other:Article Title: Resurrection of endogenous retroviruses during aging reinforces senescence.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Alexa Fluo 568 Donkey Anti-Mouse IgG (H+L) Invitrogen Cat# A-10037; RRID: AB_2534013 Alexa Fluor 488 Donkey Anti-Mouse IgG (H+L) Invitrogen Cat# A21202; RRID: AB_141607 HRP-conjugated Goat Anti-Mouse IgG (H+L) ZSGB-Bio Cat# ZB2305; RRID: AB_2747415 HRP-conjugated Goat Anti-Rabbit IgG (H+L) ZSGB-Bio Cat# ZB2301; RRID: AB_2747412 6-nm Gold-labeled Goat Anti-Mouse IgG (H+L) Jackson ImmunoResearch Cat# 115-195-146 RRID: N/A Biological samples The young and old cynomolgus monkey tissues Xieerxin Biology Resource N/A The WT and HGPS cynomolgus monkey tissues Yunnan Key Laboratory of Primate Biomedical Research N/A Human eyelid skin samples Peking Union Medical College Hospital N/A Human serum samples The First Hospital of Kunming Medical University N/A Chemicals, peptides, and recombinant proteins MEMa GIBCO Cat# 32571-101 DMEM/High Glucose HyClone Cat# SH30243.01 Non-essential amino acids (NEAA) GIBCO Cat# 11140076 Fetal bovine serum (FBS) GIBCO Cat# 42Q7980K Penicillin/streptomycin (P/S) GIBCO Cat# 15140-163 GlutaMAX GIBCO Cat# 35050079 Gelatin Sigma-Aldrich Cat# V900863 bFGF Joint Protein Central Cat# BBI-EXP-002 TrypLE Express Enzyme (1X), no phenol red GIBCO Cat# 12605010 0.25% Trypsin-EDTA (1X), Phenol Red GIBCO Cat# 25200072 Hoechst 33342 Thermo Fisher Scientific Cat# H3570 THUNDERBIRD SYBR qPCR mix TOYOBO Cat# QPS-201(-) 4% paraformaldehyde, PFA Dingguo, China Cat# AR-0211 Triton X-100 Sigma-Aldrich Cat# T9284 Crystal violet Biohao Biotechnology Co., Ltd., China Cat# C0502 TRIzol Reagent Thermo Fisher Scientific Cat# 15596018 DMSO Sigma-Aldrich Cat# D2650 NP-40 Dingguo, China Cat# DH218 Proteinase K New England Biolabs Cat# P8107S RNase A TAKARA Cat# 2158 EDTA Sigma-Aldrich Cat# EDS-500G Protease inhibitor cocktail Roche Cat# 4693159001 X-gal Amresca Cat# 0428-25G PVDF membranes Millipore Cat# IPVH00010 Protein A/G Plus-Agarose Thermo Fisher Scientific Cat# sc-2003 QX200 ddPCR EvaGreen Supermix Bio-Rad Laboratories, Inc. Cat# 186-4033 (Continued on next page) ll e2 Cell 186, 287–304.e1–e12, January 19, 2023 Article
Real-time Polymerase Chain Reaction:Article Title: Nuclear lamina erosion-induced resurrection of endogenous retroviruses underlies neuronal aging.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Normal Rabbit IgG Cell Signaling Technology Cat# 2729S; RRID: AB_1031062 Alexa FluoTM 568 Donkey Anti-Rabbit IgG (H+L) Invitrogen Cat# A-10042; RRID: AB_2534017 Alexa FluoTM 568 Donkey Anti-Mouse IgG (H+L) Invitrogen Cat# A-10037; RRID: AB_2534013 Alexa FluoTM 488 Donkey Anti-Rabbit IgG (H+L) Invitrogen Cat# A-21206; RRID: AB_2535792 Alexa FluorTM 488 Donkey Anti-Mouse IgG (H+L) Invitrogen Cat# A-21202; RRID: AB_141607 Alexa FluorTM 488 Goat Anti-Chicken IgY (H+L) Invitrogen Cat# A-11039; RRID: AB_2534096 Alexa FluorTM 488 Donkey Anti-Goat IgG (H+L) Invitrogen Cat# A-11055; RRID: AB_2534102 10-nm Gold-labeled Goat Anti-Mouse IgG (H+L) Aurion Cat# 810.022-05; RRID: N/A Biological samples The young and aged cynomolgus monkey FL tissues Xieerxin Biology Resource N/A Human FL tissues Beijing Tiantan Hospital Capital Medical University and Xuanwu Hospital Capital Medical University N/A Human CSF samples Beijing Tiantan Hospital Capital Medical University N/A Chemicals, peptides, and recombinant proteins Gelatin Sigma-Aldrich Cat# V900863 Matrigel Matrix BD Biosciences Cat# 354230 DMEM/High Glucose HyClone Cat# SH30243.01 Fetal bovine serum (FBS) GIBCO Cat# 42Q7980K DMEM/F12 Thermo Fisher Scientific Cat# 11330057 KnockOut-SR Thermo Fisher Scientific Cat# A31815-02 Non-essential amino acids (NEAA) GIBCO Cat# 11140076 GlutaMAX GIBCO Cat# 35050079 Penicillin/streptomycin (P/S) GIBCO Cat# 15140-163 bFGF Joint Protein Central Cat# BBI-EXP-002 2-Mercaptoethanol GIBCO Cat# 21985-023 Plasmocin InvivoGene Cat# ant-mpt Advanced DMEM/F12 GIBCO Cat# 12634-028 Neurobasal GIBCO Cat# 12348-017 N2 GIBCO Cat# 17502-048 B27 GIBCO Cat# 17504-044 hLIF Millipore Cat# LIF1050 SB431542 Selleck Cat# s1067 CHIR99021 TOCRIS Cat# 252917-06-9 Dorsomorphin Sigma-Aldrich Cat# P5499 Compound E Millipore Cat# 565790 dbcAMP Sigma-Aldrich Cat# D0627 Ascorbic acid Sigma-Aldrich Cat# A8960 BDNF PEPROTECH Cat# 450-02 GDNF PEPROTECH Cat# 450-10 Accumax Millipore Cat# SCR006 (Continued on next page) 22 Cell Reports 42, 112593, June 27, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER Laminin Sigma-Aldrich Cat# L2020 Hoechst 33342 Thermo Fisher Scientific Cat# H3570 THUNDERBIRD SYBR qPCR mix TOYOBO Cat# QPS-201(-) 4% paraformaldehyde, PFA Dingguo, China Cat# AR-0211 Triton X-100 Sigma-Aldrich Cat# T9284 TRIzolTM Reagent Thermo Fisher Scientific Cat# 15596018 DMSO Sigma-Aldrich Cat# D2650 NP-40 Dingguo, China Cat# DH218 Proteinase K New England Biolabs Cat# P8107S EDTA Sigma-Aldrich Cat# EDS-500G Protease inhibitor cocktail Roche Cat# 4693159001 X-Gal Amresca Cat# 0428-25G RNasin Plus RNase Inhibitor Promega Cat# N2618 SUPERase-IN RNase Inhibitor Invitrogen Cat# AM2694 VECTASHIELD Antifade Mounting Medium Vector Laboratories Cat# H-1000 Abacavir Selleckchem Cat# S3165 Critical commercial assays DynabeadsTM Protein A Thermo Fisher Scientific Cat# 10002D GoScript Reverse Transcription System Promega Cat# A5001 Lipofectamine 3000 Transfection Reagent Thermo Fisher Scientific Cat# L3000015 Human IL6 ELISA Kit BioLegend Cat# 430515 Human HERVK-Env Polyprotein ELISA Kit CUSABIO Cat# CBS-EL007812HU 2030-cGAMP ELISA Kit Cayman Cat# 501700 Human Ab1-40(Amyloid Beta 1-40) ELISA Kit Elabscience Cat# E-EL-H0542c Human Ab1-42(Amyloid Beta 1-42) ELISA Kit Elabscience Cat# E-EL-H0543c DAB Staining Kit ZSGB-BIO Cat# ZLI-9018 FD Rapid GolgiStainTM Kit FD NeuroTechnologies Cat# PK401 Proteostat Protein Aggregation Assay Enzo Cat# ENZ-51035-K100 Deposited data The raw sequencing data of young and aged cynomolgus monkey frontal cortex This study GSA: CRA006691 The raw RNA-seq data for human neurons This study GSA-human: HRA002438 Experimental models: Cell lines WT hNeurons (derived from WT hESCs (Line H9) This study N/A Experimental models: Organisms/strains C57BL/6J mice SiPeiFu (Beijing) Biotechnology Co., Ltd. N/A Oligonucleotides Primers for qPCR, qRT-PCR, and sequences of the siRNAs are shown in Table S7 This study N/A Software and algorithms ImageJ (version 1.8.0) Schneider et al.82 https://imagej.net/Welcome ZEN 3.1 ZEISS https://www.micro-shop.zeiss.com/en/us/ system/zen+software/software+zen/ zen+-+basic+software/410135-1002-310 Leica LAS AF Lite (version 2.6.0) Leica https://leica-las-af-lite.updatestar.com/ (Continued on next page) Cell Reports 42, 112593, June 27, 2023 23 .. REAGENT or RESOURCE SOURCE IDENTIFIER PhenochartTM 1.0 Phenochart https://www.akoyabio.com/support/ software/phenochart-whole-slide-viewer/ GraphPadPrism 8.0 GraphPad Software Inc. https://www.graphpad.com/ IMARIS 9.8 OXFORD INSTRUMENTs https://imaris.oxinst.cn/newrelease TrimGalore (version 0.4.5) N/A https://github.com/FelixKrueger/ TrimGalore HISAT2 (version 2.0.4) Kim et al.83 http://daehwankimlab.github.io/hisat2/ featureCounts (version 2.0.0) Liao et al.84 https://subread.sourceforge.net/ fastp (version 0.19.10) Chen et al.85 https://github.com/OpenGene/fastp bsmap (version 2.90) Xi et al.86 https://code.google.com/p/bsmap/ deepTools (version 2.5.4-2-5ee467f) Ramirez et al.87 https://deeptools.readthedocs.io/en/ develop/index.html GSEA (version 4.1.0) Subramanian et al.88 https://www.gsea-msigdb.org/gsea/ downloads.jsp DoubletFinder (version 2.0.2) McGinnis et al.89 https://github.com/chris-mcginnis-ucsf/ DoubletFinder Seurat (version 3.2.3) Butler et al.90 https://satijalab.org/seurat/articles/install. html CellBender (version 0.2.0) Fleming et al.91 https://github.com/broadinstitute/ CellBender Cell Ranger (version 3.0.0) 10x Genomics https://support.10xgenomics.com/ single-cell-gene-expression/software/ downloads/3.0/ DESeq2 (version 1.22.2) Love et al.92 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html MaxQuant (v.1.5.2.8) N/A https://www.maxquant.org/ Metascape Zhou et al.93 https://metascape.org/ Cytoscape (version 3.8.2) Shannon et al.94 https://cytoscape.org/
Protease Inhibitor:Article Title: Nuclear lamina erosion-induced resurrection of endogenous retroviruses underlies neuronal aging.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Normal Rabbit IgG Cell Signaling Technology Cat# 2729S; RRID: AB_1031062 Alexa FluoTM 568 Donkey Anti-Rabbit IgG (H+L) Invitrogen Cat# A-10042; RRID: AB_2534017 Alexa FluoTM 568 Donkey Anti-Mouse IgG (H+L) Invitrogen Cat# A-10037; RRID: AB_2534013 Alexa FluoTM 488 Donkey Anti-Rabbit IgG (H+L) Invitrogen Cat# A-21206; RRID: AB_2535792 Alexa FluorTM 488 Donkey Anti-Mouse IgG (H+L) Invitrogen Cat# A-21202; RRID: AB_141607 Alexa FluorTM 488 Goat Anti-Chicken IgY (H+L) Invitrogen Cat# A-11039; RRID: AB_2534096 Alexa FluorTM 488 Donkey Anti-Goat IgG (H+L) Invitrogen Cat# A-11055; RRID: AB_2534102 10-nm Gold-labeled Goat Anti-Mouse IgG (H+L) Aurion Cat# 810.022-05; RRID: N/A Biological samples The young and aged cynomolgus monkey FL tissues Xieerxin Biology Resource N/A Human FL tissues Beijing Tiantan Hospital Capital Medical University and Xuanwu Hospital Capital Medical University N/A Human CSF samples Beijing Tiantan Hospital Capital Medical University N/A Chemicals, peptides, and recombinant proteins Gelatin Sigma-Aldrich Cat# V900863 Matrigel Matrix BD Biosciences Cat# 354230 DMEM/High Glucose HyClone Cat# SH30243.01 Fetal bovine serum (FBS) GIBCO Cat# 42Q7980K DMEM/F12 Thermo Fisher Scientific Cat# 11330057 KnockOut-SR Thermo Fisher Scientific Cat# A31815-02 Non-essential amino acids (NEAA) GIBCO Cat# 11140076 GlutaMAX GIBCO Cat# 35050079 Penicillin/streptomycin (P/S) GIBCO Cat# 15140-163 bFGF Joint Protein Central Cat# BBI-EXP-002 2-Mercaptoethanol GIBCO Cat# 21985-023 Plasmocin InvivoGene Cat# ant-mpt Advanced DMEM/F12 GIBCO Cat# 12634-028 Neurobasal GIBCO Cat# 12348-017 N2 GIBCO Cat# 17502-048 B27 GIBCO Cat# 17504-044 hLIF Millipore Cat# LIF1050 SB431542 Selleck Cat# s1067 CHIR99021 TOCRIS Cat# 252917-06-9 Dorsomorphin Sigma-Aldrich Cat# P5499 Compound E Millipore Cat# 565790 dbcAMP Sigma-Aldrich Cat# D0627 Ascorbic acid Sigma-Aldrich Cat# A8960 BDNF PEPROTECH Cat# 450-02 GDNF PEPROTECH Cat# 450-10 Accumax Millipore Cat# SCR006 (Continued on next page) 22 Cell Reports 42, 112593, June 27, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER Laminin Sigma-Aldrich Cat# L2020 Hoechst 33342 Thermo Fisher Scientific Cat# H3570 THUNDERBIRD SYBR qPCR mix TOYOBO Cat# QPS-201(-) 4% paraformaldehyde, PFA Dingguo, China Cat# AR-0211 Triton X-100 Sigma-Aldrich Cat# T9284 TRIzolTM Reagent Thermo Fisher Scientific Cat# 15596018 DMSO Sigma-Aldrich Cat# D2650 NP-40 Dingguo, China Cat# DH218 Proteinase K New England Biolabs Cat# P8107S EDTA Sigma-Aldrich Cat# EDS-500G Protease inhibitor cocktail Roche Cat# 4693159001 X-Gal Amresca Cat# 0428-25G RNasin Plus RNase Inhibitor Promega Cat# N2618 SUPERase-IN RNase Inhibitor Invitrogen Cat# AM2694 VECTASHIELD Antifade Mounting Medium Vector Laboratories Cat# H-1000 Abacavir Selleckchem Cat# S3165 Critical commercial assays DynabeadsTM Protein A Thermo Fisher Scientific Cat# 10002D GoScript Reverse Transcription System Promega Cat# A5001 Lipofectamine 3000 Transfection Reagent Thermo Fisher Scientific Cat# L3000015 Human IL6 ELISA Kit BioLegend Cat# 430515 Human HERVK-Env Polyprotein ELISA Kit CUSABIO Cat# CBS-EL007812HU 2030-cGAMP ELISA Kit Cayman Cat# 501700 Human Ab1-40(Amyloid Beta 1-40) ELISA Kit Elabscience Cat# E-EL-H0542c Human Ab1-42(Amyloid Beta 1-42) ELISA Kit Elabscience Cat# E-EL-H0543c DAB Staining Kit ZSGB-BIO Cat# ZLI-9018 FD Rapid GolgiStainTM Kit FD NeuroTechnologies Cat# PK401 Proteostat Protein Aggregation Assay Enzo Cat# ENZ-51035-K100 Deposited data The raw sequencing data of young and aged cynomolgus monkey frontal cortex This study GSA: CRA006691 The raw RNA-seq data for human neurons This study GSA-human: HRA002438 Experimental models: Cell lines WT hNeurons (derived from WT hESCs (Line H9) This study N/A Experimental models: Organisms/strains C57BL/6J mice SiPeiFu (Beijing) Biotechnology Co., Ltd. N/A Oligonucleotides Primers for qPCR, qRT-PCR, and sequences of the siRNAs are shown in Table S7 This study N/A Software and algorithms ImageJ (version 1.8.0) Schneider et al.82 https://imagej.net/Welcome ZEN 3.1 ZEISS https://www.micro-shop.zeiss.com/en/us/ system/zen+software/software+zen/ zen+-+basic+software/410135-1002-310 Leica LAS AF Lite (version 2.6.0) Leica https://leica-las-af-lite.updatestar.com/ (Continued on next page) Cell Reports 42, 112593, June 27, 2023 23 .. REAGENT or RESOURCE SOURCE IDENTIFIER PhenochartTM 1.0 Phenochart https://www.akoyabio.com/support/ software/phenochart-whole-slide-viewer/ GraphPadPrism 8.0 GraphPad Software Inc. https://www.graphpad.com/ IMARIS 9.8 OXFORD INSTRUMENTs https://imaris.oxinst.cn/newrelease TrimGalore (version 0.4.5) N/A https://github.com/FelixKrueger/ TrimGalore HISAT2 (version 2.0.4) Kim et al.83 http://daehwankimlab.github.io/hisat2/ featureCounts (version 2.0.0) Liao et al.84 https://subread.sourceforge.net/ fastp (version 0.19.10) Chen et al.85 https://github.com/OpenGene/fastp bsmap (version 2.90) Xi et al.86 https://code.google.com/p/bsmap/ deepTools (version 2.5.4-2-5ee467f) Ramirez et al.87 https://deeptools.readthedocs.io/en/ develop/index.html GSEA (version 4.1.0) Subramanian et al.88 https://www.gsea-msigdb.org/gsea/ downloads.jsp DoubletFinder (version 2.0.2) McGinnis et al.89 https://github.com/chris-mcginnis-ucsf/ DoubletFinder Seurat (version 3.2.3) Butler et al.90 https://satijalab.org/seurat/articles/install. html CellBender (version 0.2.0) Fleming et al.91 https://github.com/broadinstitute/ CellBender Cell Ranger (version 3.0.0) 10x Genomics https://support.10xgenomics.com/ single-cell-gene-expression/software/ downloads/3.0/ DESeq2 (version 1.22.2) Love et al.92 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html MaxQuant (v.1.5.2.8) N/A https://www.maxquant.org/ Metascape Zhou et al.93 https://metascape.org/ Cytoscape (version 3.8.2) Shannon et al.94 https://cytoscape.org/
Reverse Transcription:Article Title: Nuclear lamina erosion-induced resurrection of endogenous retroviruses underlies neuronal aging.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Normal Rabbit IgG Cell Signaling Technology Cat# 2729S; RRID: AB_1031062 Alexa FluoTM 568 Donkey Anti-Rabbit IgG (H+L) Invitrogen Cat# A-10042; RRID: AB_2534017 Alexa FluoTM 568 Donkey Anti-Mouse IgG (H+L) Invitrogen Cat# A-10037; RRID: AB_2534013 Alexa FluoTM 488 Donkey Anti-Rabbit IgG (H+L) Invitrogen Cat# A-21206; RRID: AB_2535792 Alexa FluorTM 488 Donkey Anti-Mouse IgG (H+L) Invitrogen Cat# A-21202; RRID: AB_141607 Alexa FluorTM 488 Goat Anti-Chicken IgY (H+L) Invitrogen Cat# A-11039; RRID: AB_2534096 Alexa FluorTM 488 Donkey Anti-Goat IgG (H+L) Invitrogen Cat# A-11055; RRID: AB_2534102 10-nm Gold-labeled Goat Anti-Mouse IgG (H+L) Aurion Cat# 810.022-05; RRID: N/A Biological samples The young and aged cynomolgus monkey FL tissues Xieerxin Biology Resource N/A Human FL tissues Beijing Tiantan Hospital Capital Medical University and Xuanwu Hospital Capital Medical University N/A Human CSF samples Beijing Tiantan Hospital Capital Medical University N/A Chemicals, peptides, and recombinant proteins Gelatin Sigma-Aldrich Cat# V900863 Matrigel Matrix BD Biosciences Cat# 354230 DMEM/High Glucose HyClone Cat# SH30243.01 Fetal bovine serum (FBS) GIBCO Cat# 42Q7980K DMEM/F12 Thermo Fisher Scientific Cat# 11330057 KnockOut-SR Thermo Fisher Scientific Cat# A31815-02 Non-essential amino acids (NEAA) GIBCO Cat# 11140076 GlutaMAX GIBCO Cat# 35050079 Penicillin/streptomycin (P/S) GIBCO Cat# 15140-163 bFGF Joint Protein Central Cat# BBI-EXP-002 2-Mercaptoethanol GIBCO Cat# 21985-023 Plasmocin InvivoGene Cat# ant-mpt Advanced DMEM/F12 GIBCO Cat# 12634-028 Neurobasal GIBCO Cat# 12348-017 N2 GIBCO Cat# 17502-048 B27 GIBCO Cat# 17504-044 hLIF Millipore Cat# LIF1050 SB431542 Selleck Cat# s1067 CHIR99021 TOCRIS Cat# 252917-06-9 Dorsomorphin Sigma-Aldrich Cat# P5499 Compound E Millipore Cat# 565790 dbcAMP Sigma-Aldrich Cat# D0627 Ascorbic acid Sigma-Aldrich Cat# A8960 BDNF PEPROTECH Cat# 450-02 GDNF PEPROTECH Cat# 450-10 Accumax Millipore Cat# SCR006 (Continued on next page) 22 Cell Reports 42, 112593, June 27, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER Laminin Sigma-Aldrich Cat# L2020 Hoechst 33342 Thermo Fisher Scientific Cat# H3570 THUNDERBIRD SYBR qPCR mix TOYOBO Cat# QPS-201(-) 4% paraformaldehyde, PFA Dingguo, China Cat# AR-0211 Triton X-100 Sigma-Aldrich Cat# T9284 TRIzolTM Reagent Thermo Fisher Scientific Cat# 15596018 DMSO Sigma-Aldrich Cat# D2650 NP-40 Dingguo, China Cat# DH218 Proteinase K New England Biolabs Cat# P8107S EDTA Sigma-Aldrich Cat# EDS-500G Protease inhibitor cocktail Roche Cat# 4693159001 X-Gal Amresca Cat# 0428-25G RNasin Plus RNase Inhibitor Promega Cat# N2618 SUPERase-IN RNase Inhibitor Invitrogen Cat# AM2694 VECTASHIELD Antifade Mounting Medium Vector Laboratories Cat# H-1000 Abacavir Selleckchem Cat# S3165 Critical commercial assays DynabeadsTM Protein A Thermo Fisher Scientific Cat# 10002D GoScript Reverse Transcription System Promega Cat# A5001 Lipofectamine 3000 Transfection Reagent Thermo Fisher Scientific Cat# L3000015 Human IL6 ELISA Kit BioLegend Cat# 430515 Human HERVK-Env Polyprotein ELISA Kit CUSABIO Cat# CBS-EL007812HU 2030-cGAMP ELISA Kit Cayman Cat# 501700 Human Ab1-40(Amyloid Beta 1-40) ELISA Kit Elabscience Cat# E-EL-H0542c Human Ab1-42(Amyloid Beta 1-42) ELISA Kit Elabscience Cat# E-EL-H0543c DAB Staining Kit ZSGB-BIO Cat# ZLI-9018 FD Rapid GolgiStainTM Kit FD NeuroTechnologies Cat# PK401 Proteostat Protein Aggregation Assay Enzo Cat# ENZ-51035-K100 Deposited data The raw sequencing data of young and aged cynomolgus monkey frontal cortex This study GSA: CRA006691 The raw RNA-seq data for human neurons This study GSA-human: HRA002438 Experimental models: Cell lines WT hNeurons (derived from WT hESCs (Line H9) This study N/A Experimental models: Organisms/strains C57BL/6J mice SiPeiFu (Beijing) Biotechnology Co., Ltd. N/A Oligonucleotides Primers for qPCR, qRT-PCR, and sequences of the siRNAs are shown in Table S7 This study N/A Software and algorithms ImageJ (version 1.8.0) Schneider et al.82 https://imagej.net/Welcome ZEN 3.1 ZEISS https://www.micro-shop.zeiss.com/en/us/ system/zen+software/software+zen/ zen+-+basic+software/410135-1002-310 Leica LAS AF Lite (version 2.6.0) Leica https://leica-las-af-lite.updatestar.com/ (Continued on next page) Cell Reports 42, 112593, June 27, 2023 23 .. REAGENT or RESOURCE SOURCE IDENTIFIER PhenochartTM 1.0 Phenochart https://www.akoyabio.com/support/ software/phenochart-whole-slide-viewer/ GraphPadPrism 8.0 GraphPad Software Inc. https://www.graphpad.com/ IMARIS 9.8 OXFORD INSTRUMENTs https://imaris.oxinst.cn/newrelease TrimGalore (version 0.4.5) N/A https://github.com/FelixKrueger/ TrimGalore HISAT2 (version 2.0.4) Kim et al.83 http://daehwankimlab.github.io/hisat2/ featureCounts (version 2.0.0) Liao et al.84 https://subread.sourceforge.net/ fastp (version 0.19.10) Chen et al.85 https://github.com/OpenGene/fastp bsmap (version 2.90) Xi et al.86 https://code.google.com/p/bsmap/ deepTools (version 2.5.4-2-5ee467f) Ramirez et al.87 https://deeptools.readthedocs.io/en/ develop/index.html GSEA (version 4.1.0) Subramanian et al.88 https://www.gsea-msigdb.org/gsea/ downloads.jsp DoubletFinder (version 2.0.2) McGinnis et al.89 https://github.com/chris-mcginnis-ucsf/ DoubletFinder Seurat (version 3.2.3) Butler et al.90 https://satijalab.org/seurat/articles/install. html CellBender (version 0.2.0) Fleming et al.91 https://github.com/broadinstitute/ CellBender Cell Ranger (version 3.0.0) 10x Genomics https://support.10xgenomics.com/ single-cell-gene-expression/software/ downloads/3.0/ DESeq2 (version 1.22.2) Love et al.92 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html MaxQuant (v.1.5.2.8) N/A https://www.maxquant.org/ Metascape Zhou et al.93 https://metascape.org/ Cytoscape (version 3.8.2) Shannon et al.94 https://cytoscape.org/
Transfection:Article Title: Nuclear lamina erosion-induced resurrection of endogenous retroviruses underlies neuronal aging.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Normal Rabbit IgG Cell Signaling Technology Cat# 2729S; RRID: AB_1031062 Alexa FluoTM 568 Donkey Anti-Rabbit IgG (H+L) Invitrogen Cat# A-10042; RRID: AB_2534017 Alexa FluoTM 568 Donkey Anti-Mouse IgG (H+L) Invitrogen Cat# A-10037; RRID: AB_2534013 Alexa FluoTM 488 Donkey Anti-Rabbit IgG (H+L) Invitrogen Cat# A-21206; RRID: AB_2535792 Alexa FluorTM 488 Donkey Anti-Mouse IgG (H+L) Invitrogen Cat# A-21202; RRID: AB_141607 Alexa FluorTM 488 Goat Anti-Chicken IgY (H+L) Invitrogen Cat# A-11039; RRID: AB_2534096 Alexa FluorTM 488 Donkey Anti-Goat IgG (H+L) Invitrogen Cat# A-11055; RRID: AB_2534102 10-nm Gold-labeled Goat Anti-Mouse IgG (H+L) Aurion Cat# 810.022-05; RRID: N/A Biological samples The young and aged cynomolgus monkey FL tissues Xieerxin Biology Resource N/A Human FL tissues Beijing Tiantan Hospital Capital Medical University and Xuanwu Hospital Capital Medical University N/A Human CSF samples Beijing Tiantan Hospital Capital Medical University N/A Chemicals, peptides, and recombinant proteins Gelatin Sigma-Aldrich Cat# V900863 Matrigel Matrix BD Biosciences Cat# 354230 DMEM/High Glucose HyClone Cat# SH30243.01 Fetal bovine serum (FBS) GIBCO Cat# 42Q7980K DMEM/F12 Thermo Fisher Scientific Cat# 11330057 KnockOut-SR Thermo Fisher Scientific Cat# A31815-02 Non-essential amino acids (NEAA) GIBCO Cat# 11140076 GlutaMAX GIBCO Cat# 35050079 Penicillin/streptomycin (P/S) GIBCO Cat# 15140-163 bFGF Joint Protein Central Cat# BBI-EXP-002 2-Mercaptoethanol GIBCO Cat# 21985-023 Plasmocin InvivoGene Cat# ant-mpt Advanced DMEM/F12 GIBCO Cat# 12634-028 Neurobasal GIBCO Cat# 12348-017 N2 GIBCO Cat# 17502-048 B27 GIBCO Cat# 17504-044 hLIF Millipore Cat# LIF1050 SB431542 Selleck Cat# s1067 CHIR99021 TOCRIS Cat# 252917-06-9 Dorsomorphin Sigma-Aldrich Cat# P5499 Compound E Millipore Cat# 565790 dbcAMP Sigma-Aldrich Cat# D0627 Ascorbic acid Sigma-Aldrich Cat# A8960 BDNF PEPROTECH Cat# 450-02 GDNF PEPROTECH Cat# 450-10 Accumax Millipore Cat# SCR006 (Continued on next page) 22 Cell Reports 42, 112593, June 27, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER Laminin Sigma-Aldrich Cat# L2020 Hoechst 33342 Thermo Fisher Scientific Cat# H3570 THUNDERBIRD SYBR qPCR mix TOYOBO Cat# QPS-201(-) 4% paraformaldehyde, PFA Dingguo, China Cat# AR-0211 Triton X-100 Sigma-Aldrich Cat# T9284 TRIzolTM Reagent Thermo Fisher Scientific Cat# 15596018 DMSO Sigma-Aldrich Cat# D2650 NP-40 Dingguo, China Cat# DH218 Proteinase K New England Biolabs Cat# P8107S EDTA Sigma-Aldrich Cat# EDS-500G Protease inhibitor cocktail Roche Cat# 4693159001 X-Gal Amresca Cat# 0428-25G RNasin Plus RNase Inhibitor Promega Cat# N2618 SUPERase-IN RNase Inhibitor Invitrogen Cat# AM2694 VECTASHIELD Antifade Mounting Medium Vector Laboratories Cat# H-1000 Abacavir Selleckchem Cat# S3165 Critical commercial assays DynabeadsTM Protein A Thermo Fisher Scientific Cat# 10002D GoScript Reverse Transcription System Promega Cat# A5001 Lipofectamine 3000 Transfection Reagent Thermo Fisher Scientific Cat# L3000015 Human IL6 ELISA Kit BioLegend Cat# 430515 Human HERVK-Env Polyprotein ELISA Kit CUSABIO Cat# CBS-EL007812HU 2030-cGAMP ELISA Kit Cayman Cat# 501700 Human Ab1-40(Amyloid Beta 1-40) ELISA Kit Elabscience Cat# E-EL-H0542c Human Ab1-42(Amyloid Beta 1-42) ELISA Kit Elabscience Cat# E-EL-H0543c DAB Staining Kit ZSGB-BIO Cat# ZLI-9018 FD Rapid GolgiStainTM Kit FD NeuroTechnologies Cat# PK401 Proteostat Protein Aggregation Assay Enzo Cat# ENZ-51035-K100 Deposited data The raw sequencing data of young and aged cynomolgus monkey frontal cortex This study GSA: CRA006691 The raw RNA-seq data for human neurons This study GSA-human: HRA002438 Experimental models: Cell lines WT hNeurons (derived from WT hESCs (Line H9) This study N/A Experimental models: Organisms/strains C57BL/6J mice SiPeiFu (Beijing) Biotechnology Co., Ltd. N/A Oligonucleotides Primers for qPCR, qRT-PCR, and sequences of the siRNAs are shown in Table S7 This study N/A Software and algorithms ImageJ (version 1.8.0) Schneider et al.82 https://imagej.net/Welcome ZEN 3.1 ZEISS https://www.micro-shop.zeiss.com/en/us/ system/zen+software/software+zen/ zen+-+basic+software/410135-1002-310 Leica LAS AF Lite (version 2.6.0) Leica https://leica-las-af-lite.updatestar.com/ (Continued on next page) Cell Reports 42, 112593, June 27, 2023 23 .. REAGENT or RESOURCE SOURCE IDENTIFIER PhenochartTM 1.0 Phenochart https://www.akoyabio.com/support/ software/phenochart-whole-slide-viewer/ GraphPadPrism 8.0 GraphPad Software Inc. https://www.graphpad.com/ IMARIS 9.8 OXFORD INSTRUMENTs https://imaris.oxinst.cn/newrelease TrimGalore (version 0.4.5) N/A https://github.com/FelixKrueger/ TrimGalore HISAT2 (version 2.0.4) Kim et al.83 http://daehwankimlab.github.io/hisat2/ featureCounts (version 2.0.0) Liao et al.84 https://subread.sourceforge.net/ fastp (version 0.19.10) Chen et al.85 https://github.com/OpenGene/fastp bsmap (version 2.90) Xi et al.86 https://code.google.com/p/bsmap/ deepTools (version 2.5.4-2-5ee467f) Ramirez et al.87 https://deeptools.readthedocs.io/en/ develop/index.html GSEA (version 4.1.0) Subramanian et al.88 https://www.gsea-msigdb.org/gsea/ downloads.jsp DoubletFinder (version 2.0.2) McGinnis et al.89 https://github.com/chris-mcginnis-ucsf/ DoubletFinder Seurat (version 3.2.3) Butler et al.90 https://satijalab.org/seurat/articles/install. html CellBender (version 0.2.0) Fleming et al.91 https://github.com/broadinstitute/ CellBender Cell Ranger (version 3.0.0) 10x Genomics https://support.10xgenomics.com/ single-cell-gene-expression/software/ downloads/3.0/ DESeq2 (version 1.22.2) Love et al.92 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html MaxQuant (v.1.5.2.8) N/A https://www.maxquant.org/ Metascape Zhou et al.93 https://metascape.org/ Cytoscape (version 3.8.2) Shannon et al.94 https://cytoscape.org/
Enzyme-linked Immunosorbent Assay:Article Title: Nuclear lamina erosion-induced resurrection of endogenous retroviruses underlies neuronal aging.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Normal Rabbit IgG Cell Signaling Technology Cat# 2729S; RRID: AB_1031062 Alexa FluoTM 568 Donkey Anti-Rabbit IgG (H+L) Invitrogen Cat# A-10042; RRID: AB_2534017 Alexa FluoTM 568 Donkey Anti-Mouse IgG (H+L) Invitrogen Cat# A-10037; RRID: AB_2534013 Alexa FluoTM 488 Donkey Anti-Rabbit IgG (H+L) Invitrogen Cat# A-21206; RRID: AB_2535792 Alexa FluorTM 488 Donkey Anti-Mouse IgG (H+L) Invitrogen Cat# A-21202; RRID: AB_141607 Alexa FluorTM 488 Goat Anti-Chicken IgY (H+L) Invitrogen Cat# A-11039; RRID: AB_2534096 Alexa FluorTM 488 Donkey Anti-Goat IgG (H+L) Invitrogen Cat# A-11055; RRID: AB_2534102 10-nm Gold-labeled Goat Anti-Mouse IgG (H+L) Aurion Cat# 810.022-05; RRID: N/A Biological samples The young and aged cynomolgus monkey FL tissues Xieerxin Biology Resource N/A Human FL tissues Beijing Tiantan Hospital Capital Medical University and Xuanwu Hospital Capital Medical University N/A Human CSF samples Beijing Tiantan Hospital Capital Medical University N/A Chemicals, peptides, and recombinant proteins Gelatin Sigma-Aldrich Cat# V900863 Matrigel Matrix BD Biosciences Cat# 354230 DMEM/High Glucose HyClone Cat# SH30243.01 Fetal bovine serum (FBS) GIBCO Cat# 42Q7980K DMEM/F12 Thermo Fisher Scientific Cat# 11330057 KnockOut-SR Thermo Fisher Scientific Cat# A31815-02 Non-essential amino acids (NEAA) GIBCO Cat# 11140076 GlutaMAX GIBCO Cat# 35050079 Penicillin/streptomycin (P/S) GIBCO Cat# 15140-163 bFGF Joint Protein Central Cat# BBI-EXP-002 2-Mercaptoethanol GIBCO Cat# 21985-023 Plasmocin InvivoGene Cat# ant-mpt Advanced DMEM/F12 GIBCO Cat# 12634-028 Neurobasal GIBCO Cat# 12348-017 N2 GIBCO Cat# 17502-048 B27 GIBCO Cat# 17504-044 hLIF Millipore Cat# LIF1050 SB431542 Selleck Cat# s1067 CHIR99021 TOCRIS Cat# 252917-06-9 Dorsomorphin Sigma-Aldrich Cat# P5499 Compound E Millipore Cat# 565790 dbcAMP Sigma-Aldrich Cat# D0627 Ascorbic acid Sigma-Aldrich Cat# A8960 BDNF PEPROTECH Cat# 450-02 GDNF PEPROTECH Cat# 450-10 Accumax Millipore Cat# SCR006 (Continued on next page) 22 Cell Reports 42, 112593, June 27, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER Laminin Sigma-Aldrich Cat# L2020 Hoechst 33342 Thermo Fisher Scientific Cat# H3570 THUNDERBIRD SYBR qPCR mix TOYOBO Cat# QPS-201(-) 4% paraformaldehyde, PFA Dingguo, China Cat# AR-0211 Triton X-100 Sigma-Aldrich Cat# T9284 TRIzolTM Reagent Thermo Fisher Scientific Cat# 15596018 DMSO Sigma-Aldrich Cat# D2650 NP-40 Dingguo, China Cat# DH218 Proteinase K New England Biolabs Cat# P8107S EDTA Sigma-Aldrich Cat# EDS-500G Protease inhibitor cocktail Roche Cat# 4693159001 X-Gal Amresca Cat# 0428-25G RNasin Plus RNase Inhibitor Promega Cat# N2618 SUPERase-IN RNase Inhibitor Invitrogen Cat# AM2694 VECTASHIELD Antifade Mounting Medium Vector Laboratories Cat# H-1000 Abacavir Selleckchem Cat# S3165 Critical commercial assays DynabeadsTM Protein A Thermo Fisher Scientific Cat# 10002D GoScript Reverse Transcription System Promega Cat# A5001 Lipofectamine 3000 Transfection Reagent Thermo Fisher Scientific Cat# L3000015 Human IL6 ELISA Kit BioLegend Cat# 430515 Human HERVK-Env Polyprotein ELISA Kit CUSABIO Cat# CBS-EL007812HU 2030-cGAMP ELISA Kit Cayman Cat# 501700 Human Ab1-40(Amyloid Beta 1-40) ELISA Kit Elabscience Cat# E-EL-H0542c Human Ab1-42(Amyloid Beta 1-42) ELISA Kit Elabscience Cat# E-EL-H0543c DAB Staining Kit ZSGB-BIO Cat# ZLI-9018 FD Rapid GolgiStainTM Kit FD NeuroTechnologies Cat# PK401 Proteostat Protein Aggregation Assay Enzo Cat# ENZ-51035-K100 Deposited data The raw sequencing data of young and aged cynomolgus monkey frontal cortex This study GSA: CRA006691 The raw RNA-seq data for human neurons This study GSA-human: HRA002438 Experimental models: Cell lines WT hNeurons (derived from WT hESCs (Line H9) This study N/A Experimental models: Organisms/strains C57BL/6J mice SiPeiFu (Beijing) Biotechnology Co., Ltd. N/A Oligonucleotides Primers for qPCR, qRT-PCR, and sequences of the siRNAs are shown in Table S7 This study N/A Software and algorithms ImageJ (version 1.8.0) Schneider et al.82 https://imagej.net/Welcome ZEN 3.1 ZEISS https://www.micro-shop.zeiss.com/en/us/ system/zen+software/software+zen/ zen+-+basic+software/410135-1002-310 Leica LAS AF Lite (version 2.6.0) Leica https://leica-las-af-lite.updatestar.com/ (Continued on next page) Cell Reports 42, 112593, June 27, 2023 23 .. REAGENT or RESOURCE SOURCE IDENTIFIER PhenochartTM 1.0 Phenochart https://www.akoyabio.com/support/ software/phenochart-whole-slide-viewer/ GraphPadPrism 8.0 GraphPad Software Inc. https://www.graphpad.com/ IMARIS 9.8 OXFORD INSTRUMENTs https://imaris.oxinst.cn/newrelease TrimGalore (version 0.4.5) N/A https://github.com/FelixKrueger/ TrimGalore HISAT2 (version 2.0.4) Kim et al.83 http://daehwankimlab.github.io/hisat2/ featureCounts (version 2.0.0) Liao et al.84 https://subread.sourceforge.net/ fastp (version 0.19.10) Chen et al.85 https://github.com/OpenGene/fastp bsmap (version 2.90) Xi et al.86 https://code.google.com/p/bsmap/ deepTools (version 2.5.4-2-5ee467f) Ramirez et al.87 https://deeptools.readthedocs.io/en/ develop/index.html GSEA (version 4.1.0) Subramanian et al.88 https://www.gsea-msigdb.org/gsea/ downloads.jsp DoubletFinder (version 2.0.2) McGinnis et al.89 https://github.com/chris-mcginnis-ucsf/ DoubletFinder Seurat (version 3.2.3) Butler et al.90 https://satijalab.org/seurat/articles/install. html CellBender (version 0.2.0) Fleming et al.91 https://github.com/broadinstitute/ CellBender Cell Ranger (version 3.0.0) 10x Genomics https://support.10xgenomics.com/ single-cell-gene-expression/software/ downloads/3.0/ DESeq2 (version 1.22.2) Love et al.92 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html MaxQuant (v.1.5.2.8) N/A https://www.maxquant.org/ Metascape Zhou et al.93 https://metascape.org/ Cytoscape (version 3.8.2) Shannon et al.94 https://cytoscape.org/
Staining:Article Title: Nuclear lamina erosion-induced resurrection of endogenous retroviruses underlies neuronal aging.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Normal Rabbit IgG Cell Signaling Technology Cat# 2729S; RRID: AB_1031062 Alexa FluoTM 568 Donkey Anti-Rabbit IgG (H+L) Invitrogen Cat# A-10042; RRID: AB_2534017 Alexa FluoTM 568 Donkey Anti-Mouse IgG (H+L) Invitrogen Cat# A-10037; RRID: AB_2534013 Alexa FluoTM 488 Donkey Anti-Rabbit IgG (H+L) Invitrogen Cat# A-21206; RRID: AB_2535792 Alexa FluorTM 488 Donkey Anti-Mouse IgG (H+L) Invitrogen Cat# A-21202; RRID: AB_141607 Alexa FluorTM 488 Goat Anti-Chicken IgY (H+L) Invitrogen Cat# A-11039; RRID: AB_2534096 Alexa FluorTM 488 Donkey Anti-Goat IgG (H+L) Invitrogen Cat# A-11055; RRID: AB_2534102 10-nm Gold-labeled Goat Anti-Mouse IgG (H+L) Aurion Cat# 810.022-05; RRID: N/A Biological samples The young and aged cynomolgus monkey FL tissues Xieerxin Biology Resource N/A Human FL tissues Beijing Tiantan Hospital Capital Medical University and Xuanwu Hospital Capital Medical University N/A Human CSF samples Beijing Tiantan Hospital Capital Medical University N/A Chemicals, peptides, and recombinant proteins Gelatin Sigma-Aldrich Cat# V900863 Matrigel Matrix BD Biosciences Cat# 354230 DMEM/High Glucose HyClone Cat# SH30243.01 Fetal bovine serum (FBS) GIBCO Cat# 42Q7980K DMEM/F12 Thermo Fisher Scientific Cat# 11330057 KnockOut-SR Thermo Fisher Scientific Cat# A31815-02 Non-essential amino acids (NEAA) GIBCO Cat# 11140076 GlutaMAX GIBCO Cat# 35050079 Penicillin/streptomycin (P/S) GIBCO Cat# 15140-163 bFGF Joint Protein Central Cat# BBI-EXP-002 2-Mercaptoethanol GIBCO Cat# 21985-023 Plasmocin InvivoGene Cat# ant-mpt Advanced DMEM/F12 GIBCO Cat# 12634-028 Neurobasal GIBCO Cat# 12348-017 N2 GIBCO Cat# 17502-048 B27 GIBCO Cat# 17504-044 hLIF Millipore Cat# LIF1050 SB431542 Selleck Cat# s1067 CHIR99021 TOCRIS Cat# 252917-06-9 Dorsomorphin Sigma-Aldrich Cat# P5499 Compound E Millipore Cat# 565790 dbcAMP Sigma-Aldrich Cat# D0627 Ascorbic acid Sigma-Aldrich Cat# A8960 BDNF PEPROTECH Cat# 450-02 GDNF PEPROTECH Cat# 450-10 Accumax Millipore Cat# SCR006 (Continued on next page) 22 Cell Reports 42, 112593, June 27, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER Laminin Sigma-Aldrich Cat# L2020 Hoechst 33342 Thermo Fisher Scientific Cat# H3570 THUNDERBIRD SYBR qPCR mix TOYOBO Cat# QPS-201(-) 4% paraformaldehyde, PFA Dingguo, China Cat# AR-0211 Triton X-100 Sigma-Aldrich Cat# T9284 TRIzolTM Reagent Thermo Fisher Scientific Cat# 15596018 DMSO Sigma-Aldrich Cat# D2650 NP-40 Dingguo, China Cat# DH218 Proteinase K New England Biolabs Cat# P8107S EDTA Sigma-Aldrich Cat# EDS-500G Protease inhibitor cocktail Roche Cat# 4693159001 X-Gal Amresca Cat# 0428-25G RNasin Plus RNase Inhibitor Promega Cat# N2618 SUPERase-IN RNase Inhibitor Invitrogen Cat# AM2694 VECTASHIELD Antifade Mounting Medium Vector Laboratories Cat# H-1000 Abacavir Selleckchem Cat# S3165 Critical commercial assays DynabeadsTM Protein A Thermo Fisher Scientific Cat# 10002D GoScript Reverse Transcription System Promega Cat# A5001 Lipofectamine 3000 Transfection Reagent Thermo Fisher Scientific Cat# L3000015 Human IL6 ELISA Kit BioLegend Cat# 430515 Human HERVK-Env Polyprotein ELISA Kit CUSABIO Cat# CBS-EL007812HU 2030-cGAMP ELISA Kit Cayman Cat# 501700 Human Ab1-40(Amyloid Beta 1-40) ELISA Kit Elabscience Cat# E-EL-H0542c Human Ab1-42(Amyloid Beta 1-42) ELISA Kit Elabscience Cat# E-EL-H0543c DAB Staining Kit ZSGB-BIO Cat# ZLI-9018 FD Rapid GolgiStainTM Kit FD NeuroTechnologies Cat# PK401 Proteostat Protein Aggregation Assay Enzo Cat# ENZ-51035-K100 Deposited data The raw sequencing data of young and aged cynomolgus monkey frontal cortex This study GSA: CRA006691 The raw RNA-seq data for human neurons This study GSA-human: HRA002438 Experimental models: Cell lines WT hNeurons (derived from WT hESCs (Line H9) This study N/A Experimental models: Organisms/strains C57BL/6J mice SiPeiFu (Beijing) Biotechnology Co., Ltd. N/A Oligonucleotides Primers for qPCR, qRT-PCR, and sequences of the siRNAs are shown in Table S7 This study N/A Software and algorithms ImageJ (version 1.8.0) Schneider et al.82 https://imagej.net/Welcome ZEN 3.1 ZEISS https://www.micro-shop.zeiss.com/en/us/ system/zen+software/software+zen/ zen+-+basic+software/410135-1002-310 Leica LAS AF Lite (version 2.6.0) Leica https://leica-las-af-lite.updatestar.com/ (Continued on next page) Cell Reports 42, 112593, June 27, 2023 23 .. REAGENT or RESOURCE SOURCE IDENTIFIER PhenochartTM 1.0 Phenochart https://www.akoyabio.com/support/ software/phenochart-whole-slide-viewer/ GraphPadPrism 8.0 GraphPad Software Inc. https://www.graphpad.com/ IMARIS 9.8 OXFORD INSTRUMENTs https://imaris.oxinst.cn/newrelease TrimGalore (version 0.4.5) N/A https://github.com/FelixKrueger/ TrimGalore HISAT2 (version 2.0.4) Kim et al.83 http://daehwankimlab.github.io/hisat2/ featureCounts (version 2.0.0) Liao et al.84 https://subread.sourceforge.net/ fastp (version 0.19.10) Chen et al.85 https://github.com/OpenGene/fastp bsmap (version 2.90) Xi et al.86 https://code.google.com/p/bsmap/ deepTools (version 2.5.4-2-5ee467f) Ramirez et al.87 https://deeptools.readthedocs.io/en/ develop/index.html GSEA (version 4.1.0) Subramanian et al.88 https://www.gsea-msigdb.org/gsea/ downloads.jsp DoubletFinder (version 2.0.2) McGinnis et al.89 https://github.com/chris-mcginnis-ucsf/ DoubletFinder Seurat (version 3.2.3) Butler et al.90 https://satijalab.org/seurat/articles/install. html CellBender (version 0.2.0) Fleming et al.91 https://github.com/broadinstitute/ CellBender Cell Ranger (version 3.0.0) 10x Genomics https://support.10xgenomics.com/ single-cell-gene-expression/software/ downloads/3.0/ DESeq2 (version 1.22.2) Love et al.92 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html MaxQuant (v.1.5.2.8) N/A https://www.maxquant.org/ Metascape Zhou et al.93 https://metascape.org/ Cytoscape (version 3.8.2) Shannon et al.94 https://cytoscape.org/
Sequencing:Article Title: Nuclear lamina erosion-induced resurrection of endogenous retroviruses underlies neuronal aging.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Normal Rabbit IgG Cell Signaling Technology Cat# 2729S; RRID: AB_1031062 Alexa FluoTM 568 Donkey Anti-Rabbit IgG (H+L) Invitrogen Cat# A-10042; RRID: AB_2534017 Alexa FluoTM 568 Donkey Anti-Mouse IgG (H+L) Invitrogen Cat# A-10037; RRID: AB_2534013 Alexa FluoTM 488 Donkey Anti-Rabbit IgG (H+L) Invitrogen Cat# A-21206; RRID: AB_2535792 Alexa FluorTM 488 Donkey Anti-Mouse IgG (H+L) Invitrogen Cat# A-21202; RRID: AB_141607 Alexa FluorTM 488 Goat Anti-Chicken IgY (H+L) Invitrogen Cat# A-11039; RRID: AB_2534096 Alexa FluorTM 488 Donkey Anti-Goat IgG (H+L) Invitrogen Cat# A-11055; RRID: AB_2534102 10-nm Gold-labeled Goat Anti-Mouse IgG (H+L) Aurion Cat# 810.022-05; RRID: N/A Biological samples The young and aged cynomolgus monkey FL tissues Xieerxin Biology Resource N/A Human FL tissues Beijing Tiantan Hospital Capital Medical University and Xuanwu Hospital Capital Medical University N/A Human CSF samples Beijing Tiantan Hospital Capital Medical University N/A Chemicals, peptides, and recombinant proteins Gelatin Sigma-Aldrich Cat# V900863 Matrigel Matrix BD Biosciences Cat# 354230 DMEM/High Glucose HyClone Cat# SH30243.01 Fetal bovine serum (FBS) GIBCO Cat# 42Q7980K DMEM/F12 Thermo Fisher Scientific Cat# 11330057 KnockOut-SR Thermo Fisher Scientific Cat# A31815-02 Non-essential amino acids (NEAA) GIBCO Cat# 11140076 GlutaMAX GIBCO Cat# 35050079 Penicillin/streptomycin (P/S) GIBCO Cat# 15140-163 bFGF Joint Protein Central Cat# BBI-EXP-002 2-Mercaptoethanol GIBCO Cat# 21985-023 Plasmocin InvivoGene Cat# ant-mpt Advanced DMEM/F12 GIBCO Cat# 12634-028 Neurobasal GIBCO Cat# 12348-017 N2 GIBCO Cat# 17502-048 B27 GIBCO Cat# 17504-044 hLIF Millipore Cat# LIF1050 SB431542 Selleck Cat# s1067 CHIR99021 TOCRIS Cat# 252917-06-9 Dorsomorphin Sigma-Aldrich Cat# P5499 Compound E Millipore Cat# 565790 dbcAMP Sigma-Aldrich Cat# D0627 Ascorbic acid Sigma-Aldrich Cat# A8960 BDNF PEPROTECH Cat# 450-02 GDNF PEPROTECH Cat# 450-10 Accumax Millipore Cat# SCR006 (Continued on next page) 22 Cell Reports 42, 112593, June 27, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER Laminin Sigma-Aldrich Cat# L2020 Hoechst 33342 Thermo Fisher Scientific Cat# H3570 THUNDERBIRD SYBR qPCR mix TOYOBO Cat# QPS-201(-) 4% paraformaldehyde, PFA Dingguo, China Cat# AR-0211 Triton X-100 Sigma-Aldrich Cat# T9284 TRIzolTM Reagent Thermo Fisher Scientific Cat# 15596018 DMSO Sigma-Aldrich Cat# D2650 NP-40 Dingguo, China Cat# DH218 Proteinase K New England Biolabs Cat# P8107S EDTA Sigma-Aldrich Cat# EDS-500G Protease inhibitor cocktail Roche Cat# 4693159001 X-Gal Amresca Cat# 0428-25G RNasin Plus RNase Inhibitor Promega Cat# N2618 SUPERase-IN RNase Inhibitor Invitrogen Cat# AM2694 VECTASHIELD Antifade Mounting Medium Vector Laboratories Cat# H-1000 Abacavir Selleckchem Cat# S3165 Critical commercial assays DynabeadsTM Protein A Thermo Fisher Scientific Cat# 10002D GoScript Reverse Transcription System Promega Cat# A5001 Lipofectamine 3000 Transfection Reagent Thermo Fisher Scientific Cat# L3000015 Human IL6 ELISA Kit BioLegend Cat# 430515 Human HERVK-Env Polyprotein ELISA Kit CUSABIO Cat# CBS-EL007812HU 2030-cGAMP ELISA Kit Cayman Cat# 501700 Human Ab1-40(Amyloid Beta 1-40) ELISA Kit Elabscience Cat# E-EL-H0542c Human Ab1-42(Amyloid Beta 1-42) ELISA Kit Elabscience Cat# E-EL-H0543c DAB Staining Kit ZSGB-BIO Cat# ZLI-9018 FD Rapid GolgiStainTM Kit FD NeuroTechnologies Cat# PK401 Proteostat Protein Aggregation Assay Enzo Cat# ENZ-51035-K100 Deposited data The raw sequencing data of young and aged cynomolgus monkey frontal cortex This study GSA: CRA006691 The raw RNA-seq data for human neurons This study GSA-human: HRA002438 Experimental models: Cell lines WT hNeurons (derived from WT hESCs (Line H9) This study N/A Experimental models: Organisms/strains C57BL/6J mice SiPeiFu (Beijing) Biotechnology Co., Ltd. N/A Oligonucleotides Primers for qPCR, qRT-PCR, and sequences of the siRNAs are shown in Table S7 This study N/A Software and algorithms ImageJ (version 1.8.0) Schneider et al.82 https://imagej.net/Welcome ZEN 3.1 ZEISS https://www.micro-shop.zeiss.com/en/us/ system/zen+software/software+zen/ zen+-+basic+software/410135-1002-310 Leica LAS AF Lite (version 2.6.0) Leica https://leica-las-af-lite.updatestar.com/ (Continued on next page) Cell Reports 42, 112593, June 27, 2023 23 .. REAGENT or RESOURCE SOURCE IDENTIFIER PhenochartTM 1.0 Phenochart https://www.akoyabio.com/support/ software/phenochart-whole-slide-viewer/ GraphPadPrism 8.0 GraphPad Software Inc. https://www.graphpad.com/ IMARIS 9.8 OXFORD INSTRUMENTs https://imaris.oxinst.cn/newrelease TrimGalore (version 0.4.5) N/A https://github.com/FelixKrueger/ TrimGalore HISAT2 (version 2.0.4) Kim et al.83 http://daehwankimlab.github.io/hisat2/ featureCounts (version 2.0.0) Liao et al.84 https://subread.sourceforge.net/ fastp (version 0.19.10) Chen et al.85 https://github.com/OpenGene/fastp bsmap (version 2.90) Xi et al.86 https://code.google.com/p/bsmap/ deepTools (version 2.5.4-2-5ee467f) Ramirez et al.87 https://deeptools.readthedocs.io/en/ develop/index.html GSEA (version 4.1.0) Subramanian et al.88 https://www.gsea-msigdb.org/gsea/ downloads.jsp DoubletFinder (version 2.0.2) McGinnis et al.89 https://github.com/chris-mcginnis-ucsf/ DoubletFinder Seurat (version 3.2.3) Butler et al.90 https://satijalab.org/seurat/articles/install. html CellBender (version 0.2.0) Fleming et al.91 https://github.com/broadinstitute/ CellBender Cell Ranger (version 3.0.0) 10x Genomics https://support.10xgenomics.com/ single-cell-gene-expression/software/ downloads/3.0/ DESeq2 (version 1.22.2) Love et al.92 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html MaxQuant (v.1.5.2.8) N/A https://www.maxquant.org/ Metascape Zhou et al.93 https://metascape.org/ Cytoscape (version 3.8.2) Shannon et al.94 https://cytoscape.org/
RNA Sequencing:Article Title: Nuclear lamina erosion-induced resurrection of endogenous retroviruses underlies neuronal aging.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Normal Rabbit IgG Cell Signaling Technology Cat# 2729S; RRID: AB_1031062 Alexa FluoTM 568 Donkey Anti-Rabbit IgG (H+L) Invitrogen Cat# A-10042; RRID: AB_2534017 Alexa FluoTM 568 Donkey Anti-Mouse IgG (H+L) Invitrogen Cat# A-10037; RRID: AB_2534013 Alexa FluoTM 488 Donkey Anti-Rabbit IgG (H+L) Invitrogen Cat# A-21206; RRID: AB_2535792 Alexa FluorTM 488 Donkey Anti-Mouse IgG (H+L) Invitrogen Cat# A-21202; RRID: AB_141607 Alexa FluorTM 488 Goat Anti-Chicken IgY (H+L) Invitrogen Cat# A-11039; RRID: AB_2534096 Alexa FluorTM 488 Donkey Anti-Goat IgG (H+L) Invitrogen Cat# A-11055; RRID: AB_2534102 10-nm Gold-labeled Goat Anti-Mouse IgG (H+L) Aurion Cat# 810.022-05; RRID: N/A Biological samples The young and aged cynomolgus monkey FL tissues Xieerxin Biology Resource N/A Human FL tissues Beijing Tiantan Hospital Capital Medical University and Xuanwu Hospital Capital Medical University N/A Human CSF samples Beijing Tiantan Hospital Capital Medical University N/A Chemicals, peptides, and recombinant proteins Gelatin Sigma-Aldrich Cat# V900863 Matrigel Matrix BD Biosciences Cat# 354230 DMEM/High Glucose HyClone Cat# SH30243.01 Fetal bovine serum (FBS) GIBCO Cat# 42Q7980K DMEM/F12 Thermo Fisher Scientific Cat# 11330057 KnockOut-SR Thermo Fisher Scientific Cat# A31815-02 Non-essential amino acids (NEAA) GIBCO Cat# 11140076 GlutaMAX GIBCO Cat# 35050079 Penicillin/streptomycin (P/S) GIBCO Cat# 15140-163 bFGF Joint Protein Central Cat# BBI-EXP-002 2-Mercaptoethanol GIBCO Cat# 21985-023 Plasmocin InvivoGene Cat# ant-mpt Advanced DMEM/F12 GIBCO Cat# 12634-028 Neurobasal GIBCO Cat# 12348-017 N2 GIBCO Cat# 17502-048 B27 GIBCO Cat# 17504-044 hLIF Millipore Cat# LIF1050 SB431542 Selleck Cat# s1067 CHIR99021 TOCRIS Cat# 252917-06-9 Dorsomorphin Sigma-Aldrich Cat# P5499 Compound E Millipore Cat# 565790 dbcAMP Sigma-Aldrich Cat# D0627 Ascorbic acid Sigma-Aldrich Cat# A8960 BDNF PEPROTECH Cat# 450-02 GDNF PEPROTECH Cat# 450-10 Accumax Millipore Cat# SCR006 (Continued on next page) 22 Cell Reports 42, 112593, June 27, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER Laminin Sigma-Aldrich Cat# L2020 Hoechst 33342 Thermo Fisher Scientific Cat# H3570 THUNDERBIRD SYBR qPCR mix TOYOBO Cat# QPS-201(-) 4% paraformaldehyde, PFA Dingguo, China Cat# AR-0211 Triton X-100 Sigma-Aldrich Cat# T9284 TRIzolTM Reagent Thermo Fisher Scientific Cat# 15596018 DMSO Sigma-Aldrich Cat# D2650 NP-40 Dingguo, China Cat# DH218 Proteinase K New England Biolabs Cat# P8107S EDTA Sigma-Aldrich Cat# EDS-500G Protease inhibitor cocktail Roche Cat# 4693159001 X-Gal Amresca Cat# 0428-25G RNasin Plus RNase Inhibitor Promega Cat# N2618 SUPERase-IN RNase Inhibitor Invitrogen Cat# AM2694 VECTASHIELD Antifade Mounting Medium Vector Laboratories Cat# H-1000 Abacavir Selleckchem Cat# S3165 Critical commercial assays DynabeadsTM Protein A Thermo Fisher Scientific Cat# 10002D GoScript Reverse Transcription System Promega Cat# A5001 Lipofectamine 3000 Transfection Reagent Thermo Fisher Scientific Cat# L3000015 Human IL6 ELISA Kit BioLegend Cat# 430515 Human HERVK-Env Polyprotein ELISA Kit CUSABIO Cat# CBS-EL007812HU 2030-cGAMP ELISA Kit Cayman Cat# 501700 Human Ab1-40(Amyloid Beta 1-40) ELISA Kit Elabscience Cat# E-EL-H0542c Human Ab1-42(Amyloid Beta 1-42) ELISA Kit Elabscience Cat# E-EL-H0543c DAB Staining Kit ZSGB-BIO Cat# ZLI-9018 FD Rapid GolgiStainTM Kit FD NeuroTechnologies Cat# PK401 Proteostat Protein Aggregation Assay Enzo Cat# ENZ-51035-K100 Deposited data The raw sequencing data of young and aged cynomolgus monkey frontal cortex This study GSA: CRA006691 The raw RNA-seq data for human neurons This study GSA-human: HRA002438 Experimental models: Cell lines WT hNeurons (derived from WT hESCs (Line H9) This study N/A Experimental models: Organisms/strains C57BL/6J mice SiPeiFu (Beijing) Biotechnology Co., Ltd. N/A Oligonucleotides Primers for qPCR, qRT-PCR, and sequences of the siRNAs are shown in Table S7 This study N/A Software and algorithms ImageJ (version 1.8.0) Schneider et al.82 https://imagej.net/Welcome ZEN 3.1 ZEISS https://www.micro-shop.zeiss.com/en/us/ system/zen+software/software+zen/ zen+-+basic+software/410135-1002-310 Leica LAS AF Lite (version 2.6.0) Leica https://leica-las-af-lite.updatestar.com/ (Continued on next page) Cell Reports 42, 112593, June 27, 2023 23 .. REAGENT or RESOURCE SOURCE IDENTIFIER PhenochartTM 1.0 Phenochart https://www.akoyabio.com/support/ software/phenochart-whole-slide-viewer/ GraphPadPrism 8.0 GraphPad Software Inc. https://www.graphpad.com/ IMARIS 9.8 OXFORD INSTRUMENTs https://imaris.oxinst.cn/newrelease TrimGalore (version 0.4.5) N/A https://github.com/FelixKrueger/ TrimGalore HISAT2 (version 2.0.4) Kim et al.83 http://daehwankimlab.github.io/hisat2/ featureCounts (version 2.0.0) Liao et al.84 https://subread.sourceforge.net/ fastp (version 0.19.10) Chen et al.85 https://github.com/OpenGene/fastp bsmap (version 2.90) Xi et al.86 https://code.google.com/p/bsmap/ deepTools (version 2.5.4-2-5ee467f) Ramirez et al.87 https://deeptools.readthedocs.io/en/ develop/index.html GSEA (version 4.1.0) Subramanian et al.88 https://www.gsea-msigdb.org/gsea/ downloads.jsp DoubletFinder (version 2.0.2) McGinnis et al.89 https://github.com/chris-mcginnis-ucsf/ DoubletFinder Seurat (version 3.2.3) Butler et al.90 https://satijalab.org/seurat/articles/install. html CellBender (version 0.2.0) Fleming et al.91 https://github.com/broadinstitute/ CellBender Cell Ranger (version 3.0.0) 10x Genomics https://support.10xgenomics.com/ single-cell-gene-expression/software/ downloads/3.0/ DESeq2 (version 1.22.2) Love et al.92 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html MaxQuant (v.1.5.2.8) N/A https://www.maxquant.org/ Metascape Zhou et al.93 https://metascape.org/ Cytoscape (version 3.8.2) Shannon et al.94 https://cytoscape.org/
Derivative Assay:Article Title: Nuclear lamina erosion-induced resurrection of endogenous retroviruses underlies neuronal aging.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Normal Rabbit IgG Cell Signaling Technology Cat# 2729S; RRID: AB_1031062 Alexa FluoTM 568 Donkey Anti-Rabbit IgG (H+L) Invitrogen Cat# A-10042; RRID: AB_2534017 Alexa FluoTM 568 Donkey Anti-Mouse IgG (H+L) Invitrogen Cat# A-10037; RRID: AB_2534013 Alexa FluoTM 488 Donkey Anti-Rabbit IgG (H+L) Invitrogen Cat# A-21206; RRID: AB_2535792 Alexa FluorTM 488 Donkey Anti-Mouse IgG (H+L) Invitrogen Cat# A-21202; RRID: AB_141607 Alexa FluorTM 488 Goat Anti-Chicken IgY (H+L) Invitrogen Cat# A-11039; RRID: AB_2534096 Alexa FluorTM 488 Donkey Anti-Goat IgG (H+L) Invitrogen Cat# A-11055; RRID: AB_2534102 10-nm Gold-labeled Goat Anti-Mouse IgG (H+L) Aurion Cat# 810.022-05; RRID: N/A Biological samples The young and aged cynomolgus monkey FL tissues Xieerxin Biology Resource N/A Human FL tissues Beijing Tiantan Hospital Capital Medical University and Xuanwu Hospital Capital Medical University N/A Human CSF samples Beijing Tiantan Hospital Capital Medical University N/A Chemicals, peptides, and recombinant proteins Gelatin Sigma-Aldrich Cat# V900863 Matrigel Matrix BD Biosciences Cat# 354230 DMEM/High Glucose HyClone Cat# SH30243.01 Fetal bovine serum (FBS) GIBCO Cat# 42Q7980K DMEM/F12 Thermo Fisher Scientific Cat# 11330057 KnockOut-SR Thermo Fisher Scientific Cat# A31815-02 Non-essential amino acids (NEAA) GIBCO Cat# 11140076 GlutaMAX GIBCO Cat# 35050079 Penicillin/streptomycin (P/S) GIBCO Cat# 15140-163 bFGF Joint Protein Central Cat# BBI-EXP-002 2-Mercaptoethanol GIBCO Cat# 21985-023 Plasmocin InvivoGene Cat# ant-mpt Advanced DMEM/F12 GIBCO Cat# 12634-028 Neurobasal GIBCO Cat# 12348-017 N2 GIBCO Cat# 17502-048 B27 GIBCO Cat# 17504-044 hLIF Millipore Cat# LIF1050 SB431542 Selleck Cat# s1067 CHIR99021 TOCRIS Cat# 252917-06-9 Dorsomorphin Sigma-Aldrich Cat# P5499 Compound E Millipore Cat# 565790 dbcAMP Sigma-Aldrich Cat# D0627 Ascorbic acid Sigma-Aldrich Cat# A8960 BDNF PEPROTECH Cat# 450-02 GDNF PEPROTECH Cat# 450-10 Accumax Millipore Cat# SCR006 (Continued on next page) 22 Cell Reports 42, 112593, June 27, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER Laminin Sigma-Aldrich Cat# L2020 Hoechst 33342 Thermo Fisher Scientific Cat# H3570 THUNDERBIRD SYBR qPCR mix TOYOBO Cat# QPS-201(-) 4% paraformaldehyde, PFA Dingguo, China Cat# AR-0211 Triton X-100 Sigma-Aldrich Cat# T9284 TRIzolTM Reagent Thermo Fisher Scientific Cat# 15596018 DMSO Sigma-Aldrich Cat# D2650 NP-40 Dingguo, China Cat# DH218 Proteinase K New England Biolabs Cat# P8107S EDTA Sigma-Aldrich Cat# EDS-500G Protease inhibitor cocktail Roche Cat# 4693159001 X-Gal Amresca Cat# 0428-25G RNasin Plus RNase Inhibitor Promega Cat# N2618 SUPERase-IN RNase Inhibitor Invitrogen Cat# AM2694 VECTASHIELD Antifade Mounting Medium Vector Laboratories Cat# H-1000 Abacavir Selleckchem Cat# S3165 Critical commercial assays DynabeadsTM Protein A Thermo Fisher Scientific Cat# 10002D GoScript Reverse Transcription System Promega Cat# A5001 Lipofectamine 3000 Transfection Reagent Thermo Fisher Scientific Cat# L3000015 Human IL6 ELISA Kit BioLegend Cat# 430515 Human HERVK-Env Polyprotein ELISA Kit CUSABIO Cat# CBS-EL007812HU 2030-cGAMP ELISA Kit Cayman Cat# 501700 Human Ab1-40(Amyloid Beta 1-40) ELISA Kit Elabscience Cat# E-EL-H0542c Human Ab1-42(Amyloid Beta 1-42) ELISA Kit Elabscience Cat# E-EL-H0543c DAB Staining Kit ZSGB-BIO Cat# ZLI-9018 FD Rapid GolgiStainTM Kit FD NeuroTechnologies Cat# PK401 Proteostat Protein Aggregation Assay Enzo Cat# ENZ-51035-K100 Deposited data The raw sequencing data of young and aged cynomolgus monkey frontal cortex This study GSA: CRA006691 The raw RNA-seq data for human neurons This study GSA-human: HRA002438 Experimental models: Cell lines WT hNeurons (derived from WT hESCs (Line H9) This study N/A Experimental models: Organisms/strains C57BL/6J mice SiPeiFu (Beijing) Biotechnology Co., Ltd. N/A Oligonucleotides Primers for qPCR, qRT-PCR, and sequences of the siRNAs are shown in Table S7 This study N/A Software and algorithms ImageJ (version 1.8.0) Schneider et al.82 https://imagej.net/Welcome ZEN 3.1 ZEISS https://www.micro-shop.zeiss.com/en/us/ system/zen+software/software+zen/ zen+-+basic+software/410135-1002-310 Leica LAS AF Lite (version 2.6.0) Leica https://leica-las-af-lite.updatestar.com/ (Continued on next page) Cell Reports 42, 112593, June 27, 2023 23 .. REAGENT or RESOURCE SOURCE IDENTIFIER PhenochartTM 1.0 Phenochart https://www.akoyabio.com/support/ software/phenochart-whole-slide-viewer/ GraphPadPrism 8.0 GraphPad Software Inc. https://www.graphpad.com/ IMARIS 9.8 OXFORD INSTRUMENTs https://imaris.oxinst.cn/newrelease TrimGalore (version 0.4.5) N/A https://github.com/FelixKrueger/ TrimGalore HISAT2 (version 2.0.4) Kim et al.83 http://daehwankimlab.github.io/hisat2/ featureCounts (version 2.0.0) Liao et al.84 https://subread.sourceforge.net/ fastp (version 0.19.10) Chen et al.85 https://github.com/OpenGene/fastp bsmap (version 2.90) Xi et al.86 https://code.google.com/p/bsmap/ deepTools (version 2.5.4-2-5ee467f) Ramirez et al.87 https://deeptools.readthedocs.io/en/ develop/index.html GSEA (version 4.1.0) Subramanian et al.88 https://www.gsea-msigdb.org/gsea/ downloads.jsp DoubletFinder (version 2.0.2) McGinnis et al.89 https://github.com/chris-mcginnis-ucsf/ DoubletFinder Seurat (version 3.2.3) Butler et al.90 https://satijalab.org/seurat/articles/install. html CellBender (version 0.2.0) Fleming et al.91 https://github.com/broadinstitute/ CellBender Cell Ranger (version 3.0.0) 10x Genomics https://support.10xgenomics.com/ single-cell-gene-expression/software/ downloads/3.0/ DESeq2 (version 1.22.2) Love et al.92 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html MaxQuant (v.1.5.2.8) N/A https://www.maxquant.org/ Metascape Zhou et al.93 https://metascape.org/ Cytoscape (version 3.8.2) Shannon et al.94 https://cytoscape.org/
Software:Article Title: Nuclear lamina erosion-induced resurrection of endogenous retroviruses underlies neuronal aging.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Normal Rabbit IgG Cell Signaling Technology Cat# 2729S; RRID: AB_1031062 Alexa FluoTM 568 Donkey Anti-Rabbit IgG (H+L) Invitrogen Cat# A-10042; RRID: AB_2534017 Alexa FluoTM 568 Donkey Anti-Mouse IgG (H+L) Invitrogen Cat# A-10037; RRID: AB_2534013 Alexa FluoTM 488 Donkey Anti-Rabbit IgG (H+L) Invitrogen Cat# A-21206; RRID: AB_2535792 Alexa FluorTM 488 Donkey Anti-Mouse IgG (H+L) Invitrogen Cat# A-21202; RRID: AB_141607 Alexa FluorTM 488 Goat Anti-Chicken IgY (H+L) Invitrogen Cat# A-11039; RRID: AB_2534096 Alexa FluorTM 488 Donkey Anti-Goat IgG (H+L) Invitrogen Cat# A-11055; RRID: AB_2534102 10-nm Gold-labeled Goat Anti-Mouse IgG (H+L) Aurion Cat# 810.022-05; RRID: N/A Biological samples The young and aged cynomolgus monkey FL tissues Xieerxin Biology Resource N/A Human FL tissues Beijing Tiantan Hospital Capital Medical University and Xuanwu Hospital Capital Medical University N/A Human CSF samples Beijing Tiantan Hospital Capital Medical University N/A Chemicals, peptides, and recombinant proteins Gelatin Sigma-Aldrich Cat# V900863 Matrigel Matrix BD Biosciences Cat# 354230 DMEM/High Glucose HyClone Cat# SH30243.01 Fetal bovine serum (FBS) GIBCO Cat# 42Q7980K DMEM/F12 Thermo Fisher Scientific Cat# 11330057 KnockOut-SR Thermo Fisher Scientific Cat# A31815-02 Non-essential amino acids (NEAA) GIBCO Cat# 11140076 GlutaMAX GIBCO Cat# 35050079 Penicillin/streptomycin (P/S) GIBCO Cat# 15140-163 bFGF Joint Protein Central Cat# BBI-EXP-002 2-Mercaptoethanol GIBCO Cat# 21985-023 Plasmocin InvivoGene Cat# ant-mpt Advanced DMEM/F12 GIBCO Cat# 12634-028 Neurobasal GIBCO Cat# 12348-017 N2 GIBCO Cat# 17502-048 B27 GIBCO Cat# 17504-044 hLIF Millipore Cat# LIF1050 SB431542 Selleck Cat# s1067 CHIR99021 TOCRIS Cat# 252917-06-9 Dorsomorphin Sigma-Aldrich Cat# P5499 Compound E Millipore Cat# 565790 dbcAMP Sigma-Aldrich Cat# D0627 Ascorbic acid Sigma-Aldrich Cat# A8960 BDNF PEPROTECH Cat# 450-02 GDNF PEPROTECH Cat# 450-10 Accumax Millipore Cat# SCR006 (Continued on next page) 22 Cell Reports 42, 112593, June 27, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER Laminin Sigma-Aldrich Cat# L2020 Hoechst 33342 Thermo Fisher Scientific Cat# H3570 THUNDERBIRD SYBR qPCR mix TOYOBO Cat# QPS-201(-) 4% paraformaldehyde, PFA Dingguo, China Cat# AR-0211 Triton X-100 Sigma-Aldrich Cat# T9284 TRIzolTM Reagent Thermo Fisher Scientific Cat# 15596018 DMSO Sigma-Aldrich Cat# D2650 NP-40 Dingguo, China Cat# DH218 Proteinase K New England Biolabs Cat# P8107S EDTA Sigma-Aldrich Cat# EDS-500G Protease inhibitor cocktail Roche Cat# 4693159001 X-Gal Amresca Cat# 0428-25G RNasin Plus RNase Inhibitor Promega Cat# N2618 SUPERase-IN RNase Inhibitor Invitrogen Cat# AM2694 VECTASHIELD Antifade Mounting Medium Vector Laboratories Cat# H-1000 Abacavir Selleckchem Cat# S3165 Critical commercial assays DynabeadsTM Protein A Thermo Fisher Scientific Cat# 10002D GoScript Reverse Transcription System Promega Cat# A5001 Lipofectamine 3000 Transfection Reagent Thermo Fisher Scientific Cat# L3000015 Human IL6 ELISA Kit BioLegend Cat# 430515 Human HERVK-Env Polyprotein ELISA Kit CUSABIO Cat# CBS-EL007812HU 2030-cGAMP ELISA Kit Cayman Cat# 501700 Human Ab1-40(Amyloid Beta 1-40) ELISA Kit Elabscience Cat# E-EL-H0542c Human Ab1-42(Amyloid Beta 1-42) ELISA Kit Elabscience Cat# E-EL-H0543c DAB Staining Kit ZSGB-BIO Cat# ZLI-9018 FD Rapid GolgiStainTM Kit FD NeuroTechnologies Cat# PK401 Proteostat Protein Aggregation Assay Enzo Cat# ENZ-51035-K100 Deposited data The raw sequencing data of young and aged cynomolgus monkey frontal cortex This study GSA: CRA006691 The raw RNA-seq data for human neurons This study GSA-human: HRA002438 Experimental models: Cell lines WT hNeurons (derived from WT hESCs (Line H9) This study N/A Experimental models: Organisms/strains C57BL/6J mice SiPeiFu (Beijing) Biotechnology Co., Ltd. N/A Oligonucleotides Primers for qPCR, qRT-PCR, and sequences of the siRNAs are shown in Table S7 This study N/A Software and algorithms ImageJ (version 1.8.0) Schneider et al.82 https://imagej.net/Welcome ZEN 3.1 ZEISS https://www.micro-shop.zeiss.com/en/us/ system/zen+software/software+zen/ zen+-+basic+software/410135-1002-310 Leica LAS AF Lite (version 2.6.0) Leica https://leica-las-af-lite.updatestar.com/ (Continued on next page) Cell Reports 42, 112593, June 27, 2023 23 .. REAGENT or RESOURCE SOURCE IDENTIFIER PhenochartTM 1.0 Phenochart https://www.akoyabio.com/support/ software/phenochart-whole-slide-viewer/ GraphPadPrism 8.0 GraphPad Software Inc. https://www.graphpad.com/ IMARIS 9.8 OXFORD INSTRUMENTs https://imaris.oxinst.cn/newrelease TrimGalore (version 0.4.5) N/A https://github.com/FelixKrueger/ TrimGalore HISAT2 (version 2.0.4) Kim et al.83 http://daehwankimlab.github.io/hisat2/ featureCounts (version 2.0.0) Liao et al.84 https://subread.sourceforge.net/ fastp (version 0.19.10) Chen et al.85 https://github.com/OpenGene/fastp bsmap (version 2.90) Xi et al.86 https://code.google.com/p/bsmap/ deepTools (version 2.5.4-2-5ee467f) Ramirez et al.87 https://deeptools.readthedocs.io/en/ develop/index.html GSEA (version 4.1.0) Subramanian et al.88 https://www.gsea-msigdb.org/gsea/ downloads.jsp DoubletFinder (version 2.0.2) McGinnis et al.89 https://github.com/chris-mcginnis-ucsf/ DoubletFinder Seurat (version 3.2.3) Butler et al.90 https://satijalab.org/seurat/articles/install. html CellBender (version 0.2.0) Fleming et al.91 https://github.com/broadinstitute/ CellBender Cell Ranger (version 3.0.0) 10x Genomics https://support.10xgenomics.com/ single-cell-gene-expression/software/ downloads/3.0/ DESeq2 (version 1.22.2) Love et al.92 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html MaxQuant (v.1.5.2.8) N/A https://www.maxquant.org/ Metascape Zhou et al.93 https://metascape.org/ Cytoscape (version 3.8.2) Shannon et al.94 https://cytoscape.org/
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