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    ATCC cell lines hek 293t atcc
    Cell Lines Hek 293t Atcc, supplied by ATCC, used in various techniques. Bioz Stars score: 99/100, based on 38021 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/cell+lines+hek+293t+cells+atcc+crl/293T/pm42285104-590-194-198
    Average 99 stars, based on 38021 article reviews
    cell lines hek 293t atcc - by Bioz Stars, 2026-09
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    Article Title: A positive feedback loop between FGR and p65 sustains satellite glial cell activation and chronic neuropathic pain.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Protease inhibitor cocktail Beyotime Cat# P1005 Triton TM X-100 Sigma-Aldrich Cat# X100 Critical commercial assays Pierce Classic Magnetic IP/Co-IP Kit Thermo Fisher Scientific Cat# 88804 EZ-Magna ChIP G-Chromatin Immunoprecipitation Kit Millipore Cat# 17-611 miRNeasy Mini Kit QIAGEN Cat# 217004 RNAscope® 2.5 HD Reagent Kit-RED ACD Cat# 322350 Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit Agilent Cat# 5067-1511 Dual-Luciferase Reporter Assay System Promega Cat# E1910 Mouse L308 Array RayBiotech AAM-BLG-L308 Deposited data RNA-seq on mouse DRGs, SC, Brainstem, Thalamus and Prefrontal cortex after SNL/ sham surgery This paper https://ngdc.cncb.ac.cn/gsa (CRA027545 for DRG, CRA027544 for spinal cord, CRA027543 for brainstem, CRA027530 for thalamus, and CRA027528 for prefrontal cortex) Experimental models: cell lines HEK-293T cells ATCC CRL-3216; RRID: CVCL_0063 Experimental models: organisms/strains C57BL/6J SLAC Laboratory C57BL/6Slac Macaques Guangzhou Conghua Huazhen Laboratory Animal Breeding Center N/A Oligonucleotides See Table S2 for qRT-PCR primer sequences This study N/A See Table S2 for ChIP-qPCR primer sequences This study N/A See Table S2 for target sequences against p65 or Fgr This study N/A Recombinant DNA Plasmid: Fgr-flag This study N/A Plasmid: p65-myc This study N/A Plasmid: p65mut1-myc This study N/A Plasmid: p65mut2-myc This study N/A Plasmid: Pp2a-HA This study N/A Plasmid: Gfp-flag This study N/A Plasmid: pRL-TK This study N/A Plasmid: pGL3-Basic This study N/A Plasmid: pGL3-Fgr promoter This study N/A Plasmid: Gfp This study N/A Plasmid: p65 This study N/A Software and algorithms JASPAR Rauluseviciute et al. 50 https://jaspar.elixir.no MED-PC CPP software MED Associates Inc. https://med-associates.com Applied Biosystems QuantStudio5 system Thermo Fisher Scientific https://www.thermofisher.cn/ GraphPad Prism 8 GraphPad Software, Inc. https://www.graphpad.com R R Core Team https://www.r-project.org/ ImageJ Schneider et al. 78 https://imagej.nih.gov/ij/ (Continued on next page) 22 Cell Reports 45, 116899, February 24, 2026

    shRNA:

    Article Title: Modulation of the mevalonate pathway by TCR engagement regulates T follicular helper cell generation in homeostasis and autoimmunity.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Opal 520 Reagent Pack PerkinElmer FP1487001KT Opal 570 Reagent Pack PerkinElmer FP1488001KT Opal 690 Reagent Pack PerkinElmer FP1497001KT KLH MERCK Cat# H7017 Tamoxifen MERCK Cat# T5648 NP-KLH (Keyhole Limpet Hemocyanin) Biosearch Technologies Cat# N-5060-25 SRBCs (15%) Solarbio Cat# S9702 LPS MERCK Cat# 437628 Alhydrogel adjuvant 2% InvivoGen Cat# vac-alu-50 BCG Adjuvant REBIO Cat# R19021 Complete Freund’s Adjuvant (CFA) MERCK Cat# F5881 Freund’s Adjuvant, Incomplete, (IFA) MERCK Cat# F5506 Cytoxan MedChemExpress Cat# HY-17420 Critical commercial assays EasySepTM Human Naı̈ve CD4+ T Cell Isolation Kit II Stemcell Cat# 17555 CD4 MicroBeads, human Miltenyi Biotec Cat# 130-045-101 EasySepTM Mouse CD4+ T Cell Isolation Kit Stemcell Cat# 19852 EasySepTM Mouse Naı̈ve CD4+ T Cell Isolation Kit Stemcell Cat# 19765 Zombie NIRTM Fixable Viability Kit BioLegend Cat# 423106 Zombie AquaTM Fixable Viability Kit BioLegend Cat# 423102 Human Interleukin 21, IL-21 ELISA Kit CUSABIO Cat# CSB-E11707h Mouse IL-21 ELISA Ready-SET-Go!TM Kit eBioscience Cat# BMS6021 Mouse anti-double stranded DNA antibody (IgM) ELISA Kit CUSABIO Cat# CSB-E11194m Mouse anti-nuclear Antibody (IgG) ELISA Kit CUSABIO Cat# CSB-E12912m eBioscienceTM IC Fixation Buffer Invitrogen Cat# 00-8222-49 Cytofix/Cytoperm Fixation/ Permeabilization Solution Kit BD Cat# 5547222 eBioscienceTM Foxp3 / Transcription Factor Staining Buffer Set Invitrogen Cat# 00-5523-00 Leukocyte Activation Cocktail, with BD GolgiPlugTM BD Cat# 550583 VeZol Reagent Vazyme Cat# R411-01 HiScript III RT SuperMix for qPCR (+gDNA wiper) Vazyme Cat# R323-01 ChamQ Universal SYBR qPCR Master Mix Vazyme Cat# Q711-02 SuperPico ECL Master Mix Vazyme Cat# E432-02 Hyperactive pG-MNase CUT&RUN Assay Kit for PCR/qPCR Vazyme Cat# ND607 Hyperactive Universal CUT&Tag Assay Kit Vazyme Cat# TD904 Immunol Staining Fix Solution Beyotime Cat# P0100A immune-electron microscopy fixation solution Servicebio Cat# G1102 SE Cell Line 4D X Kit L (12 RCT) Lonza V4XC-1012 P3 Primary Cell 4D X Kit L Lonza V4XP-3024 Dual-Luciferase Reporter Gene Assay Kit II Beyotime RG029S (Continued on next page) ll OPEN ACCESS Article e5 Immunity 59, 1–17.e1–e12, July 14, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data Raw and analyzed data This paper www.ncbi.nlm.nih.gov/sra/PRJNA1247225 Raw and analyzed data This paper www.ncbi.nlm.nih.gov/bioproject/ PRJNA1406436 Raw and analyzed data This paper www.ncbi.nlm.nih.gov/bioproject/ PRJNA1406179 Raw and analyzed data This paper http://central.proteomexchange.org/cgi/ GetDataset?ID=PXD062705 Raw and analyzed data This paper www.ebi.ac.uk/metabolights/ MTBLS12378 Raw and analyzed data This paper 10.6084/m9.figshare.25426150 Raw and analyzed data This paper 10.6084/m9.figshare.25427467 Raw and analyzed data This paper 10.6084/m9.figshare.25427470 Raw and analyzed data NBDC JGAS000486 Experimental models: Cell lines HEK-293T cells ATCC CRL-3216 Jurkat cells ATCC TIB-152 Experimental models: Organisms/strains C57BL/6J WT The Jackson Laboratory RRID:IMSR_JAX:000664 C57BL/6J Cd4CreERT2×Ggps1flox/flox mice This paper N/A C57BL/6J Cd4CreERT2×Rabggtaflox/flox mice This paper N/A C57BL/6J Cd4CreERT2×Pggt1bflox/flox mice This paper N/A B6 CD45.1+ mice The Jackson Laboratory RRID:IMSR_JAX:002014 MRL/MpJ-Faslpr/J The Jackson Laboratory RRID:IMSR_JAX:000485 MRL/MpJ The Jackson Laboratory RRID:IMSR_JAX:000486 B6(C)-H2-Ab1bm12/KhEgJ The Jackson Laboratory RRID:IMSR_JAX:001162 Oligonucleotides shRNA and siRNA sequence: Table S1 This paper N/A Real-time qPCR primers: Table S2 This paper N/A Genotyping primers: Table S3 This paper N/A Recombinant DNA pcSLenti-EF1-Puro-CMV-3*FlagRAB35-WPRE This paper N/A pcSLenti-EF1-Puro-CMV-3*FlagRAB35(C200A, C201A)-WPRE This paper N/A pcDNA3.1-CMV-3*HA-CXCR5-mcherry This paper N/A p-CMV-RAB35 (WT)-3*Flag-EGFP This paper N/A p-CMV-RAB35 (C200A, C201A)3*Flag-EGFP This paper N/A pGL3-basic-RABGGTA-WT firefly luciferase reporter This paper N/A pGL3-basic-RABGGTA-mutation firefly luciferase reporter This paper N/A pGL3-basic-RAB35-WT firefly luciferase reporter This paper N/A pGL3-basic-RAB35-mutation firefly luciferase reporter This paper N/A pcDNA3.1(+)-HA-E2F1 Public Protein/Plasmid Library Cat# PPL01074-2b (Continued on next page) ll OPEN ACCESSArticle Immunity 59, 1–17.e1–e12, July 14, 2026 e6 ..

    Sequencing:

    Article Title: Modulation of the mevalonate pathway by TCR engagement regulates T follicular helper cell generation in homeostasis and autoimmunity.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Opal 520 Reagent Pack PerkinElmer FP1487001KT Opal 570 Reagent Pack PerkinElmer FP1488001KT Opal 690 Reagent Pack PerkinElmer FP1497001KT KLH MERCK Cat# H7017 Tamoxifen MERCK Cat# T5648 NP-KLH (Keyhole Limpet Hemocyanin) Biosearch Technologies Cat# N-5060-25 SRBCs (15%) Solarbio Cat# S9702 LPS MERCK Cat# 437628 Alhydrogel adjuvant 2% InvivoGen Cat# vac-alu-50 BCG Adjuvant REBIO Cat# R19021 Complete Freund’s Adjuvant (CFA) MERCK Cat# F5881 Freund’s Adjuvant, Incomplete, (IFA) MERCK Cat# F5506 Cytoxan MedChemExpress Cat# HY-17420 Critical commercial assays EasySepTM Human Naı̈ve CD4+ T Cell Isolation Kit II Stemcell Cat# 17555 CD4 MicroBeads, human Miltenyi Biotec Cat# 130-045-101 EasySepTM Mouse CD4+ T Cell Isolation Kit Stemcell Cat# 19852 EasySepTM Mouse Naı̈ve CD4+ T Cell Isolation Kit Stemcell Cat# 19765 Zombie NIRTM Fixable Viability Kit BioLegend Cat# 423106 Zombie AquaTM Fixable Viability Kit BioLegend Cat# 423102 Human Interleukin 21, IL-21 ELISA Kit CUSABIO Cat# CSB-E11707h Mouse IL-21 ELISA Ready-SET-Go!TM Kit eBioscience Cat# BMS6021 Mouse anti-double stranded DNA antibody (IgM) ELISA Kit CUSABIO Cat# CSB-E11194m Mouse anti-nuclear Antibody (IgG) ELISA Kit CUSABIO Cat# CSB-E12912m eBioscienceTM IC Fixation Buffer Invitrogen Cat# 00-8222-49 Cytofix/Cytoperm Fixation/ Permeabilization Solution Kit BD Cat# 5547222 eBioscienceTM Foxp3 / Transcription Factor Staining Buffer Set Invitrogen Cat# 00-5523-00 Leukocyte Activation Cocktail, with BD GolgiPlugTM BD Cat# 550583 VeZol Reagent Vazyme Cat# R411-01 HiScript III RT SuperMix for qPCR (+gDNA wiper) Vazyme Cat# R323-01 ChamQ Universal SYBR qPCR Master Mix Vazyme Cat# Q711-02 SuperPico ECL Master Mix Vazyme Cat# E432-02 Hyperactive pG-MNase CUT&RUN Assay Kit for PCR/qPCR Vazyme Cat# ND607 Hyperactive Universal CUT&Tag Assay Kit Vazyme Cat# TD904 Immunol Staining Fix Solution Beyotime Cat# P0100A immune-electron microscopy fixation solution Servicebio Cat# G1102 SE Cell Line 4D X Kit L (12 RCT) Lonza V4XC-1012 P3 Primary Cell 4D X Kit L Lonza V4XP-3024 Dual-Luciferase Reporter Gene Assay Kit II Beyotime RG029S (Continued on next page) ll OPEN ACCESS Article e5 Immunity 59, 1–17.e1–e12, July 14, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data Raw and analyzed data This paper www.ncbi.nlm.nih.gov/sra/PRJNA1247225 Raw and analyzed data This paper www.ncbi.nlm.nih.gov/bioproject/ PRJNA1406436 Raw and analyzed data This paper www.ncbi.nlm.nih.gov/bioproject/ PRJNA1406179 Raw and analyzed data This paper http://central.proteomexchange.org/cgi/ GetDataset?ID=PXD062705 Raw and analyzed data This paper www.ebi.ac.uk/metabolights/ MTBLS12378 Raw and analyzed data This paper 10.6084/m9.figshare.25426150 Raw and analyzed data This paper 10.6084/m9.figshare.25427467 Raw and analyzed data This paper 10.6084/m9.figshare.25427470 Raw and analyzed data NBDC JGAS000486 Experimental models: Cell lines HEK-293T cells ATCC CRL-3216 Jurkat cells ATCC TIB-152 Experimental models: Organisms/strains C57BL/6J WT The Jackson Laboratory RRID:IMSR_JAX:000664 C57BL/6J Cd4CreERT2×Ggps1flox/flox mice This paper N/A C57BL/6J Cd4CreERT2×Rabggtaflox/flox mice This paper N/A C57BL/6J Cd4CreERT2×Pggt1bflox/flox mice This paper N/A B6 CD45.1+ mice The Jackson Laboratory RRID:IMSR_JAX:002014 MRL/MpJ-Faslpr/J The Jackson Laboratory RRID:IMSR_JAX:000485 MRL/MpJ The Jackson Laboratory RRID:IMSR_JAX:000486 B6(C)-H2-Ab1bm12/KhEgJ The Jackson Laboratory RRID:IMSR_JAX:001162 Oligonucleotides shRNA and siRNA sequence: Table S1 This paper N/A Real-time qPCR primers: Table S2 This paper N/A Genotyping primers: Table S3 This paper N/A Recombinant DNA pcSLenti-EF1-Puro-CMV-3*FlagRAB35-WPRE This paper N/A pcSLenti-EF1-Puro-CMV-3*FlagRAB35(C200A, C201A)-WPRE This paper N/A pcDNA3.1-CMV-3*HA-CXCR5-mcherry This paper N/A p-CMV-RAB35 (WT)-3*Flag-EGFP This paper N/A p-CMV-RAB35 (C200A, C201A)3*Flag-EGFP This paper N/A pGL3-basic-RABGGTA-WT firefly luciferase reporter This paper N/A pGL3-basic-RABGGTA-mutation firefly luciferase reporter This paper N/A pGL3-basic-RAB35-WT firefly luciferase reporter This paper N/A pGL3-basic-RAB35-mutation firefly luciferase reporter This paper N/A pcDNA3.1(+)-HA-E2F1 Public Protein/Plasmid Library Cat# PPL01074-2b (Continued on next page) ll OPEN ACCESSArticle Immunity 59, 1–17.e1–e12, July 14, 2026 e6 ..

    Real-time Polymerase Chain Reaction:

    Article Title: Modulation of the mevalonate pathway by TCR engagement regulates T follicular helper cell generation in homeostasis and autoimmunity.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Opal 520 Reagent Pack PerkinElmer FP1487001KT Opal 570 Reagent Pack PerkinElmer FP1488001KT Opal 690 Reagent Pack PerkinElmer FP1497001KT KLH MERCK Cat# H7017 Tamoxifen MERCK Cat# T5648 NP-KLH (Keyhole Limpet Hemocyanin) Biosearch Technologies Cat# N-5060-25 SRBCs (15%) Solarbio Cat# S9702 LPS MERCK Cat# 437628 Alhydrogel adjuvant 2% InvivoGen Cat# vac-alu-50 BCG Adjuvant REBIO Cat# R19021 Complete Freund’s Adjuvant (CFA) MERCK Cat# F5881 Freund’s Adjuvant, Incomplete, (IFA) MERCK Cat# F5506 Cytoxan MedChemExpress Cat# HY-17420 Critical commercial assays EasySepTM Human Naı̈ve CD4+ T Cell Isolation Kit II Stemcell Cat# 17555 CD4 MicroBeads, human Miltenyi Biotec Cat# 130-045-101 EasySepTM Mouse CD4+ T Cell Isolation Kit Stemcell Cat# 19852 EasySepTM Mouse Naı̈ve CD4+ T Cell Isolation Kit Stemcell Cat# 19765 Zombie NIRTM Fixable Viability Kit BioLegend Cat# 423106 Zombie AquaTM Fixable Viability Kit BioLegend Cat# 423102 Human Interleukin 21, IL-21 ELISA Kit CUSABIO Cat# CSB-E11707h Mouse IL-21 ELISA Ready-SET-Go!TM Kit eBioscience Cat# BMS6021 Mouse anti-double stranded DNA antibody (IgM) ELISA Kit CUSABIO Cat# CSB-E11194m Mouse anti-nuclear Antibody (IgG) ELISA Kit CUSABIO Cat# CSB-E12912m eBioscienceTM IC Fixation Buffer Invitrogen Cat# 00-8222-49 Cytofix/Cytoperm Fixation/ Permeabilization Solution Kit BD Cat# 5547222 eBioscienceTM Foxp3 / Transcription Factor Staining Buffer Set Invitrogen Cat# 00-5523-00 Leukocyte Activation Cocktail, with BD GolgiPlugTM BD Cat# 550583 VeZol Reagent Vazyme Cat# R411-01 HiScript III RT SuperMix for qPCR (+gDNA wiper) Vazyme Cat# R323-01 ChamQ Universal SYBR qPCR Master Mix Vazyme Cat# Q711-02 SuperPico ECL Master Mix Vazyme Cat# E432-02 Hyperactive pG-MNase CUT&RUN Assay Kit for PCR/qPCR Vazyme Cat# ND607 Hyperactive Universal CUT&Tag Assay Kit Vazyme Cat# TD904 Immunol Staining Fix Solution Beyotime Cat# P0100A immune-electron microscopy fixation solution Servicebio Cat# G1102 SE Cell Line 4D X Kit L (12 RCT) Lonza V4XC-1012 P3 Primary Cell 4D X Kit L Lonza V4XP-3024 Dual-Luciferase Reporter Gene Assay Kit II Beyotime RG029S (Continued on next page) ll OPEN ACCESS Article e5 Immunity 59, 1–17.e1–e12, July 14, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data Raw and analyzed data This paper www.ncbi.nlm.nih.gov/sra/PRJNA1247225 Raw and analyzed data This paper www.ncbi.nlm.nih.gov/bioproject/ PRJNA1406436 Raw and analyzed data This paper www.ncbi.nlm.nih.gov/bioproject/ PRJNA1406179 Raw and analyzed data This paper http://central.proteomexchange.org/cgi/ GetDataset?ID=PXD062705 Raw and analyzed data This paper www.ebi.ac.uk/metabolights/ MTBLS12378 Raw and analyzed data This paper 10.6084/m9.figshare.25426150 Raw and analyzed data This paper 10.6084/m9.figshare.25427467 Raw and analyzed data This paper 10.6084/m9.figshare.25427470 Raw and analyzed data NBDC JGAS000486 Experimental models: Cell lines HEK-293T cells ATCC CRL-3216 Jurkat cells ATCC TIB-152 Experimental models: Organisms/strains C57BL/6J WT The Jackson Laboratory RRID:IMSR_JAX:000664 C57BL/6J Cd4CreERT2×Ggps1flox/flox mice This paper N/A C57BL/6J Cd4CreERT2×Rabggtaflox/flox mice This paper N/A C57BL/6J Cd4CreERT2×Pggt1bflox/flox mice This paper N/A B6 CD45.1+ mice The Jackson Laboratory RRID:IMSR_JAX:002014 MRL/MpJ-Faslpr/J The Jackson Laboratory RRID:IMSR_JAX:000485 MRL/MpJ The Jackson Laboratory RRID:IMSR_JAX:000486 B6(C)-H2-Ab1bm12/KhEgJ The Jackson Laboratory RRID:IMSR_JAX:001162 Oligonucleotides shRNA and siRNA sequence: Table S1 This paper N/A Real-time qPCR primers: Table S2 This paper N/A Genotyping primers: Table S3 This paper N/A Recombinant DNA pcSLenti-EF1-Puro-CMV-3*FlagRAB35-WPRE This paper N/A pcSLenti-EF1-Puro-CMV-3*FlagRAB35(C200A, C201A)-WPRE This paper N/A pcDNA3.1-CMV-3*HA-CXCR5-mcherry This paper N/A p-CMV-RAB35 (WT)-3*Flag-EGFP This paper N/A p-CMV-RAB35 (C200A, C201A)3*Flag-EGFP This paper N/A pGL3-basic-RABGGTA-WT firefly luciferase reporter This paper N/A pGL3-basic-RABGGTA-mutation firefly luciferase reporter This paper N/A pGL3-basic-RAB35-WT firefly luciferase reporter This paper N/A pGL3-basic-RAB35-mutation firefly luciferase reporter This paper N/A pcDNA3.1(+)-HA-E2F1 Public Protein/Plasmid Library Cat# PPL01074-2b (Continued on next page) ll OPEN ACCESSArticle Immunity 59, 1–17.e1–e12, July 14, 2026 e6 ..

    Recombinant:

    Article Title: Modulation of the mevalonate pathway by TCR engagement regulates T follicular helper cell generation in homeostasis and autoimmunity.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Opal 520 Reagent Pack PerkinElmer FP1487001KT Opal 570 Reagent Pack PerkinElmer FP1488001KT Opal 690 Reagent Pack PerkinElmer FP1497001KT KLH MERCK Cat# H7017 Tamoxifen MERCK Cat# T5648 NP-KLH (Keyhole Limpet Hemocyanin) Biosearch Technologies Cat# N-5060-25 SRBCs (15%) Solarbio Cat# S9702 LPS MERCK Cat# 437628 Alhydrogel adjuvant 2% InvivoGen Cat# vac-alu-50 BCG Adjuvant REBIO Cat# R19021 Complete Freund’s Adjuvant (CFA) MERCK Cat# F5881 Freund’s Adjuvant, Incomplete, (IFA) MERCK Cat# F5506 Cytoxan MedChemExpress Cat# HY-17420 Critical commercial assays EasySepTM Human Naı̈ve CD4+ T Cell Isolation Kit II Stemcell Cat# 17555 CD4 MicroBeads, human Miltenyi Biotec Cat# 130-045-101 EasySepTM Mouse CD4+ T Cell Isolation Kit Stemcell Cat# 19852 EasySepTM Mouse Naı̈ve CD4+ T Cell Isolation Kit Stemcell Cat# 19765 Zombie NIRTM Fixable Viability Kit BioLegend Cat# 423106 Zombie AquaTM Fixable Viability Kit BioLegend Cat# 423102 Human Interleukin 21, IL-21 ELISA Kit CUSABIO Cat# CSB-E11707h Mouse IL-21 ELISA Ready-SET-Go!TM Kit eBioscience Cat# BMS6021 Mouse anti-double stranded DNA antibody (IgM) ELISA Kit CUSABIO Cat# CSB-E11194m Mouse anti-nuclear Antibody (IgG) ELISA Kit CUSABIO Cat# CSB-E12912m eBioscienceTM IC Fixation Buffer Invitrogen Cat# 00-8222-49 Cytofix/Cytoperm Fixation/ Permeabilization Solution Kit BD Cat# 5547222 eBioscienceTM Foxp3 / Transcription Factor Staining Buffer Set Invitrogen Cat# 00-5523-00 Leukocyte Activation Cocktail, with BD GolgiPlugTM BD Cat# 550583 VeZol Reagent Vazyme Cat# R411-01 HiScript III RT SuperMix for qPCR (+gDNA wiper) Vazyme Cat# R323-01 ChamQ Universal SYBR qPCR Master Mix Vazyme Cat# Q711-02 SuperPico ECL Master Mix Vazyme Cat# E432-02 Hyperactive pG-MNase CUT&RUN Assay Kit for PCR/qPCR Vazyme Cat# ND607 Hyperactive Universal CUT&Tag Assay Kit Vazyme Cat# TD904 Immunol Staining Fix Solution Beyotime Cat# P0100A immune-electron microscopy fixation solution Servicebio Cat# G1102 SE Cell Line 4D X Kit L (12 RCT) Lonza V4XC-1012 P3 Primary Cell 4D X Kit L Lonza V4XP-3024 Dual-Luciferase Reporter Gene Assay Kit II Beyotime RG029S (Continued on next page) ll OPEN ACCESS Article e5 Immunity 59, 1–17.e1–e12, July 14, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data Raw and analyzed data This paper www.ncbi.nlm.nih.gov/sra/PRJNA1247225 Raw and analyzed data This paper www.ncbi.nlm.nih.gov/bioproject/ PRJNA1406436 Raw and analyzed data This paper www.ncbi.nlm.nih.gov/bioproject/ PRJNA1406179 Raw and analyzed data This paper http://central.proteomexchange.org/cgi/ GetDataset?ID=PXD062705 Raw and analyzed data This paper www.ebi.ac.uk/metabolights/ MTBLS12378 Raw and analyzed data This paper 10.6084/m9.figshare.25426150 Raw and analyzed data This paper 10.6084/m9.figshare.25427467 Raw and analyzed data This paper 10.6084/m9.figshare.25427470 Raw and analyzed data NBDC JGAS000486 Experimental models: Cell lines HEK-293T cells ATCC CRL-3216 Jurkat cells ATCC TIB-152 Experimental models: Organisms/strains C57BL/6J WT The Jackson Laboratory RRID:IMSR_JAX:000664 C57BL/6J Cd4CreERT2×Ggps1flox/flox mice This paper N/A C57BL/6J Cd4CreERT2×Rabggtaflox/flox mice This paper N/A C57BL/6J Cd4CreERT2×Pggt1bflox/flox mice This paper N/A B6 CD45.1+ mice The Jackson Laboratory RRID:IMSR_JAX:002014 MRL/MpJ-Faslpr/J The Jackson Laboratory RRID:IMSR_JAX:000485 MRL/MpJ The Jackson Laboratory RRID:IMSR_JAX:000486 B6(C)-H2-Ab1bm12/KhEgJ The Jackson Laboratory RRID:IMSR_JAX:001162 Oligonucleotides shRNA and siRNA sequence: Table S1 This paper N/A Real-time qPCR primers: Table S2 This paper N/A Genotyping primers: Table S3 This paper N/A Recombinant DNA pcSLenti-EF1-Puro-CMV-3*FlagRAB35-WPRE This paper N/A pcSLenti-EF1-Puro-CMV-3*FlagRAB35(C200A, C201A)-WPRE This paper N/A pcDNA3.1-CMV-3*HA-CXCR5-mcherry This paper N/A p-CMV-RAB35 (WT)-3*Flag-EGFP This paper N/A p-CMV-RAB35 (C200A, C201A)3*Flag-EGFP This paper N/A pGL3-basic-RABGGTA-WT firefly luciferase reporter This paper N/A pGL3-basic-RABGGTA-mutation firefly luciferase reporter This paper N/A pGL3-basic-RAB35-WT firefly luciferase reporter This paper N/A pGL3-basic-RAB35-mutation firefly luciferase reporter This paper N/A pcDNA3.1(+)-HA-E2F1 Public Protein/Plasmid Library Cat# PPL01074-2b (Continued on next page) ll OPEN ACCESSArticle Immunity 59, 1–17.e1–e12, July 14, 2026 e6 ..

    Article Title: Presynaptic Biogenesis Requires Axonal Transport of Lysosome-Related Vesicles.
    Article Snippet: LI-COR Biosciences 925-32211 Alexa 488 goat anti-mouse (used at 1:500 in IF) Invitrogen A11029 Alexa 568 goat anti-rabbit (used at 1:500 in IF) Invitrogen A11011 Chemicals, Peptides, and Recombinant Proteins siRNA smart pool mouse arl8a Dharmacon 68724 (Continued on next page) e1 Neuron 99, 1–17.e1–e7, September 19, 2018 .. REAGENT or RESOURCE SOURCE IDENTIFIER Experimental Models: Cell Lines HEK 293T cells ATCC CRL-3216 Experimental Models: Organisms/Strains w1118 as wild type Bloomington N/A OK6-GAL4, UAS-BRP-D3-Straw (UAS-BRP is a truncated BRP from aa 473-1227) Sigrist lab, see Fouquet et al., 2009 N/A UAS-Lamp1-GFP Kr€amer lab (UT Southwestern, Dallas, TX, USA) N/A UAS-BRP-D3-GFP/OK6-GAL4; Ok6-Gal4: Bloomington #64199 UAS-Spinster-RFP/+; Sweeney lab (Univ. of York, UK) N/A OK6-GAL4,UAS-BRP-D3-Straw/UAS-Arl8-GFP UAS-Arl8-GFP: Sigrist lab N/A OK6-GAL4/UAS-Lamp1-GFP as above N/A PBac(RB)Giee00336/PBac(RB)Giee00336 Bloomington #17846 OK6-GAL4/UAS-D3-Straw, PBac(RB)Giee00336 as above N/A OK6-GAL4/UAS-Arl8; PBac(RB)Giee00336/PBac(RB)Giee00336 as above N/A OK6-GAL4/UAS-Arl8 as above N/A UAS-BRP-D3-Straw/OK6-GAL4,UAS-Rab7-GFP UAS-Rab7: Bloomington #42705 UAS-BRP-D3-Straw/OK6-GAL4,UAS-Rab7-GFP as above N/A OK6-GAL4/UAS-Arl8-GFP as above N/A UAS Spinster/+, OK6-GAL4-UASDicer2/+ UAS-Dicer2: VDRC N/A UAS Spinster/+, OK6-GAL4-Dicer2/+ as above N/A OK6-GAL4-Dicer2/UAS-Arl8-RNAi UAS-Arl8-RNAi: VDRC #26085 OK6-GAL4-UAS-Dicer2/UAS-VPS39-RNAi UAS-VPS39 RNAi: VDRC #40427 OK6-GAL4/+; PBac(RB)Giee00336/PBac(RB)Giee0033 as above N/A Oligonucleotides Fwd (KpnI): 50-GACTGGTACCGAATGTTGGCCCTCATCA ACAGGATCCTC-30 MWG N/A Rev (NotI): 50-AGTGCGGCCGCCAACGACTTTGGCTTTTC GAATGTTGAATTAAC-30 MWG N/A Recombinant DNA Gateway entry vector pENTR4 (Invitrogen) Addgene #17424 pUASt-destination vector (pTW, pTWG ) DGRC 1129, 1076 cDNA encoding full length Drosophila Arl8 DGRC LD29185 GFP-Basson 95-3938 Eckardt D. Gundelfinger (LIN, Magdeburg) Dresbach et al., 2006 Arl8b-HA pcDNA3 This study N/A Arl8b-mCherry pcDNA3 This study N/A vGlut1-mCherry Franck Polleux (Columbia university, New York) Kwon et al., 2016 Lamp1-mCherry Addgene #79998; Shcherbakova et al., 2016 vGlut1-VENUS Etienne Herzog (FBN, Bordeaux) Herzog et al., 2011 Lamp1- miRFP703 Addgene #79998 Rab7-EGFP Peter van der Sluijs (UMC, Utrecht) N/A EGFP-Synapsin1a Hung-Teh Kao (Brown University, Rhode Island) N/A dArl8-GFP Sean Munro, (MRC LMB Cambridge, UK) N/A dUnc104/imac-myc Thomas Schwarz (Children’s Hospital, Boston) clone 6-4-1 (Continued on next page) Neuron 99, 1–17.e1–e7, September 19, 2018 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER Software and Algorithms ImageJ Open Source Software https://imagej.net/Welcome ImageJ Coloc 2 Open Source Software https://imagej.net/Welcome ImageJ Plugin KymoAnalyzer v.1.01 Open Source Software https://imagej.net/Welcome

    Article Title: Focal clusters of peri-synaptic matrix contribute to activity-dependent plasticity and memory in mice.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-CS56 Sigma-Aldrich C8035; RRDI:AB_476879 Anti-CS56 (for immunoblot and affinity purification) Abcam ab11570: RRDI:AB_298176 Anti-Arc/Arg3.1 Proteintech 16290-1-AP; RRDI:AB_2151832 Anti-PSD95 Abcam ab90426; RRID:AB_2050168 Anti-Versican Merck AB1032, RRID:AB_2214376 Anti-Versican (for immunoblot) Santa Cruz sc-25831; RRID:AB_2241501 Anti-aggrecan (for immunoblot) Abcam ab36861; RRID:AB_722655 Anti-Parvalbumin Synaptic Systems 195 006; RRID:AB_2619887 Anti-Chondroitin Sulfate A mAb (Clone 2H6) Cosmo Bio CAC-NU-07-001 Mouse IgM isotype control Thermo Fisher 14-4752-82; RRID:AB_470123 Mouse IgM isotype control Santa Cruz sc-3881; RRID:AB_737292 Alexa Fluor 647 Goat anti-mouse Abcam ab150115; RRID:AB_2687948 Alexa Fluor 594 Goat anti-mouse Abcam ab150116; RRID:AB_2650601 Alexa Fluor 405 Goat anti-Rabbit Abcam ab175652; RRID:AB_2687498 Alexa Fluor 647 Goat anti-Rabbit Abcam ab150079; RRID:AB_2722623 Alexa Fluor 488 Donkey anti-goat Abcam ab150129; RRID:AB_2687506 Alexa Fluor 405 Goat anti-Chicken Abcam ab175674; RRID:AB_2890171 Alexa Fluor 546 Goat anti-Mouse Thermo Fisher A-11003; RRID:AB_141370 Bacterial and virus strains pAAV_U6_VCAN_shRNA_GFP Dr. Dityatev’s group N/A pAAV_U6_scramble_shRNA_GFP Mitlöhner et al.56 N/A Competent E. coli NEB C3040H Biological samples Human postmortem Amygdala sample from healthy donor Harvard Brain Tissue Resource Center/NIH NeuroBioBank N/A Chemicals, peptides, and recombinant proteins Bovine serum albumin (BSA) Thermo Fisher BP1605100 Paraformaldehyde (PFA; powder) Sigma-Aldrich P6148 Glutaraldehyde Sigma-Aldrich G6257 Sodium cacodylate Sigma-Aldrich C0250 Hydrogen peroxide Fisher H325100 Glycine Sigma G-7403 Triton X-100 Fisher AC215680010 Goat serum Gibco 16210-064 Streptavidin - Horseradish peroxidase Invitrogen 434323 3,3’-Diaminobenzidine Tetrahydrochloride Sigma D5905-100TAB Cytoseal Thermo Fisher 8310-16 Fluomount Southern biotech 0100-01 Chondroitinase ABC amsbio AMS.E1028-10 HaltTM Protease Inhibitor Cocktail Thermo Fisher 78429 Sodium borohydride Fisher AC448501000 Formic Acid/Acetonitrile 0.1/99.9, v/v Sigma-Aldrich 159002 Ammonium hydroxide Sigma-Aldrich 221228 Blocking Buffer Li-Cor 92760001 (Continued on next page) Cell Reports 43, 114112, May 28, 2024 17 .. REAGENT or RESOURCE SOURCE IDENTIFIER NuPage Bis-Tris Thermo Fisher NP0335BOX Mercaptoethanol Sigma-Aldrich M3148 Trifluoracetic acid Sigma-Aldrich 808260 Uranyl acetate Sigma-Aldrich M1775 Embed 812 resin Electron Microscopy Sciences 14900 Fetal Bovine Serum Life Technologies 10270106 PBS pH 7.4 Life Technologies 10010015 DMEM, high glucose Life Technologies 41965062 HBSS Life Technologies 14175053 Iscoves Modified Dulbecco Media Sigma Aldrich I3390 Laminin Sigma Aldrich L2020 Poly-L-Lysine Sigma Aldrich L2636 Trypsin-EDTA (0.05%) Life Technologies 25300054 Penicillin-Streptomycin (10,000 U/mL) Life Technologies 15140122 L-Glutamine Life Technologies 25030024 B27 Supplement Life Technologies 17504044 Neurobasal Media Life Technologies 21103049 Critical commercial assays PierceTMSilver Stain kit Thermo Fisher 24612 SimplyBluTMSafeStain Thermo Fisher LC6060 Protein L Sepharose Abcam ab193261 M-270 Epoxy beads Thermo Fisher 14301 BCA protein assay Thermo Fisher A55860 DNA/RNA Extracol kit EURX 3750 1X HALT protease inhibitor Thermo FIsher P187786 High-Capacity cDNA Reverse Transcription Kit Applied BiosystemsTM 4368814 TaqMan gene expression array Thermo FIsher 4331182 TaqManTM Fast Universal PCR Master Mix Applied BiosystemsTM 4352042 Deposited data Mouse proteomic raw data This Manuscript PXD047129 https://doi.org/10.6019/PXD047129 Human proteomic data This Manuscript PXD050008 https://doi.org/10.6019/PXD050008 Experimental models: Cell lines HEK 293T cells ATCC CRL-1573 Primary hippocampal culture This manuscript N/A Experimental models: Organisms/strains c57bl/6j - Males The Jackson Laboratory 000664 B6 Cg-Tg(Thy1-YFP)HJrs/J - Males The Jackson Laboratory 003782 C57BL/6NCrl - Males Charles River 027 Oligonucleotides Gapdh TaqMan Mm99999915_g1 Vcan TaqMan Mm01283063_m1 Chst3 TaqMan Mm00489736_m1 Chst7 TaqMan Mm00491466_m1 Chst11 TaqMan Mm00517562_m1 Chst12 TaqMan Mm00546416_s1 Recombinant DNA pAAV-U6-GFP Expression Vector Cell Biolabs VPK-413 (Continued on next page) 18 Cell Reports 43, 114112, May 28, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER pAAV_U6_VCANshRNA_GFP This manuscript N/A pAAV_U6_CtrlshRNA_GFP Mitlöhner et al.56 https://doi.org/10.3390/cells9020260 pAAV_U6_scramble_shRNA_GFP Mitlöhner et al.56 https://doi.org/10.3390/cells9020260 Software and algorithms ImageJ/FIJI Schneider et al.57 https://imagej.net/software/fiji/ Prism (version 8) GraphPad https://www.graphpad.com/ scientific-software/prism PATCHMASTER HEKA https://www.heka.com/downloads/ downloads_main.html#down_patchmaster StereoInvestigator 6.0 Micro-Brightfield N/A Leica LAS-X software Leica N/A Other Vibratome Leica VT1200S Microtome American Optical 860 Cryostat Leica CM1950 Double edge, breakable style razor blades Cetim AISI 440 Low-profile disposable cryostat blades Leica DB80LX Automatic tissue homogenizer Avantor SCERSP749540-0000 Disposable pestles, PP, 1.5mL Avantor SCERSP749521-1500 5600+ QTOF mass spectrometer Sciex N/A Q-Exactive HF mass spectrometer Thermo Fisher N/A nanoAcquity UPLC Waters N/A Eksigent nanoLC.as-2 autosampler SpectraLab Others-00-001 NANOSpray III Source Sciex p/n 1034661 Acclaim PepMap100 Thermo Fisher 164946 IntegraFrit Trap Column New Objective N/A Odyssey Scanner Li-Cor N/A Bio-Rad semidry transblotters Bio-Rad N/A Standard surgical blades Word Precision Instruments 500240 SuperFrost Ultra PlusTM Gold slides Fisher scientific 11976299 PierceTM C18 Spin tips and columns Thermo Fisher 87782 EPC-10 amplifier HEKA Elektronik N/A Quant-Studio-5 device Applied Biosystems A28569 Zeiss Axio Imager M2 fluorescent microscope Zeiss M2: 430004-9902 Stereotactic frame Narishige Scientific Instrument Lab SR-6M Ultra microinfusion pump World Precision Instrument UMP3 Confocal laser scanning microscope Leica TCS SP8 Scanning electron microscope JEM 1200EX II JEOL N/A Zeiss Axioskop 2 Plus Zeiss SM100297-MG1 6 well cell culture plate Greiner Bio One GB657160

    Luciferase:

    Article Title: Modulation of the mevalonate pathway by TCR engagement regulates T follicular helper cell generation in homeostasis and autoimmunity.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Opal 520 Reagent Pack PerkinElmer FP1487001KT Opal 570 Reagent Pack PerkinElmer FP1488001KT Opal 690 Reagent Pack PerkinElmer FP1497001KT KLH MERCK Cat# H7017 Tamoxifen MERCK Cat# T5648 NP-KLH (Keyhole Limpet Hemocyanin) Biosearch Technologies Cat# N-5060-25 SRBCs (15%) Solarbio Cat# S9702 LPS MERCK Cat# 437628 Alhydrogel adjuvant 2% InvivoGen Cat# vac-alu-50 BCG Adjuvant REBIO Cat# R19021 Complete Freund’s Adjuvant (CFA) MERCK Cat# F5881 Freund’s Adjuvant, Incomplete, (IFA) MERCK Cat# F5506 Cytoxan MedChemExpress Cat# HY-17420 Critical commercial assays EasySepTM Human Naı̈ve CD4+ T Cell Isolation Kit II Stemcell Cat# 17555 CD4 MicroBeads, human Miltenyi Biotec Cat# 130-045-101 EasySepTM Mouse CD4+ T Cell Isolation Kit Stemcell Cat# 19852 EasySepTM Mouse Naı̈ve CD4+ T Cell Isolation Kit Stemcell Cat# 19765 Zombie NIRTM Fixable Viability Kit BioLegend Cat# 423106 Zombie AquaTM Fixable Viability Kit BioLegend Cat# 423102 Human Interleukin 21, IL-21 ELISA Kit CUSABIO Cat# CSB-E11707h Mouse IL-21 ELISA Ready-SET-Go!TM Kit eBioscience Cat# BMS6021 Mouse anti-double stranded DNA antibody (IgM) ELISA Kit CUSABIO Cat# CSB-E11194m Mouse anti-nuclear Antibody (IgG) ELISA Kit CUSABIO Cat# CSB-E12912m eBioscienceTM IC Fixation Buffer Invitrogen Cat# 00-8222-49 Cytofix/Cytoperm Fixation/ Permeabilization Solution Kit BD Cat# 5547222 eBioscienceTM Foxp3 / Transcription Factor Staining Buffer Set Invitrogen Cat# 00-5523-00 Leukocyte Activation Cocktail, with BD GolgiPlugTM BD Cat# 550583 VeZol Reagent Vazyme Cat# R411-01 HiScript III RT SuperMix for qPCR (+gDNA wiper) Vazyme Cat# R323-01 ChamQ Universal SYBR qPCR Master Mix Vazyme Cat# Q711-02 SuperPico ECL Master Mix Vazyme Cat# E432-02 Hyperactive pG-MNase CUT&RUN Assay Kit for PCR/qPCR Vazyme Cat# ND607 Hyperactive Universal CUT&Tag Assay Kit Vazyme Cat# TD904 Immunol Staining Fix Solution Beyotime Cat# P0100A immune-electron microscopy fixation solution Servicebio Cat# G1102 SE Cell Line 4D X Kit L (12 RCT) Lonza V4XC-1012 P3 Primary Cell 4D X Kit L Lonza V4XP-3024 Dual-Luciferase Reporter Gene Assay Kit II Beyotime RG029S (Continued on next page) ll OPEN ACCESS Article e5 Immunity 59, 1–17.e1–e12, July 14, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data Raw and analyzed data This paper www.ncbi.nlm.nih.gov/sra/PRJNA1247225 Raw and analyzed data This paper www.ncbi.nlm.nih.gov/bioproject/ PRJNA1406436 Raw and analyzed data This paper www.ncbi.nlm.nih.gov/bioproject/ PRJNA1406179 Raw and analyzed data This paper http://central.proteomexchange.org/cgi/ GetDataset?ID=PXD062705 Raw and analyzed data This paper www.ebi.ac.uk/metabolights/ MTBLS12378 Raw and analyzed data This paper 10.6084/m9.figshare.25426150 Raw and analyzed data This paper 10.6084/m9.figshare.25427467 Raw and analyzed data This paper 10.6084/m9.figshare.25427470 Raw and analyzed data NBDC JGAS000486 Experimental models: Cell lines HEK-293T cells ATCC CRL-3216 Jurkat cells ATCC TIB-152 Experimental models: Organisms/strains C57BL/6J WT The Jackson Laboratory RRID:IMSR_JAX:000664 C57BL/6J Cd4CreERT2×Ggps1flox/flox mice This paper N/A C57BL/6J Cd4CreERT2×Rabggtaflox/flox mice This paper N/A C57BL/6J Cd4CreERT2×Pggt1bflox/flox mice This paper N/A B6 CD45.1+ mice The Jackson Laboratory RRID:IMSR_JAX:002014 MRL/MpJ-Faslpr/J The Jackson Laboratory RRID:IMSR_JAX:000485 MRL/MpJ The Jackson Laboratory RRID:IMSR_JAX:000486 B6(C)-H2-Ab1bm12/KhEgJ The Jackson Laboratory RRID:IMSR_JAX:001162 Oligonucleotides shRNA and siRNA sequence: Table S1 This paper N/A Real-time qPCR primers: Table S2 This paper N/A Genotyping primers: Table S3 This paper N/A Recombinant DNA pcSLenti-EF1-Puro-CMV-3*FlagRAB35-WPRE This paper N/A pcSLenti-EF1-Puro-CMV-3*FlagRAB35(C200A, C201A)-WPRE This paper N/A pcDNA3.1-CMV-3*HA-CXCR5-mcherry This paper N/A p-CMV-RAB35 (WT)-3*Flag-EGFP This paper N/A p-CMV-RAB35 (C200A, C201A)3*Flag-EGFP This paper N/A pGL3-basic-RABGGTA-WT firefly luciferase reporter This paper N/A pGL3-basic-RABGGTA-mutation firefly luciferase reporter This paper N/A pGL3-basic-RAB35-WT firefly luciferase reporter This paper N/A pGL3-basic-RAB35-mutation firefly luciferase reporter This paper N/A pcDNA3.1(+)-HA-E2F1 Public Protein/Plasmid Library Cat# PPL01074-2b (Continued on next page) ll OPEN ACCESSArticle Immunity 59, 1–17.e1–e12, July 14, 2026 e6 ..

    RNA Sequencing:

    Article Title: Development of human alveolar epithelial cell models to study distal lung biology and disease.
    Article Snippet: Matrigel Matrix Growth Factor Reduced Corning 354230 Matrigel Membrane Matrix Corning 354234 Histogel ThermoFisher HG-4000 DAPI mounting solution Vector Laboratories H-1200 .. Raw data SuperSeries This paper GEO: GSE164515 Raw and analyzed bulk RNA-seq data SubSeries This paper GEO: GSE164513 Raw and analyzed scRNA-seq data SubSeries This paper GEO: GSE164514 Experimental models: Cell lines HEK 293T cells ATCC CRL-3216; RRID:CVCL_0063 Human A549 lung adenocarcinoma cells ATCC CRM-CCL-185; RRID:CVCL_0023 Mouse MLg fibroblasts ATCC CCL-206; RRID:CVCL_0437 AEC-FT-ROCKinh cells This paper AEC-ON-ROCKinh cells This paper AEC-TN-ROCKinh cells This paper AEC-FT cells This paper AEC-ON cells This paper AEC-TN cells This paper Experimental models: Organisms/strains NU/J mice, 6 weeks, homozygous Foxn1nu Jackson Laboratories 002019; RRID:IMSR_JAX:002019 ..

    Stable Transfection:

    Article Title: Global profiling of nascent chain interactors reveals TRIM25 as a co-translational E3 ubiquitin ligase.
    Article Snippet: Short article Global profiling of nascent chain interactors reveals TRIM25 as a co-translational E3 ubiquitin ligase

    Transduction:

    Article Title: Global profiling of nascent chain interactors reveals TRIM25 as a co-translational E3 ubiquitin ligase.
    Article Snippet: Short article Global profiling of nascent chain interactors reveals TRIM25 as a co-translational E3 ubiquitin ligase

    Polymerase Chain Reaction:

    Article Title: Global profiling of nascent chain interactors reveals TRIM25 as a co-translational E3 ubiquitin ligase.
    Article Snippet: Short article Global profiling of nascent chain interactors reveals TRIM25 as a co-translational E3 ubiquitin ligase

    Article Title: Focal clusters of peri-synaptic matrix contribute to activity-dependent plasticity and memory in mice.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-CS56 Sigma-Aldrich C8035; RRDI:AB_476879 Anti-CS56 (for immunoblot and affinity purification) Abcam ab11570: RRDI:AB_298176 Anti-Arc/Arg3.1 Proteintech 16290-1-AP; RRDI:AB_2151832 Anti-PSD95 Abcam ab90426; RRID:AB_2050168 Anti-Versican Merck AB1032, RRID:AB_2214376 Anti-Versican (for immunoblot) Santa Cruz sc-25831; RRID:AB_2241501 Anti-aggrecan (for immunoblot) Abcam ab36861; RRID:AB_722655 Anti-Parvalbumin Synaptic Systems 195 006; RRID:AB_2619887 Anti-Chondroitin Sulfate A mAb (Clone 2H6) Cosmo Bio CAC-NU-07-001 Mouse IgM isotype control Thermo Fisher 14-4752-82; RRID:AB_470123 Mouse IgM isotype control Santa Cruz sc-3881; RRID:AB_737292 Alexa Fluor 647 Goat anti-mouse Abcam ab150115; RRID:AB_2687948 Alexa Fluor 594 Goat anti-mouse Abcam ab150116; RRID:AB_2650601 Alexa Fluor 405 Goat anti-Rabbit Abcam ab175652; RRID:AB_2687498 Alexa Fluor 647 Goat anti-Rabbit Abcam ab150079; RRID:AB_2722623 Alexa Fluor 488 Donkey anti-goat Abcam ab150129; RRID:AB_2687506 Alexa Fluor 405 Goat anti-Chicken Abcam ab175674; RRID:AB_2890171 Alexa Fluor 546 Goat anti-Mouse Thermo Fisher A-11003; RRID:AB_141370 Bacterial and virus strains pAAV_U6_VCAN_shRNA_GFP Dr. Dityatev’s group N/A pAAV_U6_scramble_shRNA_GFP Mitlöhner et al.56 N/A Competent E. coli NEB C3040H Biological samples Human postmortem Amygdala sample from healthy donor Harvard Brain Tissue Resource Center/NIH NeuroBioBank N/A Chemicals, peptides, and recombinant proteins Bovine serum albumin (BSA) Thermo Fisher BP1605100 Paraformaldehyde (PFA; powder) Sigma-Aldrich P6148 Glutaraldehyde Sigma-Aldrich G6257 Sodium cacodylate Sigma-Aldrich C0250 Hydrogen peroxide Fisher H325100 Glycine Sigma G-7403 Triton X-100 Fisher AC215680010 Goat serum Gibco 16210-064 Streptavidin - Horseradish peroxidase Invitrogen 434323 3,3’-Diaminobenzidine Tetrahydrochloride Sigma D5905-100TAB Cytoseal Thermo Fisher 8310-16 Fluomount Southern biotech 0100-01 Chondroitinase ABC amsbio AMS.E1028-10 HaltTM Protease Inhibitor Cocktail Thermo Fisher 78429 Sodium borohydride Fisher AC448501000 Formic Acid/Acetonitrile 0.1/99.9, v/v Sigma-Aldrich 159002 Ammonium hydroxide Sigma-Aldrich 221228 Blocking Buffer Li-Cor 92760001 (Continued on next page) Cell Reports 43, 114112, May 28, 2024 17 .. REAGENT or RESOURCE SOURCE IDENTIFIER NuPage Bis-Tris Thermo Fisher NP0335BOX Mercaptoethanol Sigma-Aldrich M3148 Trifluoracetic acid Sigma-Aldrich 808260 Uranyl acetate Sigma-Aldrich M1775 Embed 812 resin Electron Microscopy Sciences 14900 Fetal Bovine Serum Life Technologies 10270106 PBS pH 7.4 Life Technologies 10010015 DMEM, high glucose Life Technologies 41965062 HBSS Life Technologies 14175053 Iscoves Modified Dulbecco Media Sigma Aldrich I3390 Laminin Sigma Aldrich L2020 Poly-L-Lysine Sigma Aldrich L2636 Trypsin-EDTA (0.05%) Life Technologies 25300054 Penicillin-Streptomycin (10,000 U/mL) Life Technologies 15140122 L-Glutamine Life Technologies 25030024 B27 Supplement Life Technologies 17504044 Neurobasal Media Life Technologies 21103049 Critical commercial assays PierceTMSilver Stain kit Thermo Fisher 24612 SimplyBluTMSafeStain Thermo Fisher LC6060 Protein L Sepharose Abcam ab193261 M-270 Epoxy beads Thermo Fisher 14301 BCA protein assay Thermo Fisher A55860 DNA/RNA Extracol kit EURX 3750 1X HALT protease inhibitor Thermo FIsher P187786 High-Capacity cDNA Reverse Transcription Kit Applied BiosystemsTM 4368814 TaqMan gene expression array Thermo FIsher 4331182 TaqManTM Fast Universal PCR Master Mix Applied BiosystemsTM 4352042 Deposited data Mouse proteomic raw data This Manuscript PXD047129 https://doi.org/10.6019/PXD047129 Human proteomic data This Manuscript PXD050008 https://doi.org/10.6019/PXD050008 Experimental models: Cell lines HEK 293T cells ATCC CRL-1573 Primary hippocampal culture This manuscript N/A Experimental models: Organisms/strains c57bl/6j - Males The Jackson Laboratory 000664 B6 Cg-Tg(Thy1-YFP)HJrs/J - Males The Jackson Laboratory 003782 C57BL/6NCrl - Males Charles River 027 Oligonucleotides Gapdh TaqMan Mm99999915_g1 Vcan TaqMan Mm01283063_m1 Chst3 TaqMan Mm00489736_m1 Chst7 TaqMan Mm00491466_m1 Chst11 TaqMan Mm00517562_m1 Chst12 TaqMan Mm00546416_s1 Recombinant DNA pAAV-U6-GFP Expression Vector Cell Biolabs VPK-413 (Continued on next page) 18 Cell Reports 43, 114112, May 28, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER pAAV_U6_VCANshRNA_GFP This manuscript N/A pAAV_U6_CtrlshRNA_GFP Mitlöhner et al.56 https://doi.org/10.3390/cells9020260 pAAV_U6_scramble_shRNA_GFP Mitlöhner et al.56 https://doi.org/10.3390/cells9020260 Software and algorithms ImageJ/FIJI Schneider et al.57 https://imagej.net/software/fiji/ Prism (version 8) GraphPad https://www.graphpad.com/ scientific-software/prism PATCHMASTER HEKA https://www.heka.com/downloads/ downloads_main.html#down_patchmaster StereoInvestigator 6.0 Micro-Brightfield N/A Leica LAS-X software Leica N/A Other Vibratome Leica VT1200S Microtome American Optical 860 Cryostat Leica CM1950 Double edge, breakable style razor blades Cetim AISI 440 Low-profile disposable cryostat blades Leica DB80LX Automatic tissue homogenizer Avantor SCERSP749540-0000 Disposable pestles, PP, 1.5mL Avantor SCERSP749521-1500 5600+ QTOF mass spectrometer Sciex N/A Q-Exactive HF mass spectrometer Thermo Fisher N/A nanoAcquity UPLC Waters N/A Eksigent nanoLC.as-2 autosampler SpectraLab Others-00-001 NANOSpray III Source Sciex p/n 1034661 Acclaim PepMap100 Thermo Fisher 164946 IntegraFrit Trap Column New Objective N/A Odyssey Scanner Li-Cor N/A Bio-Rad semidry transblotters Bio-Rad N/A Standard surgical blades Word Precision Instruments 500240 SuperFrost Ultra PlusTM Gold slides Fisher scientific 11976299 PierceTM C18 Spin tips and columns Thermo Fisher 87782 EPC-10 amplifier HEKA Elektronik N/A Quant-Studio-5 device Applied Biosystems A28569 Zeiss Axio Imager M2 fluorescent microscope Zeiss M2: 430004-9902 Stereotactic frame Narishige Scientific Instrument Lab SR-6M Ultra microinfusion pump World Precision Instrument UMP3 Confocal laser scanning microscope Leica TCS SP8 Scanning electron microscope JEM 1200EX II JEOL N/A Zeiss Axioskop 2 Plus Zeiss SM100297-MG1 6 well cell culture plate Greiner Bio One GB657160

    Amplification:

    Article Title: Global profiling of nascent chain interactors reveals TRIM25 as a co-translational E3 ubiquitin ligase.
    Article Snippet: Short article Global profiling of nascent chain interactors reveals TRIM25 as a co-translational E3 ubiquitin ligase

    Modification:

    Article Title: Global profiling of nascent chain interactors reveals TRIM25 as a co-translational E3 ubiquitin ligase.
    Article Snippet: Short article Global profiling of nascent chain interactors reveals TRIM25 as a co-translational E3 ubiquitin ligase

    Article Title: Focal clusters of peri-synaptic matrix contribute to activity-dependent plasticity and memory in mice.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-CS56 Sigma-Aldrich C8035; RRDI:AB_476879 Anti-CS56 (for immunoblot and affinity purification) Abcam ab11570: RRDI:AB_298176 Anti-Arc/Arg3.1 Proteintech 16290-1-AP; RRDI:AB_2151832 Anti-PSD95 Abcam ab90426; RRID:AB_2050168 Anti-Versican Merck AB1032, RRID:AB_2214376 Anti-Versican (for immunoblot) Santa Cruz sc-25831; RRID:AB_2241501 Anti-aggrecan (for immunoblot) Abcam ab36861; RRID:AB_722655 Anti-Parvalbumin Synaptic Systems 195 006; RRID:AB_2619887 Anti-Chondroitin Sulfate A mAb (Clone 2H6) Cosmo Bio CAC-NU-07-001 Mouse IgM isotype control Thermo Fisher 14-4752-82; RRID:AB_470123 Mouse IgM isotype control Santa Cruz sc-3881; RRID:AB_737292 Alexa Fluor 647 Goat anti-mouse Abcam ab150115; RRID:AB_2687948 Alexa Fluor 594 Goat anti-mouse Abcam ab150116; RRID:AB_2650601 Alexa Fluor 405 Goat anti-Rabbit Abcam ab175652; RRID:AB_2687498 Alexa Fluor 647 Goat anti-Rabbit Abcam ab150079; RRID:AB_2722623 Alexa Fluor 488 Donkey anti-goat Abcam ab150129; RRID:AB_2687506 Alexa Fluor 405 Goat anti-Chicken Abcam ab175674; RRID:AB_2890171 Alexa Fluor 546 Goat anti-Mouse Thermo Fisher A-11003; RRID:AB_141370 Bacterial and virus strains pAAV_U6_VCAN_shRNA_GFP Dr. Dityatev’s group N/A pAAV_U6_scramble_shRNA_GFP Mitlöhner et al.56 N/A Competent E. coli NEB C3040H Biological samples Human postmortem Amygdala sample from healthy donor Harvard Brain Tissue Resource Center/NIH NeuroBioBank N/A Chemicals, peptides, and recombinant proteins Bovine serum albumin (BSA) Thermo Fisher BP1605100 Paraformaldehyde (PFA; powder) Sigma-Aldrich P6148 Glutaraldehyde Sigma-Aldrich G6257 Sodium cacodylate Sigma-Aldrich C0250 Hydrogen peroxide Fisher H325100 Glycine Sigma G-7403 Triton X-100 Fisher AC215680010 Goat serum Gibco 16210-064 Streptavidin - Horseradish peroxidase Invitrogen 434323 3,3’-Diaminobenzidine Tetrahydrochloride Sigma D5905-100TAB Cytoseal Thermo Fisher 8310-16 Fluomount Southern biotech 0100-01 Chondroitinase ABC amsbio AMS.E1028-10 HaltTM Protease Inhibitor Cocktail Thermo Fisher 78429 Sodium borohydride Fisher AC448501000 Formic Acid/Acetonitrile 0.1/99.9, v/v Sigma-Aldrich 159002 Ammonium hydroxide Sigma-Aldrich 221228 Blocking Buffer Li-Cor 92760001 (Continued on next page) Cell Reports 43, 114112, May 28, 2024 17 .. REAGENT or RESOURCE SOURCE IDENTIFIER NuPage Bis-Tris Thermo Fisher NP0335BOX Mercaptoethanol Sigma-Aldrich M3148 Trifluoracetic acid Sigma-Aldrich 808260 Uranyl acetate Sigma-Aldrich M1775 Embed 812 resin Electron Microscopy Sciences 14900 Fetal Bovine Serum Life Technologies 10270106 PBS pH 7.4 Life Technologies 10010015 DMEM, high glucose Life Technologies 41965062 HBSS Life Technologies 14175053 Iscoves Modified Dulbecco Media Sigma Aldrich I3390 Laminin Sigma Aldrich L2020 Poly-L-Lysine Sigma Aldrich L2636 Trypsin-EDTA (0.05%) Life Technologies 25300054 Penicillin-Streptomycin (10,000 U/mL) Life Technologies 15140122 L-Glutamine Life Technologies 25030024 B27 Supplement Life Technologies 17504044 Neurobasal Media Life Technologies 21103049 Critical commercial assays PierceTMSilver Stain kit Thermo Fisher 24612 SimplyBluTMSafeStain Thermo Fisher LC6060 Protein L Sepharose Abcam ab193261 M-270 Epoxy beads Thermo Fisher 14301 BCA protein assay Thermo Fisher A55860 DNA/RNA Extracol kit EURX 3750 1X HALT protease inhibitor Thermo FIsher P187786 High-Capacity cDNA Reverse Transcription Kit Applied BiosystemsTM 4368814 TaqMan gene expression array Thermo FIsher 4331182 TaqManTM Fast Universal PCR Master Mix Applied BiosystemsTM 4352042 Deposited data Mouse proteomic raw data This Manuscript PXD047129 https://doi.org/10.6019/PXD047129 Human proteomic data This Manuscript PXD050008 https://doi.org/10.6019/PXD050008 Experimental models: Cell lines HEK 293T cells ATCC CRL-1573 Primary hippocampal culture This manuscript N/A Experimental models: Organisms/strains c57bl/6j - Males The Jackson Laboratory 000664 B6 Cg-Tg(Thy1-YFP)HJrs/J - Males The Jackson Laboratory 003782 C57BL/6NCrl - Males Charles River 027 Oligonucleotides Gapdh TaqMan Mm99999915_g1 Vcan TaqMan Mm01283063_m1 Chst3 TaqMan Mm00489736_m1 Chst7 TaqMan Mm00491466_m1 Chst11 TaqMan Mm00517562_m1 Chst12 TaqMan Mm00546416_s1 Recombinant DNA pAAV-U6-GFP Expression Vector Cell Biolabs VPK-413 (Continued on next page) 18 Cell Reports 43, 114112, May 28, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER pAAV_U6_VCANshRNA_GFP This manuscript N/A pAAV_U6_CtrlshRNA_GFP Mitlöhner et al.56 https://doi.org/10.3390/cells9020260 pAAV_U6_scramble_shRNA_GFP Mitlöhner et al.56 https://doi.org/10.3390/cells9020260 Software and algorithms ImageJ/FIJI Schneider et al.57 https://imagej.net/software/fiji/ Prism (version 8) GraphPad https://www.graphpad.com/ scientific-software/prism PATCHMASTER HEKA https://www.heka.com/downloads/ downloads_main.html#down_patchmaster StereoInvestigator 6.0 Micro-Brightfield N/A Leica LAS-X software Leica N/A Other Vibratome Leica VT1200S Microtome American Optical 860 Cryostat Leica CM1950 Double edge, breakable style razor blades Cetim AISI 440 Low-profile disposable cryostat blades Leica DB80LX Automatic tissue homogenizer Avantor SCERSP749540-0000 Disposable pestles, PP, 1.5mL Avantor SCERSP749521-1500 5600+ QTOF mass spectrometer Sciex N/A Q-Exactive HF mass spectrometer Thermo Fisher N/A nanoAcquity UPLC Waters N/A Eksigent nanoLC.as-2 autosampler SpectraLab Others-00-001 NANOSpray III Source Sciex p/n 1034661 Acclaim PepMap100 Thermo Fisher 164946 IntegraFrit Trap Column New Objective N/A Odyssey Scanner Li-Cor N/A Bio-Rad semidry transblotters Bio-Rad N/A Standard surgical blades Word Precision Instruments 500240 SuperFrost Ultra PlusTM Gold slides Fisher scientific 11976299 PierceTM C18 Spin tips and columns Thermo Fisher 87782 EPC-10 amplifier HEKA Elektronik N/A Quant-Studio-5 device Applied Biosystems A28569 Zeiss Axio Imager M2 fluorescent microscope Zeiss M2: 430004-9902 Stereotactic frame Narishige Scientific Instrument Lab SR-6M Ultra microinfusion pump World Precision Instrument UMP3 Confocal laser scanning microscope Leica TCS SP8 Scanning electron microscope JEM 1200EX II JEOL N/A Zeiss Axioskop 2 Plus Zeiss SM100297-MG1 6 well cell culture plate Greiner Bio One GB657160

    Electron Microscopy:

    Article Title: Focal clusters of peri-synaptic matrix contribute to activity-dependent plasticity and memory in mice.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-CS56 Sigma-Aldrich C8035; RRDI:AB_476879 Anti-CS56 (for immunoblot and affinity purification) Abcam ab11570: RRDI:AB_298176 Anti-Arc/Arg3.1 Proteintech 16290-1-AP; RRDI:AB_2151832 Anti-PSD95 Abcam ab90426; RRID:AB_2050168 Anti-Versican Merck AB1032, RRID:AB_2214376 Anti-Versican (for immunoblot) Santa Cruz sc-25831; RRID:AB_2241501 Anti-aggrecan (for immunoblot) Abcam ab36861; RRID:AB_722655 Anti-Parvalbumin Synaptic Systems 195 006; RRID:AB_2619887 Anti-Chondroitin Sulfate A mAb (Clone 2H6) Cosmo Bio CAC-NU-07-001 Mouse IgM isotype control Thermo Fisher 14-4752-82; RRID:AB_470123 Mouse IgM isotype control Santa Cruz sc-3881; RRID:AB_737292 Alexa Fluor 647 Goat anti-mouse Abcam ab150115; RRID:AB_2687948 Alexa Fluor 594 Goat anti-mouse Abcam ab150116; RRID:AB_2650601 Alexa Fluor 405 Goat anti-Rabbit Abcam ab175652; RRID:AB_2687498 Alexa Fluor 647 Goat anti-Rabbit Abcam ab150079; RRID:AB_2722623 Alexa Fluor 488 Donkey anti-goat Abcam ab150129; RRID:AB_2687506 Alexa Fluor 405 Goat anti-Chicken Abcam ab175674; RRID:AB_2890171 Alexa Fluor 546 Goat anti-Mouse Thermo Fisher A-11003; RRID:AB_141370 Bacterial and virus strains pAAV_U6_VCAN_shRNA_GFP Dr. Dityatev’s group N/A pAAV_U6_scramble_shRNA_GFP Mitlöhner et al.56 N/A Competent E. coli NEB C3040H Biological samples Human postmortem Amygdala sample from healthy donor Harvard Brain Tissue Resource Center/NIH NeuroBioBank N/A Chemicals, peptides, and recombinant proteins Bovine serum albumin (BSA) Thermo Fisher BP1605100 Paraformaldehyde (PFA; powder) Sigma-Aldrich P6148 Glutaraldehyde Sigma-Aldrich G6257 Sodium cacodylate Sigma-Aldrich C0250 Hydrogen peroxide Fisher H325100 Glycine Sigma G-7403 Triton X-100 Fisher AC215680010 Goat serum Gibco 16210-064 Streptavidin - Horseradish peroxidase Invitrogen 434323 3,3’-Diaminobenzidine Tetrahydrochloride Sigma D5905-100TAB Cytoseal Thermo Fisher 8310-16 Fluomount Southern biotech 0100-01 Chondroitinase ABC amsbio AMS.E1028-10 HaltTM Protease Inhibitor Cocktail Thermo Fisher 78429 Sodium borohydride Fisher AC448501000 Formic Acid/Acetonitrile 0.1/99.9, v/v Sigma-Aldrich 159002 Ammonium hydroxide Sigma-Aldrich 221228 Blocking Buffer Li-Cor 92760001 (Continued on next page) Cell Reports 43, 114112, May 28, 2024 17 .. REAGENT or RESOURCE SOURCE IDENTIFIER NuPage Bis-Tris Thermo Fisher NP0335BOX Mercaptoethanol Sigma-Aldrich M3148 Trifluoracetic acid Sigma-Aldrich 808260 Uranyl acetate Sigma-Aldrich M1775 Embed 812 resin Electron Microscopy Sciences 14900 Fetal Bovine Serum Life Technologies 10270106 PBS pH 7.4 Life Technologies 10010015 DMEM, high glucose Life Technologies 41965062 HBSS Life Technologies 14175053 Iscoves Modified Dulbecco Media Sigma Aldrich I3390 Laminin Sigma Aldrich L2020 Poly-L-Lysine Sigma Aldrich L2636 Trypsin-EDTA (0.05%) Life Technologies 25300054 Penicillin-Streptomycin (10,000 U/mL) Life Technologies 15140122 L-Glutamine Life Technologies 25030024 B27 Supplement Life Technologies 17504044 Neurobasal Media Life Technologies 21103049 Critical commercial assays PierceTMSilver Stain kit Thermo Fisher 24612 SimplyBluTMSafeStain Thermo Fisher LC6060 Protein L Sepharose Abcam ab193261 M-270 Epoxy beads Thermo Fisher 14301 BCA protein assay Thermo Fisher A55860 DNA/RNA Extracol kit EURX 3750 1X HALT protease inhibitor Thermo FIsher P187786 High-Capacity cDNA Reverse Transcription Kit Applied BiosystemsTM 4368814 TaqMan gene expression array Thermo FIsher 4331182 TaqManTM Fast Universal PCR Master Mix Applied BiosystemsTM 4352042 Deposited data Mouse proteomic raw data This Manuscript PXD047129 https://doi.org/10.6019/PXD047129 Human proteomic data This Manuscript PXD050008 https://doi.org/10.6019/PXD050008 Experimental models: Cell lines HEK 293T cells ATCC CRL-1573 Primary hippocampal culture This manuscript N/A Experimental models: Organisms/strains c57bl/6j - Males The Jackson Laboratory 000664 B6 Cg-Tg(Thy1-YFP)HJrs/J - Males The Jackson Laboratory 003782 C57BL/6NCrl - Males Charles River 027 Oligonucleotides Gapdh TaqMan Mm99999915_g1 Vcan TaqMan Mm01283063_m1 Chst3 TaqMan Mm00489736_m1 Chst7 TaqMan Mm00491466_m1 Chst11 TaqMan Mm00517562_m1 Chst12 TaqMan Mm00546416_s1 Recombinant DNA pAAV-U6-GFP Expression Vector Cell Biolabs VPK-413 (Continued on next page) 18 Cell Reports 43, 114112, May 28, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER pAAV_U6_VCANshRNA_GFP This manuscript N/A pAAV_U6_CtrlshRNA_GFP Mitlöhner et al.56 https://doi.org/10.3390/cells9020260 pAAV_U6_scramble_shRNA_GFP Mitlöhner et al.56 https://doi.org/10.3390/cells9020260 Software and algorithms ImageJ/FIJI Schneider et al.57 https://imagej.net/software/fiji/ Prism (version 8) GraphPad https://www.graphpad.com/ scientific-software/prism PATCHMASTER HEKA https://www.heka.com/downloads/ downloads_main.html#down_patchmaster StereoInvestigator 6.0 Micro-Brightfield N/A Leica LAS-X software Leica N/A Other Vibratome Leica VT1200S Microtome American Optical 860 Cryostat Leica CM1950 Double edge, breakable style razor blades Cetim AISI 440 Low-profile disposable cryostat blades Leica DB80LX Automatic tissue homogenizer Avantor SCERSP749540-0000 Disposable pestles, PP, 1.5mL Avantor SCERSP749521-1500 5600+ QTOF mass spectrometer Sciex N/A Q-Exactive HF mass spectrometer Thermo Fisher N/A nanoAcquity UPLC Waters N/A Eksigent nanoLC.as-2 autosampler SpectraLab Others-00-001 NANOSpray III Source Sciex p/n 1034661 Acclaim PepMap100 Thermo Fisher 164946 IntegraFrit Trap Column New Objective N/A Odyssey Scanner Li-Cor N/A Bio-Rad semidry transblotters Bio-Rad N/A Standard surgical blades Word Precision Instruments 500240 SuperFrost Ultra PlusTM Gold slides Fisher scientific 11976299 PierceTM C18 Spin tips and columns Thermo Fisher 87782 EPC-10 amplifier HEKA Elektronik N/A Quant-Studio-5 device Applied Biosystems A28569 Zeiss Axio Imager M2 fluorescent microscope Zeiss M2: 430004-9902 Stereotactic frame Narishige Scientific Instrument Lab SR-6M Ultra microinfusion pump World Precision Instrument UMP3 Confocal laser scanning microscope Leica TCS SP8 Scanning electron microscope JEM 1200EX II JEOL N/A Zeiss Axioskop 2 Plus Zeiss SM100297-MG1 6 well cell culture plate Greiner Bio One GB657160

    Staining:

    Article Title: Focal clusters of peri-synaptic matrix contribute to activity-dependent plasticity and memory in mice.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-CS56 Sigma-Aldrich C8035; RRDI:AB_476879 Anti-CS56 (for immunoblot and affinity purification) Abcam ab11570: RRDI:AB_298176 Anti-Arc/Arg3.1 Proteintech 16290-1-AP; RRDI:AB_2151832 Anti-PSD95 Abcam ab90426; RRID:AB_2050168 Anti-Versican Merck AB1032, RRID:AB_2214376 Anti-Versican (for immunoblot) Santa Cruz sc-25831; RRID:AB_2241501 Anti-aggrecan (for immunoblot) Abcam ab36861; RRID:AB_722655 Anti-Parvalbumin Synaptic Systems 195 006; RRID:AB_2619887 Anti-Chondroitin Sulfate A mAb (Clone 2H6) Cosmo Bio CAC-NU-07-001 Mouse IgM isotype control Thermo Fisher 14-4752-82; RRID:AB_470123 Mouse IgM isotype control Santa Cruz sc-3881; RRID:AB_737292 Alexa Fluor 647 Goat anti-mouse Abcam ab150115; RRID:AB_2687948 Alexa Fluor 594 Goat anti-mouse Abcam ab150116; RRID:AB_2650601 Alexa Fluor 405 Goat anti-Rabbit Abcam ab175652; RRID:AB_2687498 Alexa Fluor 647 Goat anti-Rabbit Abcam ab150079; RRID:AB_2722623 Alexa Fluor 488 Donkey anti-goat Abcam ab150129; RRID:AB_2687506 Alexa Fluor 405 Goat anti-Chicken Abcam ab175674; RRID:AB_2890171 Alexa Fluor 546 Goat anti-Mouse Thermo Fisher A-11003; RRID:AB_141370 Bacterial and virus strains pAAV_U6_VCAN_shRNA_GFP Dr. Dityatev’s group N/A pAAV_U6_scramble_shRNA_GFP Mitlöhner et al.56 N/A Competent E. coli NEB C3040H Biological samples Human postmortem Amygdala sample from healthy donor Harvard Brain Tissue Resource Center/NIH NeuroBioBank N/A Chemicals, peptides, and recombinant proteins Bovine serum albumin (BSA) Thermo Fisher BP1605100 Paraformaldehyde (PFA; powder) Sigma-Aldrich P6148 Glutaraldehyde Sigma-Aldrich G6257 Sodium cacodylate Sigma-Aldrich C0250 Hydrogen peroxide Fisher H325100 Glycine Sigma G-7403 Triton X-100 Fisher AC215680010 Goat serum Gibco 16210-064 Streptavidin - Horseradish peroxidase Invitrogen 434323 3,3’-Diaminobenzidine Tetrahydrochloride Sigma D5905-100TAB Cytoseal Thermo Fisher 8310-16 Fluomount Southern biotech 0100-01 Chondroitinase ABC amsbio AMS.E1028-10 HaltTM Protease Inhibitor Cocktail Thermo Fisher 78429 Sodium borohydride Fisher AC448501000 Formic Acid/Acetonitrile 0.1/99.9, v/v Sigma-Aldrich 159002 Ammonium hydroxide Sigma-Aldrich 221228 Blocking Buffer Li-Cor 92760001 (Continued on next page) Cell Reports 43, 114112, May 28, 2024 17 .. REAGENT or RESOURCE SOURCE IDENTIFIER NuPage Bis-Tris Thermo Fisher NP0335BOX Mercaptoethanol Sigma-Aldrich M3148 Trifluoracetic acid Sigma-Aldrich 808260 Uranyl acetate Sigma-Aldrich M1775 Embed 812 resin Electron Microscopy Sciences 14900 Fetal Bovine Serum Life Technologies 10270106 PBS pH 7.4 Life Technologies 10010015 DMEM, high glucose Life Technologies 41965062 HBSS Life Technologies 14175053 Iscoves Modified Dulbecco Media Sigma Aldrich I3390 Laminin Sigma Aldrich L2020 Poly-L-Lysine Sigma Aldrich L2636 Trypsin-EDTA (0.05%) Life Technologies 25300054 Penicillin-Streptomycin (10,000 U/mL) Life Technologies 15140122 L-Glutamine Life Technologies 25030024 B27 Supplement Life Technologies 17504044 Neurobasal Media Life Technologies 21103049 Critical commercial assays PierceTMSilver Stain kit Thermo Fisher 24612 SimplyBluTMSafeStain Thermo Fisher LC6060 Protein L Sepharose Abcam ab193261 M-270 Epoxy beads Thermo Fisher 14301 BCA protein assay Thermo Fisher A55860 DNA/RNA Extracol kit EURX 3750 1X HALT protease inhibitor Thermo FIsher P187786 High-Capacity cDNA Reverse Transcription Kit Applied BiosystemsTM 4368814 TaqMan gene expression array Thermo FIsher 4331182 TaqManTM Fast Universal PCR Master Mix Applied BiosystemsTM 4352042 Deposited data Mouse proteomic raw data This Manuscript PXD047129 https://doi.org/10.6019/PXD047129 Human proteomic data This Manuscript PXD050008 https://doi.org/10.6019/PXD050008 Experimental models: Cell lines HEK 293T cells ATCC CRL-1573 Primary hippocampal culture This manuscript N/A Experimental models: Organisms/strains c57bl/6j - Males The Jackson Laboratory 000664 B6 Cg-Tg(Thy1-YFP)HJrs/J - Males The Jackson Laboratory 003782 C57BL/6NCrl - Males Charles River 027 Oligonucleotides Gapdh TaqMan Mm99999915_g1 Vcan TaqMan Mm01283063_m1 Chst3 TaqMan Mm00489736_m1 Chst7 TaqMan Mm00491466_m1 Chst11 TaqMan Mm00517562_m1 Chst12 TaqMan Mm00546416_s1 Recombinant DNA pAAV-U6-GFP Expression Vector Cell Biolabs VPK-413 (Continued on next page) 18 Cell Reports 43, 114112, May 28, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER pAAV_U6_VCANshRNA_GFP This manuscript N/A pAAV_U6_CtrlshRNA_GFP Mitlöhner et al.56 https://doi.org/10.3390/cells9020260 pAAV_U6_scramble_shRNA_GFP Mitlöhner et al.56 https://doi.org/10.3390/cells9020260 Software and algorithms ImageJ/FIJI Schneider et al.57 https://imagej.net/software/fiji/ Prism (version 8) GraphPad https://www.graphpad.com/ scientific-software/prism PATCHMASTER HEKA https://www.heka.com/downloads/ downloads_main.html#down_patchmaster StereoInvestigator 6.0 Micro-Brightfield N/A Leica LAS-X software Leica N/A Other Vibratome Leica VT1200S Microtome American Optical 860 Cryostat Leica CM1950 Double edge, breakable style razor blades Cetim AISI 440 Low-profile disposable cryostat blades Leica DB80LX Automatic tissue homogenizer Avantor SCERSP749540-0000 Disposable pestles, PP, 1.5mL Avantor SCERSP749521-1500 5600+ QTOF mass spectrometer Sciex N/A Q-Exactive HF mass spectrometer Thermo Fisher N/A nanoAcquity UPLC Waters N/A Eksigent nanoLC.as-2 autosampler SpectraLab Others-00-001 NANOSpray III Source Sciex p/n 1034661 Acclaim PepMap100 Thermo Fisher 164946 IntegraFrit Trap Column New Objective N/A Odyssey Scanner Li-Cor N/A Bio-Rad semidry transblotters Bio-Rad N/A Standard surgical blades Word Precision Instruments 500240 SuperFrost Ultra PlusTM Gold slides Fisher scientific 11976299 PierceTM C18 Spin tips and columns Thermo Fisher 87782 EPC-10 amplifier HEKA Elektronik N/A Quant-Studio-5 device Applied Biosystems A28569 Zeiss Axio Imager M2 fluorescent microscope Zeiss M2: 430004-9902 Stereotactic frame Narishige Scientific Instrument Lab SR-6M Ultra microinfusion pump World Precision Instrument UMP3 Confocal laser scanning microscope Leica TCS SP8 Scanning electron microscope JEM 1200EX II JEOL N/A Zeiss Axioskop 2 Plus Zeiss SM100297-MG1 6 well cell culture plate Greiner Bio One GB657160

    Bicinchoninic Acid Protein Assay:

    Article Title: Focal clusters of peri-synaptic matrix contribute to activity-dependent plasticity and memory in mice.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-CS56 Sigma-Aldrich C8035; RRDI:AB_476879 Anti-CS56 (for immunoblot and affinity purification) Abcam ab11570: RRDI:AB_298176 Anti-Arc/Arg3.1 Proteintech 16290-1-AP; RRDI:AB_2151832 Anti-PSD95 Abcam ab90426; RRID:AB_2050168 Anti-Versican Merck AB1032, RRID:AB_2214376 Anti-Versican (for immunoblot) Santa Cruz sc-25831; RRID:AB_2241501 Anti-aggrecan (for immunoblot) Abcam ab36861; RRID:AB_722655 Anti-Parvalbumin Synaptic Systems 195 006; RRID:AB_2619887 Anti-Chondroitin Sulfate A mAb (Clone 2H6) Cosmo Bio CAC-NU-07-001 Mouse IgM isotype control Thermo Fisher 14-4752-82; RRID:AB_470123 Mouse IgM isotype control Santa Cruz sc-3881; RRID:AB_737292 Alexa Fluor 647 Goat anti-mouse Abcam ab150115; RRID:AB_2687948 Alexa Fluor 594 Goat anti-mouse Abcam ab150116; RRID:AB_2650601 Alexa Fluor 405 Goat anti-Rabbit Abcam ab175652; RRID:AB_2687498 Alexa Fluor 647 Goat anti-Rabbit Abcam ab150079; RRID:AB_2722623 Alexa Fluor 488 Donkey anti-goat Abcam ab150129; RRID:AB_2687506 Alexa Fluor 405 Goat anti-Chicken Abcam ab175674; RRID:AB_2890171 Alexa Fluor 546 Goat anti-Mouse Thermo Fisher A-11003; RRID:AB_141370 Bacterial and virus strains pAAV_U6_VCAN_shRNA_GFP Dr. Dityatev’s group N/A pAAV_U6_scramble_shRNA_GFP Mitlöhner et al.56 N/A Competent E. coli NEB C3040H Biological samples Human postmortem Amygdala sample from healthy donor Harvard Brain Tissue Resource Center/NIH NeuroBioBank N/A Chemicals, peptides, and recombinant proteins Bovine serum albumin (BSA) Thermo Fisher BP1605100 Paraformaldehyde (PFA; powder) Sigma-Aldrich P6148 Glutaraldehyde Sigma-Aldrich G6257 Sodium cacodylate Sigma-Aldrich C0250 Hydrogen peroxide Fisher H325100 Glycine Sigma G-7403 Triton X-100 Fisher AC215680010 Goat serum Gibco 16210-064 Streptavidin - Horseradish peroxidase Invitrogen 434323 3,3’-Diaminobenzidine Tetrahydrochloride Sigma D5905-100TAB Cytoseal Thermo Fisher 8310-16 Fluomount Southern biotech 0100-01 Chondroitinase ABC amsbio AMS.E1028-10 HaltTM Protease Inhibitor Cocktail Thermo Fisher 78429 Sodium borohydride Fisher AC448501000 Formic Acid/Acetonitrile 0.1/99.9, v/v Sigma-Aldrich 159002 Ammonium hydroxide Sigma-Aldrich 221228 Blocking Buffer Li-Cor 92760001 (Continued on next page) Cell Reports 43, 114112, May 28, 2024 17 .. REAGENT or RESOURCE SOURCE IDENTIFIER NuPage Bis-Tris Thermo Fisher NP0335BOX Mercaptoethanol Sigma-Aldrich M3148 Trifluoracetic acid Sigma-Aldrich 808260 Uranyl acetate Sigma-Aldrich M1775 Embed 812 resin Electron Microscopy Sciences 14900 Fetal Bovine Serum Life Technologies 10270106 PBS pH 7.4 Life Technologies 10010015 DMEM, high glucose Life Technologies 41965062 HBSS Life Technologies 14175053 Iscoves Modified Dulbecco Media Sigma Aldrich I3390 Laminin Sigma Aldrich L2020 Poly-L-Lysine Sigma Aldrich L2636 Trypsin-EDTA (0.05%) Life Technologies 25300054 Penicillin-Streptomycin (10,000 U/mL) Life Technologies 15140122 L-Glutamine Life Technologies 25030024 B27 Supplement Life Technologies 17504044 Neurobasal Media Life Technologies 21103049 Critical commercial assays PierceTMSilver Stain kit Thermo Fisher 24612 SimplyBluTMSafeStain Thermo Fisher LC6060 Protein L Sepharose Abcam ab193261 M-270 Epoxy beads Thermo Fisher 14301 BCA protein assay Thermo Fisher A55860 DNA/RNA Extracol kit EURX 3750 1X HALT protease inhibitor Thermo FIsher P187786 High-Capacity cDNA Reverse Transcription Kit Applied BiosystemsTM 4368814 TaqMan gene expression array Thermo FIsher 4331182 TaqManTM Fast Universal PCR Master Mix Applied BiosystemsTM 4352042 Deposited data Mouse proteomic raw data This Manuscript PXD047129 https://doi.org/10.6019/PXD047129 Human proteomic data This Manuscript PXD050008 https://doi.org/10.6019/PXD050008 Experimental models: Cell lines HEK 293T cells ATCC CRL-1573 Primary hippocampal culture This manuscript N/A Experimental models: Organisms/strains c57bl/6j - Males The Jackson Laboratory 000664 B6 Cg-Tg(Thy1-YFP)HJrs/J - Males The Jackson Laboratory 003782 C57BL/6NCrl - Males Charles River 027 Oligonucleotides Gapdh TaqMan Mm99999915_g1 Vcan TaqMan Mm01283063_m1 Chst3 TaqMan Mm00489736_m1 Chst7 TaqMan Mm00491466_m1 Chst11 TaqMan Mm00517562_m1 Chst12 TaqMan Mm00546416_s1 Recombinant DNA pAAV-U6-GFP Expression Vector Cell Biolabs VPK-413 (Continued on next page) 18 Cell Reports 43, 114112, May 28, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER pAAV_U6_VCANshRNA_GFP This manuscript N/A pAAV_U6_CtrlshRNA_GFP Mitlöhner et al.56 https://doi.org/10.3390/cells9020260 pAAV_U6_scramble_shRNA_GFP Mitlöhner et al.56 https://doi.org/10.3390/cells9020260 Software and algorithms ImageJ/FIJI Schneider et al.57 https://imagej.net/software/fiji/ Prism (version 8) GraphPad https://www.graphpad.com/ scientific-software/prism PATCHMASTER HEKA https://www.heka.com/downloads/ downloads_main.html#down_patchmaster StereoInvestigator 6.0 Micro-Brightfield N/A Leica LAS-X software Leica N/A Other Vibratome Leica VT1200S Microtome American Optical 860 Cryostat Leica CM1950 Double edge, breakable style razor blades Cetim AISI 440 Low-profile disposable cryostat blades Leica DB80LX Automatic tissue homogenizer Avantor SCERSP749540-0000 Disposable pestles, PP, 1.5mL Avantor SCERSP749521-1500 5600+ QTOF mass spectrometer Sciex N/A Q-Exactive HF mass spectrometer Thermo Fisher N/A nanoAcquity UPLC Waters N/A Eksigent nanoLC.as-2 autosampler SpectraLab Others-00-001 NANOSpray III Source Sciex p/n 1034661 Acclaim PepMap100 Thermo Fisher 164946 IntegraFrit Trap Column New Objective N/A Odyssey Scanner Li-Cor N/A Bio-Rad semidry transblotters Bio-Rad N/A Standard surgical blades Word Precision Instruments 500240 SuperFrost Ultra PlusTM Gold slides Fisher scientific 11976299 PierceTM C18 Spin tips and columns Thermo Fisher 87782 EPC-10 amplifier HEKA Elektronik N/A Quant-Studio-5 device Applied Biosystems A28569 Zeiss Axio Imager M2 fluorescent microscope Zeiss M2: 430004-9902 Stereotactic frame Narishige Scientific Instrument Lab SR-6M Ultra microinfusion pump World Precision Instrument UMP3 Confocal laser scanning microscope Leica TCS SP8 Scanning electron microscope JEM 1200EX II JEOL N/A Zeiss Axioskop 2 Plus Zeiss SM100297-MG1 6 well cell culture plate Greiner Bio One GB657160

    Protease Inhibitor:

    Article Title: Focal clusters of peri-synaptic matrix contribute to activity-dependent plasticity and memory in mice.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-CS56 Sigma-Aldrich C8035; RRDI:AB_476879 Anti-CS56 (for immunoblot and affinity purification) Abcam ab11570: RRDI:AB_298176 Anti-Arc/Arg3.1 Proteintech 16290-1-AP; RRDI:AB_2151832 Anti-PSD95 Abcam ab90426; RRID:AB_2050168 Anti-Versican Merck AB1032, RRID:AB_2214376 Anti-Versican (for immunoblot) Santa Cruz sc-25831; RRID:AB_2241501 Anti-aggrecan (for immunoblot) Abcam ab36861; RRID:AB_722655 Anti-Parvalbumin Synaptic Systems 195 006; RRID:AB_2619887 Anti-Chondroitin Sulfate A mAb (Clone 2H6) Cosmo Bio CAC-NU-07-001 Mouse IgM isotype control Thermo Fisher 14-4752-82; RRID:AB_470123 Mouse IgM isotype control Santa Cruz sc-3881; RRID:AB_737292 Alexa Fluor 647 Goat anti-mouse Abcam ab150115; RRID:AB_2687948 Alexa Fluor 594 Goat anti-mouse Abcam ab150116; RRID:AB_2650601 Alexa Fluor 405 Goat anti-Rabbit Abcam ab175652; RRID:AB_2687498 Alexa Fluor 647 Goat anti-Rabbit Abcam ab150079; RRID:AB_2722623 Alexa Fluor 488 Donkey anti-goat Abcam ab150129; RRID:AB_2687506 Alexa Fluor 405 Goat anti-Chicken Abcam ab175674; RRID:AB_2890171 Alexa Fluor 546 Goat anti-Mouse Thermo Fisher A-11003; RRID:AB_141370 Bacterial and virus strains pAAV_U6_VCAN_shRNA_GFP Dr. Dityatev’s group N/A pAAV_U6_scramble_shRNA_GFP Mitlöhner et al.56 N/A Competent E. coli NEB C3040H Biological samples Human postmortem Amygdala sample from healthy donor Harvard Brain Tissue Resource Center/NIH NeuroBioBank N/A Chemicals, peptides, and recombinant proteins Bovine serum albumin (BSA) Thermo Fisher BP1605100 Paraformaldehyde (PFA; powder) Sigma-Aldrich P6148 Glutaraldehyde Sigma-Aldrich G6257 Sodium cacodylate Sigma-Aldrich C0250 Hydrogen peroxide Fisher H325100 Glycine Sigma G-7403 Triton X-100 Fisher AC215680010 Goat serum Gibco 16210-064 Streptavidin - Horseradish peroxidase Invitrogen 434323 3,3’-Diaminobenzidine Tetrahydrochloride Sigma D5905-100TAB Cytoseal Thermo Fisher 8310-16 Fluomount Southern biotech 0100-01 Chondroitinase ABC amsbio AMS.E1028-10 HaltTM Protease Inhibitor Cocktail Thermo Fisher 78429 Sodium borohydride Fisher AC448501000 Formic Acid/Acetonitrile 0.1/99.9, v/v Sigma-Aldrich 159002 Ammonium hydroxide Sigma-Aldrich 221228 Blocking Buffer Li-Cor 92760001 (Continued on next page) Cell Reports 43, 114112, May 28, 2024 17 .. REAGENT or RESOURCE SOURCE IDENTIFIER NuPage Bis-Tris Thermo Fisher NP0335BOX Mercaptoethanol Sigma-Aldrich M3148 Trifluoracetic acid Sigma-Aldrich 808260 Uranyl acetate Sigma-Aldrich M1775 Embed 812 resin Electron Microscopy Sciences 14900 Fetal Bovine Serum Life Technologies 10270106 PBS pH 7.4 Life Technologies 10010015 DMEM, high glucose Life Technologies 41965062 HBSS Life Technologies 14175053 Iscoves Modified Dulbecco Media Sigma Aldrich I3390 Laminin Sigma Aldrich L2020 Poly-L-Lysine Sigma Aldrich L2636 Trypsin-EDTA (0.05%) Life Technologies 25300054 Penicillin-Streptomycin (10,000 U/mL) Life Technologies 15140122 L-Glutamine Life Technologies 25030024 B27 Supplement Life Technologies 17504044 Neurobasal Media Life Technologies 21103049 Critical commercial assays PierceTMSilver Stain kit Thermo Fisher 24612 SimplyBluTMSafeStain Thermo Fisher LC6060 Protein L Sepharose Abcam ab193261 M-270 Epoxy beads Thermo Fisher 14301 BCA protein assay Thermo Fisher A55860 DNA/RNA Extracol kit EURX 3750 1X HALT protease inhibitor Thermo FIsher P187786 High-Capacity cDNA Reverse Transcription Kit Applied BiosystemsTM 4368814 TaqMan gene expression array Thermo FIsher 4331182 TaqManTM Fast Universal PCR Master Mix Applied BiosystemsTM 4352042 Deposited data Mouse proteomic raw data This Manuscript PXD047129 https://doi.org/10.6019/PXD047129 Human proteomic data This Manuscript PXD050008 https://doi.org/10.6019/PXD050008 Experimental models: Cell lines HEK 293T cells ATCC CRL-1573 Primary hippocampal culture This manuscript N/A Experimental models: Organisms/strains c57bl/6j - Males The Jackson Laboratory 000664 B6 Cg-Tg(Thy1-YFP)HJrs/J - Males The Jackson Laboratory 003782 C57BL/6NCrl - Males Charles River 027 Oligonucleotides Gapdh TaqMan Mm99999915_g1 Vcan TaqMan Mm01283063_m1 Chst3 TaqMan Mm00489736_m1 Chst7 TaqMan Mm00491466_m1 Chst11 TaqMan Mm00517562_m1 Chst12 TaqMan Mm00546416_s1 Recombinant DNA pAAV-U6-GFP Expression Vector Cell Biolabs VPK-413 (Continued on next page) 18 Cell Reports 43, 114112, May 28, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER pAAV_U6_VCANshRNA_GFP This manuscript N/A pAAV_U6_CtrlshRNA_GFP Mitlöhner et al.56 https://doi.org/10.3390/cells9020260 pAAV_U6_scramble_shRNA_GFP Mitlöhner et al.56 https://doi.org/10.3390/cells9020260 Software and algorithms ImageJ/FIJI Schneider et al.57 https://imagej.net/software/fiji/ Prism (version 8) GraphPad https://www.graphpad.com/ scientific-software/prism PATCHMASTER HEKA https://www.heka.com/downloads/ downloads_main.html#down_patchmaster StereoInvestigator 6.0 Micro-Brightfield N/A Leica LAS-X software Leica N/A Other Vibratome Leica VT1200S Microtome American Optical 860 Cryostat Leica CM1950 Double edge, breakable style razor blades Cetim AISI 440 Low-profile disposable cryostat blades Leica DB80LX Automatic tissue homogenizer Avantor SCERSP749540-0000 Disposable pestles, PP, 1.5mL Avantor SCERSP749521-1500 5600+ QTOF mass spectrometer Sciex N/A Q-Exactive HF mass spectrometer Thermo Fisher N/A nanoAcquity UPLC Waters N/A Eksigent nanoLC.as-2 autosampler SpectraLab Others-00-001 NANOSpray III Source Sciex p/n 1034661 Acclaim PepMap100 Thermo Fisher 164946 IntegraFrit Trap Column New Objective N/A Odyssey Scanner Li-Cor N/A Bio-Rad semidry transblotters Bio-Rad N/A Standard surgical blades Word Precision Instruments 500240 SuperFrost Ultra PlusTM Gold slides Fisher scientific 11976299 PierceTM C18 Spin tips and columns Thermo Fisher 87782 EPC-10 amplifier HEKA Elektronik N/A Quant-Studio-5 device Applied Biosystems A28569 Zeiss Axio Imager M2 fluorescent microscope Zeiss M2: 430004-9902 Stereotactic frame Narishige Scientific Instrument Lab SR-6M Ultra microinfusion pump World Precision Instrument UMP3 Confocal laser scanning microscope Leica TCS SP8 Scanning electron microscope JEM 1200EX II JEOL N/A Zeiss Axioskop 2 Plus Zeiss SM100297-MG1 6 well cell culture plate Greiner Bio One GB657160

    Reverse Transcription:

    Article Title: Focal clusters of peri-synaptic matrix contribute to activity-dependent plasticity and memory in mice.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-CS56 Sigma-Aldrich C8035; RRDI:AB_476879 Anti-CS56 (for immunoblot and affinity purification) Abcam ab11570: RRDI:AB_298176 Anti-Arc/Arg3.1 Proteintech 16290-1-AP; RRDI:AB_2151832 Anti-PSD95 Abcam ab90426; RRID:AB_2050168 Anti-Versican Merck AB1032, RRID:AB_2214376 Anti-Versican (for immunoblot) Santa Cruz sc-25831; RRID:AB_2241501 Anti-aggrecan (for immunoblot) Abcam ab36861; RRID:AB_722655 Anti-Parvalbumin Synaptic Systems 195 006; RRID:AB_2619887 Anti-Chondroitin Sulfate A mAb (Clone 2H6) Cosmo Bio CAC-NU-07-001 Mouse IgM isotype control Thermo Fisher 14-4752-82; RRID:AB_470123 Mouse IgM isotype control Santa Cruz sc-3881; RRID:AB_737292 Alexa Fluor 647 Goat anti-mouse Abcam ab150115; RRID:AB_2687948 Alexa Fluor 594 Goat anti-mouse Abcam ab150116; RRID:AB_2650601 Alexa Fluor 405 Goat anti-Rabbit Abcam ab175652; RRID:AB_2687498 Alexa Fluor 647 Goat anti-Rabbit Abcam ab150079; RRID:AB_2722623 Alexa Fluor 488 Donkey anti-goat Abcam ab150129; RRID:AB_2687506 Alexa Fluor 405 Goat anti-Chicken Abcam ab175674; RRID:AB_2890171 Alexa Fluor 546 Goat anti-Mouse Thermo Fisher A-11003; RRID:AB_141370 Bacterial and virus strains pAAV_U6_VCAN_shRNA_GFP Dr. Dityatev’s group N/A pAAV_U6_scramble_shRNA_GFP Mitlöhner et al.56 N/A Competent E. coli NEB C3040H Biological samples Human postmortem Amygdala sample from healthy donor Harvard Brain Tissue Resource Center/NIH NeuroBioBank N/A Chemicals, peptides, and recombinant proteins Bovine serum albumin (BSA) Thermo Fisher BP1605100 Paraformaldehyde (PFA; powder) Sigma-Aldrich P6148 Glutaraldehyde Sigma-Aldrich G6257 Sodium cacodylate Sigma-Aldrich C0250 Hydrogen peroxide Fisher H325100 Glycine Sigma G-7403 Triton X-100 Fisher AC215680010 Goat serum Gibco 16210-064 Streptavidin - Horseradish peroxidase Invitrogen 434323 3,3’-Diaminobenzidine Tetrahydrochloride Sigma D5905-100TAB Cytoseal Thermo Fisher 8310-16 Fluomount Southern biotech 0100-01 Chondroitinase ABC amsbio AMS.E1028-10 HaltTM Protease Inhibitor Cocktail Thermo Fisher 78429 Sodium borohydride Fisher AC448501000 Formic Acid/Acetonitrile 0.1/99.9, v/v Sigma-Aldrich 159002 Ammonium hydroxide Sigma-Aldrich 221228 Blocking Buffer Li-Cor 92760001 (Continued on next page) Cell Reports 43, 114112, May 28, 2024 17 .. REAGENT or RESOURCE SOURCE IDENTIFIER NuPage Bis-Tris Thermo Fisher NP0335BOX Mercaptoethanol Sigma-Aldrich M3148 Trifluoracetic acid Sigma-Aldrich 808260 Uranyl acetate Sigma-Aldrich M1775 Embed 812 resin Electron Microscopy Sciences 14900 Fetal Bovine Serum Life Technologies 10270106 PBS pH 7.4 Life Technologies 10010015 DMEM, high glucose Life Technologies 41965062 HBSS Life Technologies 14175053 Iscoves Modified Dulbecco Media Sigma Aldrich I3390 Laminin Sigma Aldrich L2020 Poly-L-Lysine Sigma Aldrich L2636 Trypsin-EDTA (0.05%) Life Technologies 25300054 Penicillin-Streptomycin (10,000 U/mL) Life Technologies 15140122 L-Glutamine Life Technologies 25030024 B27 Supplement Life Technologies 17504044 Neurobasal Media Life Technologies 21103049 Critical commercial assays PierceTMSilver Stain kit Thermo Fisher 24612 SimplyBluTMSafeStain Thermo Fisher LC6060 Protein L Sepharose Abcam ab193261 M-270 Epoxy beads Thermo Fisher 14301 BCA protein assay Thermo Fisher A55860 DNA/RNA Extracol kit EURX 3750 1X HALT protease inhibitor Thermo FIsher P187786 High-Capacity cDNA Reverse Transcription Kit Applied BiosystemsTM 4368814 TaqMan gene expression array Thermo FIsher 4331182 TaqManTM Fast Universal PCR Master Mix Applied BiosystemsTM 4352042 Deposited data Mouse proteomic raw data This Manuscript PXD047129 https://doi.org/10.6019/PXD047129 Human proteomic data This Manuscript PXD050008 https://doi.org/10.6019/PXD050008 Experimental models: Cell lines HEK 293T cells ATCC CRL-1573 Primary hippocampal culture This manuscript N/A Experimental models: Organisms/strains c57bl/6j - Males The Jackson Laboratory 000664 B6 Cg-Tg(Thy1-YFP)HJrs/J - Males The Jackson Laboratory 003782 C57BL/6NCrl - Males Charles River 027 Oligonucleotides Gapdh TaqMan Mm99999915_g1 Vcan TaqMan Mm01283063_m1 Chst3 TaqMan Mm00489736_m1 Chst7 TaqMan Mm00491466_m1 Chst11 TaqMan Mm00517562_m1 Chst12 TaqMan Mm00546416_s1 Recombinant DNA pAAV-U6-GFP Expression Vector Cell Biolabs VPK-413 (Continued on next page) 18 Cell Reports 43, 114112, May 28, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER pAAV_U6_VCANshRNA_GFP This manuscript N/A pAAV_U6_CtrlshRNA_GFP Mitlöhner et al.56 https://doi.org/10.3390/cells9020260 pAAV_U6_scramble_shRNA_GFP Mitlöhner et al.56 https://doi.org/10.3390/cells9020260 Software and algorithms ImageJ/FIJI Schneider et al.57 https://imagej.net/software/fiji/ Prism (version 8) GraphPad https://www.graphpad.com/ scientific-software/prism PATCHMASTER HEKA https://www.heka.com/downloads/ downloads_main.html#down_patchmaster StereoInvestigator 6.0 Micro-Brightfield N/A Leica LAS-X software Leica N/A Other Vibratome Leica VT1200S Microtome American Optical 860 Cryostat Leica CM1950 Double edge, breakable style razor blades Cetim AISI 440 Low-profile disposable cryostat blades Leica DB80LX Automatic tissue homogenizer Avantor SCERSP749540-0000 Disposable pestles, PP, 1.5mL Avantor SCERSP749521-1500 5600+ QTOF mass spectrometer Sciex N/A Q-Exactive HF mass spectrometer Thermo Fisher N/A nanoAcquity UPLC Waters N/A Eksigent nanoLC.as-2 autosampler SpectraLab Others-00-001 NANOSpray III Source Sciex p/n 1034661 Acclaim PepMap100 Thermo Fisher 164946 IntegraFrit Trap Column New Objective N/A Odyssey Scanner Li-Cor N/A Bio-Rad semidry transblotters Bio-Rad N/A Standard surgical blades Word Precision Instruments 500240 SuperFrost Ultra PlusTM Gold slides Fisher scientific 11976299 PierceTM C18 Spin tips and columns Thermo Fisher 87782 EPC-10 amplifier HEKA Elektronik N/A Quant-Studio-5 device Applied Biosystems A28569 Zeiss Axio Imager M2 fluorescent microscope Zeiss M2: 430004-9902 Stereotactic frame Narishige Scientific Instrument Lab SR-6M Ultra microinfusion pump World Precision Instrument UMP3 Confocal laser scanning microscope Leica TCS SP8 Scanning electron microscope JEM 1200EX II JEOL N/A Zeiss Axioskop 2 Plus Zeiss SM100297-MG1 6 well cell culture plate Greiner Bio One GB657160

    Gene Expression:

    Article Title: Focal clusters of peri-synaptic matrix contribute to activity-dependent plasticity and memory in mice.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-CS56 Sigma-Aldrich C8035; RRDI:AB_476879 Anti-CS56 (for immunoblot and affinity purification) Abcam ab11570: RRDI:AB_298176 Anti-Arc/Arg3.1 Proteintech 16290-1-AP; RRDI:AB_2151832 Anti-PSD95 Abcam ab90426; RRID:AB_2050168 Anti-Versican Merck AB1032, RRID:AB_2214376 Anti-Versican (for immunoblot) Santa Cruz sc-25831; RRID:AB_2241501 Anti-aggrecan (for immunoblot) Abcam ab36861; RRID:AB_722655 Anti-Parvalbumin Synaptic Systems 195 006; RRID:AB_2619887 Anti-Chondroitin Sulfate A mAb (Clone 2H6) Cosmo Bio CAC-NU-07-001 Mouse IgM isotype control Thermo Fisher 14-4752-82; RRID:AB_470123 Mouse IgM isotype control Santa Cruz sc-3881; RRID:AB_737292 Alexa Fluor 647 Goat anti-mouse Abcam ab150115; RRID:AB_2687948 Alexa Fluor 594 Goat anti-mouse Abcam ab150116; RRID:AB_2650601 Alexa Fluor 405 Goat anti-Rabbit Abcam ab175652; RRID:AB_2687498 Alexa Fluor 647 Goat anti-Rabbit Abcam ab150079; RRID:AB_2722623 Alexa Fluor 488 Donkey anti-goat Abcam ab150129; RRID:AB_2687506 Alexa Fluor 405 Goat anti-Chicken Abcam ab175674; RRID:AB_2890171 Alexa Fluor 546 Goat anti-Mouse Thermo Fisher A-11003; RRID:AB_141370 Bacterial and virus strains pAAV_U6_VCAN_shRNA_GFP Dr. Dityatev’s group N/A pAAV_U6_scramble_shRNA_GFP Mitlöhner et al.56 N/A Competent E. coli NEB C3040H Biological samples Human postmortem Amygdala sample from healthy donor Harvard Brain Tissue Resource Center/NIH NeuroBioBank N/A Chemicals, peptides, and recombinant proteins Bovine serum albumin (BSA) Thermo Fisher BP1605100 Paraformaldehyde (PFA; powder) Sigma-Aldrich P6148 Glutaraldehyde Sigma-Aldrich G6257 Sodium cacodylate Sigma-Aldrich C0250 Hydrogen peroxide Fisher H325100 Glycine Sigma G-7403 Triton X-100 Fisher AC215680010 Goat serum Gibco 16210-064 Streptavidin - Horseradish peroxidase Invitrogen 434323 3,3’-Diaminobenzidine Tetrahydrochloride Sigma D5905-100TAB Cytoseal Thermo Fisher 8310-16 Fluomount Southern biotech 0100-01 Chondroitinase ABC amsbio AMS.E1028-10 HaltTM Protease Inhibitor Cocktail Thermo Fisher 78429 Sodium borohydride Fisher AC448501000 Formic Acid/Acetonitrile 0.1/99.9, v/v Sigma-Aldrich 159002 Ammonium hydroxide Sigma-Aldrich 221228 Blocking Buffer Li-Cor 92760001 (Continued on next page) Cell Reports 43, 114112, May 28, 2024 17 .. REAGENT or RESOURCE SOURCE IDENTIFIER NuPage Bis-Tris Thermo Fisher NP0335BOX Mercaptoethanol Sigma-Aldrich M3148 Trifluoracetic acid Sigma-Aldrich 808260 Uranyl acetate Sigma-Aldrich M1775 Embed 812 resin Electron Microscopy Sciences 14900 Fetal Bovine Serum Life Technologies 10270106 PBS pH 7.4 Life Technologies 10010015 DMEM, high glucose Life Technologies 41965062 HBSS Life Technologies 14175053 Iscoves Modified Dulbecco Media Sigma Aldrich I3390 Laminin Sigma Aldrich L2020 Poly-L-Lysine Sigma Aldrich L2636 Trypsin-EDTA (0.05%) Life Technologies 25300054 Penicillin-Streptomycin (10,000 U/mL) Life Technologies 15140122 L-Glutamine Life Technologies 25030024 B27 Supplement Life Technologies 17504044 Neurobasal Media Life Technologies 21103049 Critical commercial assays PierceTMSilver Stain kit Thermo Fisher 24612 SimplyBluTMSafeStain Thermo Fisher LC6060 Protein L Sepharose Abcam ab193261 M-270 Epoxy beads Thermo Fisher 14301 BCA protein assay Thermo Fisher A55860 DNA/RNA Extracol kit EURX 3750 1X HALT protease inhibitor Thermo FIsher P187786 High-Capacity cDNA Reverse Transcription Kit Applied BiosystemsTM 4368814 TaqMan gene expression array Thermo FIsher 4331182 TaqManTM Fast Universal PCR Master Mix Applied BiosystemsTM 4352042 Deposited data Mouse proteomic raw data This Manuscript PXD047129 https://doi.org/10.6019/PXD047129 Human proteomic data This Manuscript PXD050008 https://doi.org/10.6019/PXD050008 Experimental models: Cell lines HEK 293T cells ATCC CRL-1573 Primary hippocampal culture This manuscript N/A Experimental models: Organisms/strains c57bl/6j - Males The Jackson Laboratory 000664 B6 Cg-Tg(Thy1-YFP)HJrs/J - Males The Jackson Laboratory 003782 C57BL/6NCrl - Males Charles River 027 Oligonucleotides Gapdh TaqMan Mm99999915_g1 Vcan TaqMan Mm01283063_m1 Chst3 TaqMan Mm00489736_m1 Chst7 TaqMan Mm00491466_m1 Chst11 TaqMan Mm00517562_m1 Chst12 TaqMan Mm00546416_s1 Recombinant DNA pAAV-U6-GFP Expression Vector Cell Biolabs VPK-413 (Continued on next page) 18 Cell Reports 43, 114112, May 28, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER pAAV_U6_VCANshRNA_GFP This manuscript N/A pAAV_U6_CtrlshRNA_GFP Mitlöhner et al.56 https://doi.org/10.3390/cells9020260 pAAV_U6_scramble_shRNA_GFP Mitlöhner et al.56 https://doi.org/10.3390/cells9020260 Software and algorithms ImageJ/FIJI Schneider et al.57 https://imagej.net/software/fiji/ Prism (version 8) GraphPad https://www.graphpad.com/ scientific-software/prism PATCHMASTER HEKA https://www.heka.com/downloads/ downloads_main.html#down_patchmaster StereoInvestigator 6.0 Micro-Brightfield N/A Leica LAS-X software Leica N/A Other Vibratome Leica VT1200S Microtome American Optical 860 Cryostat Leica CM1950 Double edge, breakable style razor blades Cetim AISI 440 Low-profile disposable cryostat blades Leica DB80LX Automatic tissue homogenizer Avantor SCERSP749540-0000 Disposable pestles, PP, 1.5mL Avantor SCERSP749521-1500 5600+ QTOF mass spectrometer Sciex N/A Q-Exactive HF mass spectrometer Thermo Fisher N/A nanoAcquity UPLC Waters N/A Eksigent nanoLC.as-2 autosampler SpectraLab Others-00-001 NANOSpray III Source Sciex p/n 1034661 Acclaim PepMap100 Thermo Fisher 164946 IntegraFrit Trap Column New Objective N/A Odyssey Scanner Li-Cor N/A Bio-Rad semidry transblotters Bio-Rad N/A Standard surgical blades Word Precision Instruments 500240 SuperFrost Ultra PlusTM Gold slides Fisher scientific 11976299 PierceTM C18 Spin tips and columns Thermo Fisher 87782 EPC-10 amplifier HEKA Elektronik N/A Quant-Studio-5 device Applied Biosystems A28569 Zeiss Axio Imager M2 fluorescent microscope Zeiss M2: 430004-9902 Stereotactic frame Narishige Scientific Instrument Lab SR-6M Ultra microinfusion pump World Precision Instrument UMP3 Confocal laser scanning microscope Leica TCS SP8 Scanning electron microscope JEM 1200EX II JEOL N/A Zeiss Axioskop 2 Plus Zeiss SM100297-MG1 6 well cell culture plate Greiner Bio One GB657160

    Expressing:

    Article Title: Focal clusters of peri-synaptic matrix contribute to activity-dependent plasticity and memory in mice.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-CS56 Sigma-Aldrich C8035; RRDI:AB_476879 Anti-CS56 (for immunoblot and affinity purification) Abcam ab11570: RRDI:AB_298176 Anti-Arc/Arg3.1 Proteintech 16290-1-AP; RRDI:AB_2151832 Anti-PSD95 Abcam ab90426; RRID:AB_2050168 Anti-Versican Merck AB1032, RRID:AB_2214376 Anti-Versican (for immunoblot) Santa Cruz sc-25831; RRID:AB_2241501 Anti-aggrecan (for immunoblot) Abcam ab36861; RRID:AB_722655 Anti-Parvalbumin Synaptic Systems 195 006; RRID:AB_2619887 Anti-Chondroitin Sulfate A mAb (Clone 2H6) Cosmo Bio CAC-NU-07-001 Mouse IgM isotype control Thermo Fisher 14-4752-82; RRID:AB_470123 Mouse IgM isotype control Santa Cruz sc-3881; RRID:AB_737292 Alexa Fluor 647 Goat anti-mouse Abcam ab150115; RRID:AB_2687948 Alexa Fluor 594 Goat anti-mouse Abcam ab150116; RRID:AB_2650601 Alexa Fluor 405 Goat anti-Rabbit Abcam ab175652; RRID:AB_2687498 Alexa Fluor 647 Goat anti-Rabbit Abcam ab150079; RRID:AB_2722623 Alexa Fluor 488 Donkey anti-goat Abcam ab150129; RRID:AB_2687506 Alexa Fluor 405 Goat anti-Chicken Abcam ab175674; RRID:AB_2890171 Alexa Fluor 546 Goat anti-Mouse Thermo Fisher A-11003; RRID:AB_141370 Bacterial and virus strains pAAV_U6_VCAN_shRNA_GFP Dr. Dityatev’s group N/A pAAV_U6_scramble_shRNA_GFP Mitlöhner et al.56 N/A Competent E. coli NEB C3040H Biological samples Human postmortem Amygdala sample from healthy donor Harvard Brain Tissue Resource Center/NIH NeuroBioBank N/A Chemicals, peptides, and recombinant proteins Bovine serum albumin (BSA) Thermo Fisher BP1605100 Paraformaldehyde (PFA; powder) Sigma-Aldrich P6148 Glutaraldehyde Sigma-Aldrich G6257 Sodium cacodylate Sigma-Aldrich C0250 Hydrogen peroxide Fisher H325100 Glycine Sigma G-7403 Triton X-100 Fisher AC215680010 Goat serum Gibco 16210-064 Streptavidin - Horseradish peroxidase Invitrogen 434323 3,3’-Diaminobenzidine Tetrahydrochloride Sigma D5905-100TAB Cytoseal Thermo Fisher 8310-16 Fluomount Southern biotech 0100-01 Chondroitinase ABC amsbio AMS.E1028-10 HaltTM Protease Inhibitor Cocktail Thermo Fisher 78429 Sodium borohydride Fisher AC448501000 Formic Acid/Acetonitrile 0.1/99.9, v/v Sigma-Aldrich 159002 Ammonium hydroxide Sigma-Aldrich 221228 Blocking Buffer Li-Cor 92760001 (Continued on next page) Cell Reports 43, 114112, May 28, 2024 17 .. REAGENT or RESOURCE SOURCE IDENTIFIER NuPage Bis-Tris Thermo Fisher NP0335BOX Mercaptoethanol Sigma-Aldrich M3148 Trifluoracetic acid Sigma-Aldrich 808260 Uranyl acetate Sigma-Aldrich M1775 Embed 812 resin Electron Microscopy Sciences 14900 Fetal Bovine Serum Life Technologies 10270106 PBS pH 7.4 Life Technologies 10010015 DMEM, high glucose Life Technologies 41965062 HBSS Life Technologies 14175053 Iscoves Modified Dulbecco Media Sigma Aldrich I3390 Laminin Sigma Aldrich L2020 Poly-L-Lysine Sigma Aldrich L2636 Trypsin-EDTA (0.05%) Life Technologies 25300054 Penicillin-Streptomycin (10,000 U/mL) Life Technologies 15140122 L-Glutamine Life Technologies 25030024 B27 Supplement Life Technologies 17504044 Neurobasal Media Life Technologies 21103049 Critical commercial assays PierceTMSilver Stain kit Thermo Fisher 24612 SimplyBluTMSafeStain Thermo Fisher LC6060 Protein L Sepharose Abcam ab193261 M-270 Epoxy beads Thermo Fisher 14301 BCA protein assay Thermo Fisher A55860 DNA/RNA Extracol kit EURX 3750 1X HALT protease inhibitor Thermo FIsher P187786 High-Capacity cDNA Reverse Transcription Kit Applied BiosystemsTM 4368814 TaqMan gene expression array Thermo FIsher 4331182 TaqManTM Fast Universal PCR Master Mix Applied BiosystemsTM 4352042 Deposited data Mouse proteomic raw data This Manuscript PXD047129 https://doi.org/10.6019/PXD047129 Human proteomic data This Manuscript PXD050008 https://doi.org/10.6019/PXD050008 Experimental models: Cell lines HEK 293T cells ATCC CRL-1573 Primary hippocampal culture This manuscript N/A Experimental models: Organisms/strains c57bl/6j - Males The Jackson Laboratory 000664 B6 Cg-Tg(Thy1-YFP)HJrs/J - Males The Jackson Laboratory 003782 C57BL/6NCrl - Males Charles River 027 Oligonucleotides Gapdh TaqMan Mm99999915_g1 Vcan TaqMan Mm01283063_m1 Chst3 TaqMan Mm00489736_m1 Chst7 TaqMan Mm00491466_m1 Chst11 TaqMan Mm00517562_m1 Chst12 TaqMan Mm00546416_s1 Recombinant DNA pAAV-U6-GFP Expression Vector Cell Biolabs VPK-413 (Continued on next page) 18 Cell Reports 43, 114112, May 28, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER pAAV_U6_VCANshRNA_GFP This manuscript N/A pAAV_U6_CtrlshRNA_GFP Mitlöhner et al.56 https://doi.org/10.3390/cells9020260 pAAV_U6_scramble_shRNA_GFP Mitlöhner et al.56 https://doi.org/10.3390/cells9020260 Software and algorithms ImageJ/FIJI Schneider et al.57 https://imagej.net/software/fiji/ Prism (version 8) GraphPad https://www.graphpad.com/ scientific-software/prism PATCHMASTER HEKA https://www.heka.com/downloads/ downloads_main.html#down_patchmaster StereoInvestigator 6.0 Micro-Brightfield N/A Leica LAS-X software Leica N/A Other Vibratome Leica VT1200S Microtome American Optical 860 Cryostat Leica CM1950 Double edge, breakable style razor blades Cetim AISI 440 Low-profile disposable cryostat blades Leica DB80LX Automatic tissue homogenizer Avantor SCERSP749540-0000 Disposable pestles, PP, 1.5mL Avantor SCERSP749521-1500 5600+ QTOF mass spectrometer Sciex N/A Q-Exactive HF mass spectrometer Thermo Fisher N/A nanoAcquity UPLC Waters N/A Eksigent nanoLC.as-2 autosampler SpectraLab Others-00-001 NANOSpray III Source Sciex p/n 1034661 Acclaim PepMap100 Thermo Fisher 164946 IntegraFrit Trap Column New Objective N/A Odyssey Scanner Li-Cor N/A Bio-Rad semidry transblotters Bio-Rad N/A Standard surgical blades Word Precision Instruments 500240 SuperFrost Ultra PlusTM Gold slides Fisher scientific 11976299 PierceTM C18 Spin tips and columns Thermo Fisher 87782 EPC-10 amplifier HEKA Elektronik N/A Quant-Studio-5 device Applied Biosystems A28569 Zeiss Axio Imager M2 fluorescent microscope Zeiss M2: 430004-9902 Stereotactic frame Narishige Scientific Instrument Lab SR-6M Ultra microinfusion pump World Precision Instrument UMP3 Confocal laser scanning microscope Leica TCS SP8 Scanning electron microscope JEM 1200EX II JEOL N/A Zeiss Axioskop 2 Plus Zeiss SM100297-MG1 6 well cell culture plate Greiner Bio One GB657160



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