/zenodo.7659070 The Gene Ontology resource Geneontology.org v. 2023-01-01 Prism GraphPad v. 9.3.1
Article Title: High-Content Screening of Synaptic Density Modulators in Primary Neuronal Cultures.
Article Snippet: See the T erm s and C onditions (https://onlinelibrary.w iley.com /term s-and-conditions) on W iley O nline L ibrary for rules of use; O A articles are governed by the applicable C reative C om m ons L icense 2.5% (w/v) bovine serum albumin (BSA) in DPBS with 0.1% (v/v) Triton X-100 Primary antibodies: Chicken anti-Homer1 (Synaptic Systems, cat. no. 160006) Guinea pig anti-Synaptophysin (Synaptic Systems, cat. no. 101004) Mouse anti-MAP2 (Synaptic Systems, cat. no. 188011) 1× DPBS Secondary antibodies: Donkey anti-chicken Alexa 488 (Jackson ImmunoResearch, cat. no. 703-545-155) Goat anti-guinea pig Alexa 555 (Life Technologies, cat. no. A21435) Donkey anti-mouse Alexa 647 (Jackson ImmunoResearch, cat. no. 715-605-151) 16-channel pipet (Finnpipette F1; Thermo Scientific, cat. no. 4661090N) Aluminum sealing tape (Dutscher, cat. no. 106570, or similar) PlateHUB rotating plate-storage carousel (Agilent, model G5500-23447) Plate washer associated with liquid handler (BioTek, model EL406) Wash_Primary.pro and Wash_Secondary.pro programs (see Supporting Information) VWorks automation control software (Agilent) Aspirate.LHC and Aspirate-Dispense.LHC subroutines (see Supporting Information) Direct Drive Robot (Agilent) NOTE: Use sterile pipet tips with filters (Finntip 50; Thermo Scientific, cat. no. 94052060).
Recombinant:Article Title: Deciphering the nanoscale architecture of presynaptic actin using a micropatterned presynapse-on-glass model
Article Snippet: Primary antibodies used are chicken anti-map2 (1:1,000, ab5392, RRID:AB_2138153; Abcam), mouse anti-ß2-spectrin (1:100, clone 42/aa 2101-2189, #612563, RRID:AB_399854; BD Bioscience), guinea pig anti-synaptophysin (1:400, 101 004, RRID:AB_1210382; Synaptic Systems), mouse anti-synaptotag-min1 (1:600, clone 604.2/aa 1-12, 105 311, RRID:AB_993036; Synaptic Systems), rabbit anti-adducin alpha (1:100, ab40760, RRID:AB_722627; Abcam), mouse anti-bassoon (1:200, clone SAP7F407, ab82958, RRID:AB_1860018; Abcam), rabbit anti-GFP (1:750, ab290, RRID:AB_303395; Abcam), mouse anti-GFP (1:750, clone 9F9.F9, ab1218, RRID:AB_298911; Abcam), rabbit anti-munc13-1 (1:500, 126 103, RRID:AB_887733; Synaptic Systems).
Article Title: Rapid Aging in the Perforant Path Projections to the Rodent Dentate Gyrus
Article Snippet: Primary antisera included rabbit anti-phosphorylated FAK (1:1000; catalog #ab39967, Abcam), anti-GluN2A (1:25,000; catalog #AB1555, EMD-Millipore), and anti-TrkB (1:2000; catalog #07–225, EMD-Millipore); guinea pig anti-synaptophysin (1:2500; catalog #101004, SySy Systems); and mouse anti-PSD-95 (1:1000; catalog #MA1-045, Thermo Fisher Scientific).
Article Title: Disrupted presynaptic nectin1-based neuronal adhesion in the entorhinal-hippocampal circuit contributes to early-life stress-induced memory deficits
Article Snippet: Primary rabbit anti-nectin1 (1:1000, sc-28639, Santa Cruz Biotechnology, Santa Cruz, CA, USA), rabbit anti-nectin3 (1:1000, ab63931, Abcam, Cambridge, UK), and guinea pig anti-synaptophysin (1:500, 101004, Synaptic Systems, Göttingen, Germany) antibodies were used.
Article Title: Rapid Aging in the Perforant Path Projections to the Rodent Dentate Gyrus
Article Snippet: Primary antisera included rabbit antiphosphorylated FAK (1:1000; catalog #ab39967, Abcam), anti-GluN2A (1:25,000; catalog #AB1555, EMD-Millipore), and anti-TrkB (1:2000; catalog #07–225, EMD-Millipore); guinea pig anti-synaptophysin (1:2500; catalog #101004, SySy Systems); and mouse anti-PSD-95 (1:1000; catalog #MA1-045, Thermo Fisher Scientific).
Article Title: KIF21B binds Myosin Va for Spine Entry and regulates Actin Dynamics to control Homeostatic Synaptic Downscaling
Article Snippet: Rabbit anti-KIF21B (1:1,000; Sigma-Aldrich, Taufkirchen, Germany), Mouse anti-Homer1 (1:1,000; Synaptic Systems, Göttingen, Germany), mouse anti-GluA2 extracellular (1:1,000; Millipore, Darmstadt, Germany), rabbit anti-MyoVa (1:1,000; Sigma-Aldrich, Taufkirchen, Germany), rabbit anti-MyoVI (1:1,000; Sigma-Aldrich, Taufkirchen, Germany), mouse anti-PSD95 (1:100; Thermo Fisher Scientific, Dreieich, Germany), goat anti-Shank1-3 (1:1,000; Abcam, Cambridge, UK), guinea pig anti-Synaptophysin (1:1,000; Synaptic Systems, Göttingen, Germany), rabbit anti-KIF21A (1:1,000; Dianova, Hamburg, Germany).
Article Title: N-glycoproteomics of brain synapses and synaptic vesicles.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies SV2 mAb DSHB SV2 (RRID:AB_2315387) Syt1 mAb DSHB mAb 48 (RRID:AB_2199314) Guinea pig anti-synaptophysin Synaptic Systems 104 211 (RRID:AB_1210382) Goat anti-mouse HRP-conjugated secondary Ab Bio-Rad 1706516 Goat anti-guinea pig HRP-conjugated secondary Ab Thermo Fisher A18769 Chemicals, peptides, and recombinant proteins Protein G Sepharose fast flow Cytiva 17061801 Dynabeads M-270 epoxy Thermo Fisher 14302D cOmplete mini, EDTA-free Sigma (Roche) 04693159001 Dynabeads M-270 carboxylic acid Thermo Fisher 14305D Trypsin Promega V5111 SOLA SAX 10 mg cartridge Thermo Fisher 60109–003 PNGase F NEB P0708 Procainamide Sigma SML2088 Sodium cyanoborohydride, 5 M in 1 M NaOH Sigma 296945 OASIS HLB 30 mg cartridge Waters WAT094225 a(1–2,3,6) mannosidase NEB P0768 a(1–3,4) fucosidase NEB P0769 a(1–2) fucosidase NEB P0724 a(1–2,4,6) fucosidase O NEB P0749 b(1–3,4) galactosidase NEB P0746 b-GlcNAcase S NEB P0744 Deposited data LC-MS raw data deposited at MassIVE This paper https://doi.org/10.25345/C5TB0Z526 Experimental models: Organisms/strains Mouse: C57B6/J Jackson Laboratory 000664 (RRID:IMSR_JAX:000664) Software and algorithms FragPipe Nesvizhskii Lab v. 17.1 Agilent ChemStation Agilent LTS 01.11 R/Rstudio CRAN/Posit v. 2021.09.0 R scripts used in this paper This paper https://doi.org/10.5281/zenodo.7659070 The Gene Ontology resource Geneontology.org v. 2023-01-01 Prism GraphPad v. 9.3.1
Article Title: High-Content Screening of Synaptic Density Modulators in Primary Neuronal Cultures.
Article Snippet: See the T erm s and C onditions (https://onlinelibrary.w iley.com /term s-and-conditions) on W iley O nline L ibrary for rules of use; O A articles are governed by the applicable C reative C om m ons L icense 2.5% (w/v) bovine serum albumin (BSA) in DPBS with 0.1% (v/v) Triton X-100 Primary antibodies: Chicken anti-Homer1 (Synaptic Systems, cat. no. 160006) Guinea pig anti-Synaptophysin (Synaptic Systems, cat. no. 101004) Mouse anti-MAP2 (Synaptic Systems, cat. no. 188011) 1× DPBS Secondary antibodies: Donkey anti-chicken Alexa 488 (Jackson ImmunoResearch, cat. no. 703-545-155) Goat anti-guinea pig Alexa 555 (Life Technologies, cat. no. A21435) Donkey anti-mouse Alexa 647 (Jackson ImmunoResearch, cat. no. 715-605-151) 16-channel pipet (Finnpipette F1; Thermo Scientific, cat. no. 4661090N) Aluminum sealing tape (Dutscher, cat. no. 106570, or similar) PlateHUB rotating plate-storage carousel (Agilent, model G5500-23447) Plate washer associated with liquid handler (BioTek, model EL406) Wash_Primary.pro and Wash_Secondary.pro programs (see Supporting Information) VWorks automation control software (Agilent) Aspirate.LHC and Aspirate-Dispense.LHC subroutines (see Supporting Information) Direct Drive Robot (Agilent) NOTE: Use sterile pipet tips with filters (Finntip 50; Thermo Scientific, cat. no. 94052060).
Liquid Chromatography with Mass Spectroscopy:Article Title: Deciphering the nanoscale architecture of presynaptic actin using a micropatterned presynapse-on-glass model
Article Snippet: Primary antibodies used are chicken anti-map2 (1:1,000, ab5392, RRID:AB_2138153; Abcam), mouse anti-ß2-spectrin (1:100, clone 42/aa 2101-2189, #612563, RRID:AB_399854; BD Bioscience), guinea pig anti-synaptophysin (1:400, 101 004, RRID:AB_1210382; Synaptic Systems), mouse anti-synaptotag-min1 (1:600, clone 604.2/aa 1-12, 105 311, RRID:AB_993036; Synaptic Systems), rabbit anti-adducin alpha (1:100, ab40760, RRID:AB_722627; Abcam), mouse anti-bassoon (1:200, clone SAP7F407, ab82958, RRID:AB_1860018; Abcam), rabbit anti-GFP (1:750, ab290, RRID:AB_303395; Abcam), mouse anti-GFP (1:750, clone 9F9.F9, ab1218, RRID:AB_298911; Abcam), rabbit anti-munc13-1 (1:500, 126 103, RRID:AB_887733; Synaptic Systems).
Article Title: Rapid Aging in the Perforant Path Projections to the Rodent Dentate Gyrus
Article Snippet: Primary antisera included rabbit anti-phosphorylated FAK (1:1000; catalog #ab39967, Abcam), anti-GluN2A (1:25,000; catalog #AB1555, EMD-Millipore), and anti-TrkB (1:2000; catalog #07–225, EMD-Millipore); guinea pig anti-synaptophysin (1:2500; catalog #101004, SySy Systems); and mouse anti-PSD-95 (1:1000; catalog #MA1-045, Thermo Fisher Scientific).
Article Title: Disrupted presynaptic nectin1-based neuronal adhesion in the entorhinal-hippocampal circuit contributes to early-life stress-induced memory deficits
Article Snippet: Primary rabbit anti-nectin1 (1:1000, sc-28639, Santa Cruz Biotechnology, Santa Cruz, CA, USA), rabbit anti-nectin3 (1:1000, ab63931, Abcam, Cambridge, UK), and guinea pig anti-synaptophysin (1:500, 101004, Synaptic Systems, Göttingen, Germany) antibodies were used.
Article Title: Rapid Aging in the Perforant Path Projections to the Rodent Dentate Gyrus
Article Snippet: Primary antisera included rabbit antiphosphorylated FAK (1:1000; catalog #ab39967, Abcam), anti-GluN2A (1:25,000; catalog #AB1555, EMD-Millipore), and anti-TrkB (1:2000; catalog #07–225, EMD-Millipore); guinea pig anti-synaptophysin (1:2500; catalog #101004, SySy Systems); and mouse anti-PSD-95 (1:1000; catalog #MA1-045, Thermo Fisher Scientific).
Article Title: KIF21B binds Myosin Va for Spine Entry and regulates Actin Dynamics to control Homeostatic Synaptic Downscaling
Article Snippet: Rabbit anti-KIF21B (1:1,000; Sigma-Aldrich, Taufkirchen, Germany), Mouse anti-Homer1 (1:1,000; Synaptic Systems, Göttingen, Germany), mouse anti-GluA2 extracellular (1:1,000; Millipore, Darmstadt, Germany), rabbit anti-MyoVa (1:1,000; Sigma-Aldrich, Taufkirchen, Germany), rabbit anti-MyoVI (1:1,000; Sigma-Aldrich, Taufkirchen, Germany), mouse anti-PSD95 (1:100; Thermo Fisher Scientific, Dreieich, Germany), goat anti-Shank1-3 (1:1,000; Abcam, Cambridge, UK), guinea pig anti-Synaptophysin (1:1,000; Synaptic Systems, Göttingen, Germany), rabbit anti-KIF21A (1:1,000; Dianova, Hamburg, Germany).
Article Title: N-glycoproteomics of brain synapses and synaptic vesicles.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies SV2 mAb DSHB SV2 (RRID:AB_2315387) Syt1 mAb DSHB mAb 48 (RRID:AB_2199314) Guinea pig anti-synaptophysin Synaptic Systems 104 211 (RRID:AB_1210382) Goat anti-mouse HRP-conjugated secondary Ab Bio-Rad 1706516 Goat anti-guinea pig HRP-conjugated secondary Ab Thermo Fisher A18769 Chemicals, peptides, and recombinant proteins Protein G Sepharose fast flow Cytiva 17061801 Dynabeads M-270 epoxy Thermo Fisher 14302D cOmplete mini, EDTA-free Sigma (Roche) 04693159001 Dynabeads M-270 carboxylic acid Thermo Fisher 14305D Trypsin Promega V5111 SOLA SAX 10 mg cartridge Thermo Fisher 60109–003 PNGase F NEB P0708 Procainamide Sigma SML2088 Sodium cyanoborohydride, 5 M in 1 M NaOH Sigma 296945 OASIS HLB 30 mg cartridge Waters WAT094225 a(1–2,3,6) mannosidase NEB P0768 a(1–3,4) fucosidase NEB P0769 a(1–2) fucosidase NEB P0724 a(1–2,4,6) fucosidase O NEB P0749 b(1–3,4) galactosidase NEB P0746 b-GlcNAcase S NEB P0744 Deposited data LC-MS raw data deposited at MassIVE This paper https://doi.org/10.25345/C5TB0Z526 Experimental models: Organisms/strains Mouse: C57B6/J Jackson Laboratory 000664 (RRID:IMSR_JAX:000664) Software and algorithms FragPipe Nesvizhskii Lab v. 17.1 Agilent ChemStation Agilent LTS 01.11 R/Rstudio CRAN/Posit v. 2021.09.0 R scripts used in this paper This paper https://doi.org/10.5281/zenodo.7659070 The Gene Ontology resource Geneontology.org v. 2023-01-01 Prism GraphPad v. 9.3.1
Article Title: High-Content Screening of Synaptic Density Modulators in Primary Neuronal Cultures.
Article Snippet: See the T erm s and C onditions (https://onlinelibrary.w iley.com /term s-and-conditions) on W iley O nline L ibrary for rules of use; O A articles are governed by the applicable C reative C om m ons L icense 2.5% (w/v) bovine serum albumin (BSA) in DPBS with 0.1% (v/v) Triton X-100 Primary antibodies: Chicken anti-Homer1 (Synaptic Systems, cat. no. 160006) Guinea pig anti-Synaptophysin (Synaptic Systems, cat. no. 101004) Mouse anti-MAP2 (Synaptic Systems, cat. no. 188011) 1× DPBS Secondary antibodies: Donkey anti-chicken Alexa 488 (Jackson ImmunoResearch, cat. no. 703-545-155) Goat anti-guinea pig Alexa 555 (Life Technologies, cat. no. A21435) Donkey anti-mouse Alexa 647 (Jackson ImmunoResearch, cat. no. 715-605-151) 16-channel pipet (Finnpipette F1; Thermo Scientific, cat. no. 4661090N) Aluminum sealing tape (Dutscher, cat. no. 106570, or similar) PlateHUB rotating plate-storage carousel (Agilent, model G5500-23447) Plate washer associated with liquid handler (BioTek, model EL406) Wash_Primary.pro and Wash_Secondary.pro programs (see Supporting Information) VWorks automation control software (Agilent) Aspirate.LHC and Aspirate-Dispense.LHC subroutines (see Supporting Information) Direct Drive Robot (Agilent) NOTE: Use sterile pipet tips with filters (Finntip 50; Thermo Scientific, cat. no. 94052060).
Western Blot:Article Title: Deciphering the nanoscale architecture of presynaptic actin using a micropatterned presynapse-on-glass model
Article Snippet: Primary antibodies used are chicken anti-map2 (1:1,000, ab5392, RRID:AB_2138153; Abcam), mouse anti-ß2-spectrin (1:100, clone 42/aa 2101-2189, #612563, RRID:AB_399854; BD Bioscience), guinea pig anti-synaptophysin (1:400, 101 004, RRID:AB_1210382; Synaptic Systems), mouse anti-synaptotag-min1 (1:600, clone 604.2/aa 1-12, 105 311, RRID:AB_993036; Synaptic Systems), rabbit anti-adducin alpha (1:100, ab40760, RRID:AB_722627; Abcam), mouse anti-bassoon (1:200, clone SAP7F407, ab82958, RRID:AB_1860018; Abcam), rabbit anti-GFP (1:750, ab290, RRID:AB_303395; Abcam), mouse anti-GFP (1:750, clone 9F9.F9, ab1218, RRID:AB_298911; Abcam), rabbit anti-munc13-1 (1:500, 126 103, RRID:AB_887733; Synaptic Systems).
Article Title: Rapid Aging in the Perforant Path Projections to the Rodent Dentate Gyrus
Article Snippet: Primary antisera included rabbit anti-phosphorylated FAK (1:1000; catalog #ab39967, Abcam), anti-GluN2A (1:25,000; catalog #AB1555, EMD-Millipore), and anti-TrkB (1:2000; catalog #07–225, EMD-Millipore); guinea pig anti-synaptophysin (1:2500; catalog #101004, SySy Systems); and mouse anti-PSD-95 (1:1000; catalog #MA1-045, Thermo Fisher Scientific).
Article Title: Disrupted presynaptic nectin1-based neuronal adhesion in the entorhinal-hippocampal circuit contributes to early-life stress-induced memory deficits
Article Snippet: Primary rabbit anti-nectin1 (1:1000, sc-28639, Santa Cruz Biotechnology, Santa Cruz, CA, USA), rabbit anti-nectin3 (1:1000, ab63931, Abcam, Cambridge, UK), and guinea pig anti-synaptophysin (1:500, 101004, Synaptic Systems, Göttingen, Germany) antibodies were used.
Article Title: Rapid Aging in the Perforant Path Projections to the Rodent Dentate Gyrus
Article Snippet: Primary antisera included rabbit antiphosphorylated FAK (1:1000; catalog #ab39967, Abcam), anti-GluN2A (1:25,000; catalog #AB1555, EMD-Millipore), and anti-TrkB (1:2000; catalog #07–225, EMD-Millipore); guinea pig anti-synaptophysin (1:2500; catalog #101004, SySy Systems); and mouse anti-PSD-95 (1:1000; catalog #MA1-045, Thermo Fisher Scientific).
Article Title: KIF21B binds Myosin Va for Spine Entry and regulates Actin Dynamics to control Homeostatic Synaptic Downscaling
Article Snippet: Rabbit anti-KIF21B (1:1,000; Sigma-Aldrich, Taufkirchen, Germany), Mouse anti-Homer1 (1:1,000; Synaptic Systems, Göttingen, Germany), mouse anti-GluA2 extracellular (1:1,000; Millipore, Darmstadt, Germany), rabbit anti-MyoVa (1:1,000; Sigma-Aldrich, Taufkirchen, Germany), rabbit anti-MyoVI (1:1,000; Sigma-Aldrich, Taufkirchen, Germany), mouse anti-PSD95 (1:100; Thermo Fisher Scientific, Dreieich, Germany), goat anti-Shank1-3 (1:1,000; Abcam, Cambridge, UK), guinea pig anti-Synaptophysin (1:1,000; Synaptic Systems, Göttingen, Germany), rabbit anti-KIF21A (1:1,000; Dianova, Hamburg, Germany).
Article Title: N-glycoproteomics of brain synapses and synaptic vesicles.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies SV2 mAb DSHB SV2 (RRID:AB_2315387) Syt1 mAb DSHB mAb 48 (RRID:AB_2199314) Guinea pig anti-synaptophysin Synaptic Systems 104 211 (RRID:AB_1210382) Goat anti-mouse HRP-conjugated secondary Ab Bio-Rad 1706516 Goat anti-guinea pig HRP-conjugated secondary Ab Thermo Fisher A18769 Chemicals, peptides, and recombinant proteins Protein G Sepharose fast flow Cytiva 17061801 Dynabeads M-270 epoxy Thermo Fisher 14302D cOmplete mini, EDTA-free Sigma (Roche) 04693159001 Dynabeads M-270 carboxylic acid Thermo Fisher 14305D Trypsin Promega V5111 SOLA SAX 10 mg cartridge Thermo Fisher 60109–003 PNGase F NEB P0708 Procainamide Sigma SML2088 Sodium cyanoborohydride, 5 M in 1 M NaOH Sigma 296945 OASIS HLB 30 mg cartridge Waters WAT094225 a(1–2,3,6) mannosidase NEB P0768 a(1–3,4) fucosidase NEB P0769 a(1–2) fucosidase NEB P0724 a(1–2,4,6) fucosidase O NEB P0749 b(1–3,4) galactosidase NEB P0746 b-GlcNAcase S NEB P0744 Deposited data LC-MS raw data deposited at MassIVE This paper https://doi.org/10.25345/C5TB0Z526 Experimental models: Organisms/strains Mouse: C57B6/J Jackson Laboratory 000664 (RRID:IMSR_JAX:000664) Software and algorithms FragPipe Nesvizhskii Lab v. 17.1 Agilent ChemStation Agilent LTS 01.11 R/Rstudio CRAN/Posit v. 2021.09.0 R scripts used in this paper This paper https://doi.org/10.5281/zenodo.7659070 The Gene Ontology resource Geneontology.org v. 2023-01-01 Prism GraphPad v. 9.3.1
Article Title: High-Content Screening of Synaptic Density Modulators in Primary Neuronal Cultures.
Article Snippet: See the T erm s and C onditions (https://onlinelibrary.w iley.com /term s-and-conditions) on W iley O nline L ibrary for rules of use; O A articles are governed by the applicable C reative C om m ons L icense 2.5% (w/v) bovine serum albumin (BSA) in DPBS with 0.1% (v/v) Triton X-100 Primary antibodies: Chicken anti-Homer1 (Synaptic Systems, cat. no. 160006) Guinea pig anti-Synaptophysin (Synaptic Systems, cat. no. 101004) Mouse anti-MAP2 (Synaptic Systems, cat. no. 188011) 1× DPBS Secondary antibodies: Donkey anti-chicken Alexa 488 (Jackson ImmunoResearch, cat. no. 703-545-155) Goat anti-guinea pig Alexa 555 (Life Technologies, cat. no. A21435) Donkey anti-mouse Alexa 647 (Jackson ImmunoResearch, cat. no. 715-605-151) 16-channel pipet (Finnpipette F1; Thermo Scientific, cat. no. 4661090N) Aluminum sealing tape (Dutscher, cat. no. 106570, or similar) PlateHUB rotating plate-storage carousel (Agilent, model G5500-23447) Plate washer associated with liquid handler (BioTek, model EL406) Wash_Primary.pro and Wash_Secondary.pro programs (see Supporting Information) VWorks automation control software (Agilent) Aspirate.LHC and Aspirate-Dispense.LHC subroutines (see Supporting Information) Direct Drive Robot (Agilent) NOTE: Use sterile pipet tips with filters (Finntip 50; Thermo Scientific, cat. no. 94052060).
Immuno-Electron Microscopy:Article Title: Deciphering the nanoscale architecture of presynaptic actin using a micropatterned presynapse-on-glass model
Article Snippet: Primary antibodies used are chicken anti-map2 (1:1,000, ab5392, RRID:AB_2138153; Abcam), mouse anti-ß2-spectrin (1:100, clone 42/aa 2101-2189, #612563, RRID:AB_399854; BD Bioscience), guinea pig anti-synaptophysin (1:400, 101 004, RRID:AB_1210382; Synaptic Systems), mouse anti-synaptotag-min1 (1:600, clone 604.2/aa 1-12, 105 311, RRID:AB_993036; Synaptic Systems), rabbit anti-adducin alpha (1:100, ab40760, RRID:AB_722627; Abcam), mouse anti-bassoon (1:200, clone SAP7F407, ab82958, RRID:AB_1860018; Abcam), rabbit anti-GFP (1:750, ab290, RRID:AB_303395; Abcam), mouse anti-GFP (1:750, clone 9F9.F9, ab1218, RRID:AB_298911; Abcam), rabbit anti-munc13-1 (1:500, 126 103, RRID:AB_887733; Synaptic Systems).
Article Title: Rapid Aging in the Perforant Path Projections to the Rodent Dentate Gyrus
Article Snippet: Primary antisera included rabbit anti-phosphorylated FAK (1:1000; catalog #ab39967, Abcam), anti-GluN2A (1:25,000; catalog #AB1555, EMD-Millipore), and anti-TrkB (1:2000; catalog #07–225, EMD-Millipore); guinea pig anti-synaptophysin (1:2500; catalog #101004, SySy Systems); and mouse anti-PSD-95 (1:1000; catalog #MA1-045, Thermo Fisher Scientific).
Article Title: Disrupted presynaptic nectin1-based neuronal adhesion in the entorhinal-hippocampal circuit contributes to early-life stress-induced memory deficits
Article Snippet: Primary rabbit anti-nectin1 (1:1000, sc-28639, Santa Cruz Biotechnology, Santa Cruz, CA, USA), rabbit anti-nectin3 (1:1000, ab63931, Abcam, Cambridge, UK), and guinea pig anti-synaptophysin (1:500, 101004, Synaptic Systems, Göttingen, Germany) antibodies were used.
Article Title: Rapid Aging in the Perforant Path Projections to the Rodent Dentate Gyrus
Article Snippet: Primary antisera included rabbit antiphosphorylated FAK (1:1000; catalog #ab39967, Abcam), anti-GluN2A (1:25,000; catalog #AB1555, EMD-Millipore), and anti-TrkB (1:2000; catalog #07–225, EMD-Millipore); guinea pig anti-synaptophysin (1:2500; catalog #101004, SySy Systems); and mouse anti-PSD-95 (1:1000; catalog #MA1-045, Thermo Fisher Scientific).
Article Title: KIF21B binds Myosin Va for Spine Entry and regulates Actin Dynamics to control Homeostatic Synaptic Downscaling
Article Snippet: Rabbit anti-KIF21B (1:1,000; Sigma-Aldrich, Taufkirchen, Germany), Mouse anti-Homer1 (1:1,000; Synaptic Systems, Göttingen, Germany), mouse anti-GluA2 extracellular (1:1,000; Millipore, Darmstadt, Germany), rabbit anti-MyoVa (1:1,000; Sigma-Aldrich, Taufkirchen, Germany), rabbit anti-MyoVI (1:1,000; Sigma-Aldrich, Taufkirchen, Germany), mouse anti-PSD95 (1:100; Thermo Fisher Scientific, Dreieich, Germany), goat anti-Shank1-3 (1:1,000; Abcam, Cambridge, UK), guinea pig anti-Synaptophysin (1:1,000; Synaptic Systems, Göttingen, Germany), rabbit anti-KIF21A (1:1,000; Dianova, Hamburg, Germany).
Article Title: N-glycoproteomics of brain synapses and synaptic vesicles.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies SV2 mAb DSHB SV2 (RRID:AB_2315387) Syt1 mAb DSHB mAb 48 (RRID:AB_2199314) Guinea pig anti-synaptophysin Synaptic Systems 104 211 (RRID:AB_1210382) Goat anti-mouse HRP-conjugated secondary Ab Bio-Rad 1706516 Goat anti-guinea pig HRP-conjugated secondary Ab Thermo Fisher A18769 Chemicals, peptides, and recombinant proteins Protein G Sepharose fast flow Cytiva 17061801 Dynabeads M-270 epoxy Thermo Fisher 14302D cOmplete mini, EDTA-free Sigma (Roche) 04693159001 Dynabeads M-270 carboxylic acid Thermo Fisher 14305D Trypsin Promega V5111 SOLA SAX 10 mg cartridge Thermo Fisher 60109–003 PNGase F NEB P0708 Procainamide Sigma SML2088 Sodium cyanoborohydride, 5 M in 1 M NaOH Sigma 296945 OASIS HLB 30 mg cartridge Waters WAT094225 a(1–2,3,6) mannosidase NEB P0768 a(1–3,4) fucosidase NEB P0769 a(1–2) fucosidase NEB P0724 a(1–2,4,6) fucosidase O NEB P0749 b(1–3,4) galactosidase NEB P0746 b-GlcNAcase S NEB P0744 Deposited data LC-MS raw data deposited at MassIVE This paper https://doi.org/10.25345/C5TB0Z526 Experimental models: Organisms/strains Mouse: C57B6/J Jackson Laboratory 000664 (RRID:IMSR_JAX:000664) Software and algorithms FragPipe Nesvizhskii Lab v. 17.1 Agilent ChemStation Agilent LTS 01.11 R/Rstudio CRAN/Posit v. 2021.09.0 R scripts used in this paper This paper https://doi.org/10.5281/zenodo.7659070 The Gene Ontology resource Geneontology.org v. 2023-01-01 Prism GraphPad v. 9.3.1
Article Title: High-Content Screening of Synaptic Density Modulators in Primary Neuronal Cultures.
Article Snippet: See the T erm s and C onditions (https://onlinelibrary.w iley.com /term s-and-conditions) on W iley O nline L ibrary for rules of use; O A articles are governed by the applicable C reative C om m ons L icense 2.5% (w/v) bovine serum albumin (BSA) in DPBS with 0.1% (v/v) Triton X-100 Primary antibodies: Chicken anti-Homer1 (Synaptic Systems, cat. no. 160006) Guinea pig anti-Synaptophysin (Synaptic Systems, cat. no. 101004) Mouse anti-MAP2 (Synaptic Systems, cat. no. 188011) 1× DPBS Secondary antibodies: Donkey anti-chicken Alexa 488 (Jackson ImmunoResearch, cat. no. 703-545-155) Goat anti-guinea pig Alexa 555 (Life Technologies, cat. no. A21435) Donkey anti-mouse Alexa 647 (Jackson ImmunoResearch, cat. no. 715-605-151) 16-channel pipet (Finnpipette F1; Thermo Scientific, cat. no. 4661090N) Aluminum sealing tape (Dutscher, cat. no. 106570, or similar) PlateHUB rotating plate-storage carousel (Agilent, model G5500-23447) Plate washer associated with liquid handler (BioTek, model EL406) Wash_Primary.pro and Wash_Secondary.pro programs (see Supporting Information) VWorks automation control software (Agilent) Aspirate.LHC and Aspirate-Dispense.LHC subroutines (see Supporting Information) Direct Drive Robot (Agilent) NOTE: Use sterile pipet tips with filters (Finntip 50; Thermo Scientific, cat. no. 94052060).
Immunostaining:Article Title: Deciphering the nanoscale architecture of presynaptic actin using a micropatterned presynapse-on-glass model
Article Snippet: Primary antibodies used are chicken anti-map2 (1:1,000, ab5392, RRID:AB_2138153; Abcam), mouse anti-ß2-spectrin (1:100, clone 42/aa 2101-2189, #612563, RRID:AB_399854; BD Bioscience), guinea pig anti-synaptophysin (1:400, 101 004, RRID:AB_1210382; Synaptic Systems), mouse anti-synaptotag-min1 (1:600, clone 604.2/aa 1-12, 105 311, RRID:AB_993036; Synaptic Systems), rabbit anti-adducin alpha (1:100, ab40760, RRID:AB_722627; Abcam), mouse anti-bassoon (1:200, clone SAP7F407, ab82958, RRID:AB_1860018; Abcam), rabbit anti-GFP (1:750, ab290, RRID:AB_303395; Abcam), mouse anti-GFP (1:750, clone 9F9.F9, ab1218, RRID:AB_298911; Abcam), rabbit anti-munc13-1 (1:500, 126 103, RRID:AB_887733; Synaptic Systems).
Article Title: Rapid Aging in the Perforant Path Projections to the Rodent Dentate Gyrus
Article Snippet: Primary antisera included rabbit anti-phosphorylated FAK (1:1000; catalog #ab39967, Abcam), anti-GluN2A (1:25,000; catalog #AB1555, EMD-Millipore), and anti-TrkB (1:2000; catalog #07–225, EMD-Millipore); guinea pig anti-synaptophysin (1:2500; catalog #101004, SySy Systems); and mouse anti-PSD-95 (1:1000; catalog #MA1-045, Thermo Fisher Scientific).
Article Title: Disrupted presynaptic nectin1-based neuronal adhesion in the entorhinal-hippocampal circuit contributes to early-life stress-induced memory deficits
Article Snippet: Primary rabbit anti-nectin1 (1:1000, sc-28639, Santa Cruz Biotechnology, Santa Cruz, CA, USA), rabbit anti-nectin3 (1:1000, ab63931, Abcam, Cambridge, UK), and guinea pig anti-synaptophysin (1:500, 101004, Synaptic Systems, Göttingen, Germany) antibodies were used.
Article Title: Rapid Aging in the Perforant Path Projections to the Rodent Dentate Gyrus
Article Snippet: Primary antisera included rabbit antiphosphorylated FAK (1:1000; catalog #ab39967, Abcam), anti-GluN2A (1:25,000; catalog #AB1555, EMD-Millipore), and anti-TrkB (1:2000; catalog #07–225, EMD-Millipore); guinea pig anti-synaptophysin (1:2500; catalog #101004, SySy Systems); and mouse anti-PSD-95 (1:1000; catalog #MA1-045, Thermo Fisher Scientific).
Article Title: KIF21B binds Myosin Va for Spine Entry and regulates Actin Dynamics to control Homeostatic Synaptic Downscaling
Article Snippet: Rabbit anti-KIF21B (1:1,000; Sigma-Aldrich, Taufkirchen, Germany), Mouse anti-Homer1 (1:1,000; Synaptic Systems, Göttingen, Germany), mouse anti-GluA2 extracellular (1:1,000; Millipore, Darmstadt, Germany), rabbit anti-MyoVa (1:1,000; Sigma-Aldrich, Taufkirchen, Germany), rabbit anti-MyoVI (1:1,000; Sigma-Aldrich, Taufkirchen, Germany), mouse anti-PSD95 (1:100; Thermo Fisher Scientific, Dreieich, Germany), goat anti-Shank1-3 (1:1,000; Abcam, Cambridge, UK), guinea pig anti-Synaptophysin (1:1,000; Synaptic Systems, Göttingen, Germany), rabbit anti-KIF21A (1:1,000; Dianova, Hamburg, Germany).
Article Title: N-glycoproteomics of brain synapses and synaptic vesicles.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies SV2 mAb DSHB SV2 (RRID:AB_2315387) Syt1 mAb DSHB mAb 48 (RRID:AB_2199314) Guinea pig anti-synaptophysin Synaptic Systems 104 211 (RRID:AB_1210382) Goat anti-mouse HRP-conjugated secondary Ab Bio-Rad 1706516 Goat anti-guinea pig HRP-conjugated secondary Ab Thermo Fisher A18769 Chemicals, peptides, and recombinant proteins Protein G Sepharose fast flow Cytiva 17061801 Dynabeads M-270 epoxy Thermo Fisher 14302D cOmplete mini, EDTA-free Sigma (Roche) 04693159001 Dynabeads M-270 carboxylic acid Thermo Fisher 14305D Trypsin Promega V5111 SOLA SAX 10 mg cartridge Thermo Fisher 60109–003 PNGase F NEB P0708 Procainamide Sigma SML2088 Sodium cyanoborohydride, 5 M in 1 M NaOH Sigma 296945 OASIS HLB 30 mg cartridge Waters WAT094225 a(1–2,3,6) mannosidase NEB P0768 a(1–3,4) fucosidase NEB P0769 a(1–2) fucosidase NEB P0724 a(1–2,4,6) fucosidase O NEB P0749 b(1–3,4) galactosidase NEB P0746 b-GlcNAcase S NEB P0744 Deposited data LC-MS raw data deposited at MassIVE This paper https://doi.org/10.25345/C5TB0Z526 Experimental models: Organisms/strains Mouse: C57B6/J Jackson Laboratory 000664 (RRID:IMSR_JAX:000664) Software and algorithms FragPipe Nesvizhskii Lab v. 17.1 Agilent ChemStation Agilent LTS 01.11 R/Rstudio CRAN/Posit v. 2021.09.0 R scripts used in this paper This paper https://doi.org/10.5281/zenodo.7659070 The Gene Ontology resource Geneontology.org v. 2023-01-01 Prism GraphPad v. 9.3.1
Article Title: High-Content Screening of Synaptic Density Modulators in Primary Neuronal Cultures.
Article Snippet: See the T erm s and C onditions (https://onlinelibrary.w iley.com /term s-and-conditions) on W iley O nline L ibrary for rules of use; O A articles are governed by the applicable C reative C om m ons L icense 2.5% (w/v) bovine serum albumin (BSA) in DPBS with 0.1% (v/v) Triton X-100 Primary antibodies: Chicken anti-Homer1 (Synaptic Systems, cat. no. 160006) Guinea pig anti-Synaptophysin (Synaptic Systems, cat. no. 101004) Mouse anti-MAP2 (Synaptic Systems, cat. no. 188011) 1× DPBS Secondary antibodies: Donkey anti-chicken Alexa 488 (Jackson ImmunoResearch, cat. no. 703-545-155) Goat anti-guinea pig Alexa 555 (Life Technologies, cat. no. A21435) Donkey anti-mouse Alexa 647 (Jackson ImmunoResearch, cat. no. 715-605-151) 16-channel pipet (Finnpipette F1; Thermo Scientific, cat. no. 4661090N) Aluminum sealing tape (Dutscher, cat. no. 106570, or similar) PlateHUB rotating plate-storage carousel (Agilent, model G5500-23447) Plate washer associated with liquid handler (BioTek, model EL406) Wash_Primary.pro and Wash_Secondary.pro programs (see Supporting Information) VWorks automation control software (Agilent) Aspirate.LHC and Aspirate-Dispense.LHC subroutines (see Supporting Information) Direct Drive Robot (Agilent) NOTE: Use sterile pipet tips with filters (Finntip 50; Thermo Scientific, cat. no. 94052060).
Immunofluorescence:Article Title: Deciphering the nanoscale architecture of presynaptic actin using a micropatterned presynapse-on-glass model
Article Snippet: Primary antibodies used are chicken anti-map2 (1:1,000, ab5392, RRID:AB_2138153; Abcam), mouse anti-ß2-spectrin (1:100, clone 42/aa 2101-2189, #612563, RRID:AB_399854; BD Bioscience), guinea pig anti-synaptophysin (1:400, 101 004, RRID:AB_1210382; Synaptic Systems), mouse anti-synaptotag-min1 (1:600, clone 604.2/aa 1-12, 105 311, RRID:AB_993036; Synaptic Systems), rabbit anti-adducin alpha (1:100, ab40760, RRID:AB_722627; Abcam), mouse anti-bassoon (1:200, clone SAP7F407, ab82958, RRID:AB_1860018; Abcam), rabbit anti-GFP (1:750, ab290, RRID:AB_303395; Abcam), mouse anti-GFP (1:750, clone 9F9.F9, ab1218, RRID:AB_298911; Abcam), rabbit anti-munc13-1 (1:500, 126 103, RRID:AB_887733; Synaptic Systems).
Article Title: Rapid Aging in the Perforant Path Projections to the Rodent Dentate Gyrus
Article Snippet: Primary antisera included rabbit anti-phosphorylated FAK (1:1000; catalog #ab39967, Abcam), anti-GluN2A (1:25,000; catalog #AB1555, EMD-Millipore), and anti-TrkB (1:2000; catalog #07–225, EMD-Millipore); guinea pig anti-synaptophysin (1:2500; catalog #101004, SySy Systems); and mouse anti-PSD-95 (1:1000; catalog #MA1-045, Thermo Fisher Scientific).
Article Title: Disrupted presynaptic nectin1-based neuronal adhesion in the entorhinal-hippocampal circuit contributes to early-life stress-induced memory deficits
Article Snippet: Primary rabbit anti-nectin1 (1:1000, sc-28639, Santa Cruz Biotechnology, Santa Cruz, CA, USA), rabbit anti-nectin3 (1:1000, ab63931, Abcam, Cambridge, UK), and guinea pig anti-synaptophysin (1:500, 101004, Synaptic Systems, Göttingen, Germany) antibodies were used.
Article Title: Rapid Aging in the Perforant Path Projections to the Rodent Dentate Gyrus
Article Snippet: Primary antisera included rabbit antiphosphorylated FAK (1:1000; catalog #ab39967, Abcam), anti-GluN2A (1:25,000; catalog #AB1555, EMD-Millipore), and anti-TrkB (1:2000; catalog #07–225, EMD-Millipore); guinea pig anti-synaptophysin (1:2500; catalog #101004, SySy Systems); and mouse anti-PSD-95 (1:1000; catalog #MA1-045, Thermo Fisher Scientific).
Article Title: KIF21B binds Myosin Va for Spine Entry and regulates Actin Dynamics to control Homeostatic Synaptic Downscaling
Article Snippet: Rabbit anti-KIF21B (1:1,000; Sigma-Aldrich, Taufkirchen, Germany), Mouse anti-Homer1 (1:1,000; Synaptic Systems, Göttingen, Germany), mouse anti-GluA2 extracellular (1:1,000; Millipore, Darmstadt, Germany), rabbit anti-MyoVa (1:1,000; Sigma-Aldrich, Taufkirchen, Germany), rabbit anti-MyoVI (1:1,000; Sigma-Aldrich, Taufkirchen, Germany), mouse anti-PSD95 (1:100; Thermo Fisher Scientific, Dreieich, Germany), goat anti-Shank1-3 (1:1,000; Abcam, Cambridge, UK), guinea pig anti-Synaptophysin (1:1,000; Synaptic Systems, Göttingen, Germany), rabbit anti-KIF21A (1:1,000; Dianova, Hamburg, Germany).
Article Title: N-glycoproteomics of brain synapses and synaptic vesicles.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies SV2 mAb DSHB SV2 (RRID:AB_2315387) Syt1 mAb DSHB mAb 48 (RRID:AB_2199314) Guinea pig anti-synaptophysin Synaptic Systems 104 211 (RRID:AB_1210382) Goat anti-mouse HRP-conjugated secondary Ab Bio-Rad 1706516 Goat anti-guinea pig HRP-conjugated secondary Ab Thermo Fisher A18769 Chemicals, peptides, and recombinant proteins Protein G Sepharose fast flow Cytiva 17061801 Dynabeads M-270 epoxy Thermo Fisher 14302D cOmplete mini, EDTA-free Sigma (Roche) 04693159001 Dynabeads M-270 carboxylic acid Thermo Fisher 14305D Trypsin Promega V5111 SOLA SAX 10 mg cartridge Thermo Fisher 60109–003 PNGase F NEB P0708 Procainamide Sigma SML2088 Sodium cyanoborohydride, 5 M in 1 M NaOH Sigma 296945 OASIS HLB 30 mg cartridge Waters WAT094225 a(1–2,3,6) mannosidase NEB P0768 a(1–3,4) fucosidase NEB P0769 a(1–2) fucosidase NEB P0724 a(1–2,4,6) fucosidase O NEB P0749 b(1–3,4) galactosidase NEB P0746 b-GlcNAcase S NEB P0744 Deposited data LC-MS raw data deposited at MassIVE This paper https://doi.org/10.25345/C5TB0Z526 Experimental models: Organisms/strains Mouse: C57B6/J Jackson Laboratory 000664 (RRID:IMSR_JAX:000664) Software and algorithms FragPipe Nesvizhskii Lab v. 17.1 Agilent ChemStation Agilent LTS 01.11 R/Rstudio CRAN/Posit v. 2021.09.0 R scripts used in this paper This paper https://doi.org/10.5281/zenodo.7659070 The Gene Ontology resource Geneontology.org v. 2023-01-01 Prism GraphPad v. 9.3.1
Article Title: High-Content Screening of Synaptic Density Modulators in Primary Neuronal Cultures.
Article Snippet: See the T erm s and C onditions (https://onlinelibrary.w iley.com /term s-and-conditions) on W iley O nline L ibrary for rules of use; O A articles are governed by the applicable C reative C om m ons L icense 2.5% (w/v) bovine serum albumin (BSA) in DPBS with 0.1% (v/v) Triton X-100 Primary antibodies: Chicken anti-Homer1 (Synaptic Systems, cat. no. 160006) Guinea pig anti-Synaptophysin (Synaptic Systems, cat. no. 101004) Mouse anti-MAP2 (Synaptic Systems, cat. no. 188011) 1× DPBS Secondary antibodies: Donkey anti-chicken Alexa 488 (Jackson ImmunoResearch, cat. no. 703-545-155) Goat anti-guinea pig Alexa 555 (Life Technologies, cat. no. A21435) Donkey anti-mouse Alexa 647 (Jackson ImmunoResearch, cat. no. 715-605-151) 16-channel pipet (Finnpipette F1; Thermo Scientific, cat. no. 4661090N) Aluminum sealing tape (Dutscher, cat. no. 106570, or similar) PlateHUB rotating plate-storage carousel (Agilent, model G5500-23447) Plate washer associated with liquid handler (BioTek, model EL406) Wash_Primary.pro and Wash_Secondary.pro programs (see Supporting Information) VWorks automation control software (Agilent) Aspirate.LHC and Aspirate-Dispense.LHC subroutines (see Supporting Information) Direct Drive Robot (Agilent) NOTE: Use sterile pipet tips with filters (Finntip 50; Thermo Scientific, cat. no. 94052060).
Marker:Article Title: Deciphering the nanoscale architecture of presynaptic actin using a micropatterned presynapse-on-glass model
Article Snippet: Primary antibodies used are chicken anti-map2 (1:1,000, ab5392, RRID:AB_2138153; Abcam), mouse anti-ß2-spectrin (1:100, clone 42/aa 2101-2189, #612563, RRID:AB_399854; BD Bioscience), guinea pig anti-synaptophysin (1:400, 101 004, RRID:AB_1210382; Synaptic Systems), mouse anti-synaptotag-min1 (1:600, clone 604.2/aa 1-12, 105 311, RRID:AB_993036; Synaptic Systems), rabbit anti-adducin alpha (1:100, ab40760, RRID:AB_722627; Abcam), mouse anti-bassoon (1:200, clone SAP7F407, ab82958, RRID:AB_1860018; Abcam), rabbit anti-GFP (1:750, ab290, RRID:AB_303395; Abcam), mouse anti-GFP (1:750, clone 9F9.F9, ab1218, RRID:AB_298911; Abcam), rabbit anti-munc13-1 (1:500, 126 103, RRID:AB_887733; Synaptic Systems).
Article Title: Rapid Aging in the Perforant Path Projections to the Rodent Dentate Gyrus
Article Snippet: Primary antisera included rabbit anti-phosphorylated FAK (1:1000; catalog #ab39967, Abcam), anti-GluN2A (1:25,000; catalog #AB1555, EMD-Millipore), and anti-TrkB (1:2000; catalog #07–225, EMD-Millipore); guinea pig anti-synaptophysin (1:2500; catalog #101004, SySy Systems); and mouse anti-PSD-95 (1:1000; catalog #MA1-045, Thermo Fisher Scientific).
Article Title: Disrupted presynaptic nectin1-based neuronal adhesion in the entorhinal-hippocampal circuit contributes to early-life stress-induced memory deficits
Article Snippet: Primary rabbit anti-nectin1 (1:1000, sc-28639, Santa Cruz Biotechnology, Santa Cruz, CA, USA), rabbit anti-nectin3 (1:1000, ab63931, Abcam, Cambridge, UK), and guinea pig anti-synaptophysin (1:500, 101004, Synaptic Systems, Göttingen, Germany) antibodies were used.
Article Title: Rapid Aging in the Perforant Path Projections to the Rodent Dentate Gyrus
Article Snippet: Primary antisera included rabbit antiphosphorylated FAK (1:1000; catalog #ab39967, Abcam), anti-GluN2A (1:25,000; catalog #AB1555, EMD-Millipore), and anti-TrkB (1:2000; catalog #07–225, EMD-Millipore); guinea pig anti-synaptophysin (1:2500; catalog #101004, SySy Systems); and mouse anti-PSD-95 (1:1000; catalog #MA1-045, Thermo Fisher Scientific).
Article Title: KIF21B binds Myosin Va for Spine Entry and regulates Actin Dynamics to control Homeostatic Synaptic Downscaling
Article Snippet: Rabbit anti-KIF21B (1:1,000; Sigma-Aldrich, Taufkirchen, Germany), Mouse anti-Homer1 (1:1,000; Synaptic Systems, Göttingen, Germany), mouse anti-GluA2 extracellular (1:1,000; Millipore, Darmstadt, Germany), rabbit anti-MyoVa (1:1,000; Sigma-Aldrich, Taufkirchen, Germany), rabbit anti-MyoVI (1:1,000; Sigma-Aldrich, Taufkirchen, Germany), mouse anti-PSD95 (1:100; Thermo Fisher Scientific, Dreieich, Germany), goat anti-Shank1-3 (1:1,000; Abcam, Cambridge, UK), guinea pig anti-Synaptophysin (1:1,000; Synaptic Systems, Göttingen, Germany), rabbit anti-KIF21A (1:1,000; Dianova, Hamburg, Germany).
Article Title: N-glycoproteomics of brain synapses and synaptic vesicles.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies SV2 mAb DSHB SV2 (RRID:AB_2315387) Syt1 mAb DSHB mAb 48 (RRID:AB_2199314) Guinea pig anti-synaptophysin Synaptic Systems 104 211 (RRID:AB_1210382) Goat anti-mouse HRP-conjugated secondary Ab Bio-Rad 1706516 Goat anti-guinea pig HRP-conjugated secondary Ab Thermo Fisher A18769 Chemicals, peptides, and recombinant proteins Protein G Sepharose fast flow Cytiva 17061801 Dynabeads M-270 epoxy Thermo Fisher 14302D cOmplete mini, EDTA-free Sigma (Roche) 04693159001 Dynabeads M-270 carboxylic acid Thermo Fisher 14305D Trypsin Promega V5111 SOLA SAX 10 mg cartridge Thermo Fisher 60109–003 PNGase F NEB P0708 Procainamide Sigma SML2088 Sodium cyanoborohydride, 5 M in 1 M NaOH Sigma 296945 OASIS HLB 30 mg cartridge Waters WAT094225 a(1–2,3,6) mannosidase NEB P0768 a(1–3,4) fucosidase NEB P0769 a(1–2) fucosidase NEB P0724 a(1–2,4,6) fucosidase O NEB P0749 b(1–3,4) galactosidase NEB P0746 b-GlcNAcase S NEB P0744 Deposited data LC-MS raw data deposited at MassIVE This paper https://doi.org/10.25345/C5TB0Z526 Experimental models: Organisms/strains Mouse: C57B6/J Jackson Laboratory 000664 (RRID:IMSR_JAX:000664) Software and algorithms FragPipe Nesvizhskii Lab v. 17.1 Agilent ChemStation Agilent LTS 01.11 R/Rstudio CRAN/Posit v. 2021.09.0 R scripts used in this paper This paper https://doi.org/10.5281/zenodo.7659070 The Gene Ontology resource Geneontology.org v. 2023-01-01 Prism GraphPad v. 9.3.1
Article Title: High-Content Screening of Synaptic Density Modulators in Primary Neuronal Cultures.
Article Snippet: See the T erm s and C onditions (https://onlinelibrary.w iley.com /term s-and-conditions) on W iley O nline L ibrary for rules of use; O A articles are governed by the applicable C reative C om m ons L icense 2.5% (w/v) bovine serum albumin (BSA) in DPBS with 0.1% (v/v) Triton X-100 Primary antibodies: Chicken anti-Homer1 (Synaptic Systems, cat. no. 160006) Guinea pig anti-Synaptophysin (Synaptic Systems, cat. no. 101004) Mouse anti-MAP2 (Synaptic Systems, cat. no. 188011) 1× DPBS Secondary antibodies: Donkey anti-chicken Alexa 488 (Jackson ImmunoResearch, cat. no. 703-545-155) Goat anti-guinea pig Alexa 555 (Life Technologies, cat. no. A21435) Donkey anti-mouse Alexa 647 (Jackson ImmunoResearch, cat. no. 715-605-151) 16-channel pipet (Finnpipette F1; Thermo Scientific, cat. no. 4661090N) Aluminum sealing tape (Dutscher, cat. no. 106570, or similar) PlateHUB rotating plate-storage carousel (Agilent, model G5500-23447) Plate washer associated with liquid handler (BioTek, model EL406) Wash_Primary.pro and Wash_Secondary.pro programs (see Supporting Information) VWorks automation control software (Agilent) Aspirate.LHC and Aspirate-Dispense.LHC subroutines (see Supporting Information) Direct Drive Robot (Agilent) NOTE: Use sterile pipet tips with filters (Finntip 50; Thermo Scientific, cat. no. 94052060).
Immunolabeling:Article Title: Deciphering the nanoscale architecture of presynaptic actin using a micropatterned presynapse-on-glass model
Article Snippet: Primary antibodies used are chicken anti-map2 (1:1,000, ab5392, RRID:AB_2138153; Abcam), mouse anti-ß2-spectrin (1:100, clone 42/aa 2101-2189, #612563, RRID:AB_399854; BD Bioscience), guinea pig anti-synaptophysin (1:400, 101 004, RRID:AB_1210382; Synaptic Systems), mouse anti-synaptotag-min1 (1:600, clone 604.2/aa 1-12, 105 311, RRID:AB_993036; Synaptic Systems), rabbit anti-adducin alpha (1:100, ab40760, RRID:AB_722627; Abcam), mouse anti-bassoon (1:200, clone SAP7F407, ab82958, RRID:AB_1860018; Abcam), rabbit anti-GFP (1:750, ab290, RRID:AB_303395; Abcam), mouse anti-GFP (1:750, clone 9F9.F9, ab1218, RRID:AB_298911; Abcam), rabbit anti-munc13-1 (1:500, 126 103, RRID:AB_887733; Synaptic Systems).
Article Title: Rapid Aging in the Perforant Path Projections to the Rodent Dentate Gyrus
Article Snippet: Primary antisera included rabbit anti-phosphorylated FAK (1:1000; catalog #ab39967, Abcam), anti-GluN2A (1:25,000; catalog #AB1555, EMD-Millipore), and anti-TrkB (1:2000; catalog #07–225, EMD-Millipore); guinea pig anti-synaptophysin (1:2500; catalog #101004, SySy Systems); and mouse anti-PSD-95 (1:1000; catalog #MA1-045, Thermo Fisher Scientific).
Article Title: Disrupted presynaptic nectin1-based neuronal adhesion in the entorhinal-hippocampal circuit contributes to early-life stress-induced memory deficits
Article Snippet: Primary rabbit anti-nectin1 (1:1000, sc-28639, Santa Cruz Biotechnology, Santa Cruz, CA, USA), rabbit anti-nectin3 (1:1000, ab63931, Abcam, Cambridge, UK), and guinea pig anti-synaptophysin (1:500, 101004, Synaptic Systems, Göttingen, Germany) antibodies were used.
Article Title: Rapid Aging in the Perforant Path Projections to the Rodent Dentate Gyrus
Article Snippet: Primary antisera included rabbit antiphosphorylated FAK (1:1000; catalog #ab39967, Abcam), anti-GluN2A (1:25,000; catalog #AB1555, EMD-Millipore), and anti-TrkB (1:2000; catalog #07–225, EMD-Millipore); guinea pig anti-synaptophysin (1:2500; catalog #101004, SySy Systems); and mouse anti-PSD-95 (1:1000; catalog #MA1-045, Thermo Fisher Scientific).
Article Title: KIF21B binds Myosin Va for Spine Entry and regulates Actin Dynamics to control Homeostatic Synaptic Downscaling
Article Snippet: Rabbit anti-KIF21B (1:1,000; Sigma-Aldrich, Taufkirchen, Germany), Mouse anti-Homer1 (1:1,000; Synaptic Systems, Göttingen, Germany), mouse anti-GluA2 extracellular (1:1,000; Millipore, Darmstadt, Germany), rabbit anti-MyoVa (1:1,000; Sigma-Aldrich, Taufkirchen, Germany), rabbit anti-MyoVI (1:1,000; Sigma-Aldrich, Taufkirchen, Germany), mouse anti-PSD95 (1:100; Thermo Fisher Scientific, Dreieich, Germany), goat anti-Shank1-3 (1:1,000; Abcam, Cambridge, UK), guinea pig anti-Synaptophysin (1:1,000; Synaptic Systems, Göttingen, Germany), rabbit anti-KIF21A (1:1,000; Dianova, Hamburg, Germany).
Article Title: N-glycoproteomics of brain synapses and synaptic vesicles.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies SV2 mAb DSHB SV2 (RRID:AB_2315387) Syt1 mAb DSHB mAb 48 (RRID:AB_2199314) Guinea pig anti-synaptophysin Synaptic Systems 104 211 (RRID:AB_1210382) Goat anti-mouse HRP-conjugated secondary Ab Bio-Rad 1706516 Goat anti-guinea pig HRP-conjugated secondary Ab Thermo Fisher A18769 Chemicals, peptides, and recombinant proteins Protein G Sepharose fast flow Cytiva 17061801 Dynabeads M-270 epoxy Thermo Fisher 14302D cOmplete mini, EDTA-free Sigma (Roche) 04693159001 Dynabeads M-270 carboxylic acid Thermo Fisher 14305D Trypsin Promega V5111 SOLA SAX 10 mg cartridge Thermo Fisher 60109–003 PNGase F NEB P0708 Procainamide Sigma SML2088 Sodium cyanoborohydride, 5 M in 1 M NaOH Sigma 296945 OASIS HLB 30 mg cartridge Waters WAT094225 a(1–2,3,6) mannosidase NEB P0768 a(1–3,4) fucosidase NEB P0769 a(1–2) fucosidase NEB P0724 a(1–2,4,6) fucosidase O NEB P0749 b(1–3,4) galactosidase NEB P0746 b-GlcNAcase S NEB P0744 Deposited data LC-MS raw data deposited at MassIVE This paper https://doi.org/10.25345/C5TB0Z526 Experimental models: Organisms/strains Mouse: C57B6/J Jackson Laboratory 000664 (RRID:IMSR_JAX:000664) Software and algorithms FragPipe Nesvizhskii Lab v. 17.1 Agilent ChemStation Agilent LTS 01.11 R/Rstudio CRAN/Posit v. 2021.09.0 R scripts used in this paper This paper https://doi.org/10.5281/zenodo.7659070 The Gene Ontology resource Geneontology.org v. 2023-01-01 Prism GraphPad v. 9.3.1
Article Title: High-Content Screening of Synaptic Density Modulators in Primary Neuronal Cultures.
Article Snippet: See the T erm s and C onditions (https://onlinelibrary.w iley.com /term s-and-conditions) on W iley O nline L ibrary for rules of use; O A articles are governed by the applicable C reative C om m ons L icense 2.5% (w/v) bovine serum albumin (BSA) in DPBS with 0.1% (v/v) Triton X-100 Primary antibodies: Chicken anti-Homer1 (Synaptic Systems, cat. no. 160006) Guinea pig anti-Synaptophysin (Synaptic Systems, cat. no. 101004) Mouse anti-MAP2 (Synaptic Systems, cat. no. 188011) 1× DPBS Secondary antibodies: Donkey anti-chicken Alexa 488 (Jackson ImmunoResearch, cat. no. 703-545-155) Goat anti-guinea pig Alexa 555 (Life Technologies, cat. no. A21435) Donkey anti-mouse Alexa 647 (Jackson ImmunoResearch, cat. no. 715-605-151) 16-channel pipet (Finnpipette F1; Thermo Scientific, cat. no. 4661090N) Aluminum sealing tape (Dutscher, cat. no. 106570, or similar) PlateHUB rotating plate-storage carousel (Agilent, model G5500-23447) Plate washer associated with liquid handler (BioTek, model EL406) Wash_Primary.pro and Wash_Secondary.pro programs (see Supporting Information) VWorks automation control software (Agilent) Aspirate.LHC and Aspirate-Dispense.LHC subroutines (see Supporting Information) Direct Drive Robot (Agilent) NOTE: Use sterile pipet tips with filters (Finntip 50; Thermo Scientific, cat. no. 94052060).
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