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p egfp c3 empty vector plasmid  (Addgene inc)


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    Structured Review

    Addgene inc p egfp c3 empty vector plasmid
    P Egfp C3 Empty Vector Plasmid, supplied by Addgene inc, used in various techniques. Bioz Stars score: 93/100, based on 24 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/pegfp+empty+vector/pEGFP(C3)-Nup153-N+(Plasmid+%2364318)/pmc09998969-158-16-21
    Average 93 stars, based on 24 article reviews
    p egfp c3 empty vector plasmid - by Bioz Stars, 2026-10
    93/100 stars

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    Real-time Polymerase Chain Reaction:

    Article Title: Hormone-induced enhancer assembly requires an optimal level of hormone receptor multivalent interactions.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER CircLigase ssDNA Ligase Epicentre Cat# CL4111K Ape1 New England BioLabs Cat# M0282S Phusion High-Fidelity DNA Polymerase New England BioLabs Cat# M0530L Gibson Assembly Master Mix New England BioLabs Cat# E2611L Proteinase K, recombinant, PCR Grade Roche Cat# 3115879001 RNase Sigma-Aldrich Cat# R6513 TRIzol LS Reagent Life Technologies Cat# 10296028 T4 PNK New England BioLabs Cat# M0201S DNase I Life Technologies Cat# AM2222 Benzonase Nuclease EMD Millipore Cat# 70746 MyOne Streptavidin T1 Dynabeads Life Technologies Cat# 65602 Nanolink Streptavidin Magnetic beads Solulink Cat# M-1002-010 AcTEV Protease Life Technologies Cat# 12575015 PEG8000 Sigma-Aldrich Cat# 89510 BioRad protein assay BioRAD Cat# 5000001 Critical commercial assays pCR 8/GW/TOPO TA Cloning Kit Life Technologies Cat# K250020 Gateway LR Clonase II Enzyme mix Life Technologies Cat# 11791100 Dual-Glo Luciferase Assay System Promega Cat# E2940 Antifade mountant with DAPI Life Technologies Cat# P36931 RNeasy Mini Kit Qiagen Cat# 74106 iScript Select cDNA Synthesis Kit BioRAD Cat# 1708897 SsoAdvanced Universal SYBR Green Supermix BioRAD Cat# 1725275 QIAquick spin columns Qiagen Cat# 28115 KAPA Hyper Prep kit Kapa Biosystems Cat# KK8504 Nextera DNA Library Prep Kit Illumina Cat# FC-121-1030 Deposited data Raw and processed sequencing data for ChIP-seq This paper GEO: GSE215161 Raw and processed sequencing data for ATAC-seq This paper GEO: GSE215160 Raw and processed sequencing data for GRO-seq This paper GEO: GSE215162 AR ChIP-seq Malinen et al.39 GEO: GSE83860 H3K27ac ChIP-seq Hazelett et al.40 GEO: GSE51621 Experimental models: Cell lines Human: LNCaP ATCC Cat# CRL-1740 Human: U2OS ATCC Cat# HTB-96 Human: SH-SY5Y ATCC Cat# CRL-2266 Human: HEK293T ATCC Cat# CRL-3216 Human: U2OS 2-6-3 Janicki et al.51 N/A Human: LNCaP-pInducer20-AR stable lines for wildtype and mutants This paper N/A Human: LNCaP-TetR stable line This paper N/A Human: LNCaP-TetR-BioID-AR stable lines for wt, DIDR, and pQ69 This paper N/A Human: LNCaP-BirA-TetR stable line This paper N/A (Continued on next page) e2 Molecular Cell 83, 3438–3456.e1–e12, October 5, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER Human: LNCaP-BirA-TetR-BLRP-AR stable lines for wt, DIDR, and pQ69 This paper N/A Oligonucleotides Primers or oligos for qPCR and GRO-seq see method details This paper N/A Recombinant DNA shAR Sigma-Aldrich TRCN0000003718 shControl Sigma-Aldrich SHC002 shControl Sigma-Aldrich SHC202 pET-His-GFP-gw This paper N/A pET-His-GFP-ARNTD for wildtype and mutants This paper N/A pEGFP-C3-gw This paper N/A pEGFP-C3-AR for wildtype and mutants This paper N/A pCRY2PHR-mCherryN1 Addgene Plasmid ID: #26866 pCRY2PHR-mCherry-gw This paper N/A pCRY2PHR-mCherry-AR for NTD andDIDR This paper N/A eYFP-gw-LacI This paper N/A eYFP-AR-LacI for wt, DIDR, 7FS, and pQ69 This paper N/A mCherry-gw This paper N/A mCherry-AR for wt, DIDR, and 7FS This paper N/A mCherry-MED1 This paper N/A pHalo-gw-NLS This paper N/A pHalo-ARNTDwt-NLS This paper N/A pHalo-ARNTDpQ69-NLS This paper N/A pInducer20 Addgene Plasmid ID: #44012 pInducer20-AR for wildtype and mutants This paper N/A pCMV-Renilla-3XARE-TATA-luciferase This paper N/A pRetroX-mycBioID-MCS This paper N/A pRetroX-mycBioID-AR for wt, DIDR, and pQ69 This paper N/A pRetroX-BLRP-MCS This paper N/A pRetroX-BLRP-AR for wt, DIDR, and pQ69 This paper N/A pCL-Ampho Novus Biologicals Cat# NBP2-29541 pMD2.G Addgene Plasmid ID: #12259 psPAX2 Addgene Plasmid ID: #12260 Software and algorithms SLIMfast Teves et al.72 https://doi.org/10.7554/eLife.22280.022 ImageJ Macros script and MATLAB code for quantifying protein binding residence times from SPT data Chong et al.13 https://doi.org/10.5281/zenodo.8292534 Bowtie v1.1.2 Langmead et al.73 http://bowtie-bio.sourceforge.net/ index.shtml MACS2 v2.1.1.20160309 Zhang et al.74 https://github.com/taoliu/MACS ChIPseeker v1.10.3 Yu et al.75 https://bioconductor.org/packages/ release/bioc/html/ChIPseeker.html Integrative Genomics Viewer (IGV) Robinson et al.76 https://software.broadinstitute.org/ software/igv/ MaxQuant software v1.5.5.1 Max-Planck-Institute of Biochemistry https://www.biochem.mpg.de/227318/ MaxQuant (Continued on next page) Molecular Cell 83, 3438–3456.e1–e12, October 5, 2023 e3 .. REAGENT or RESOURCE SOURCE IDENTIFIER Prism 5 GraphPad https://graphpad-prism.software.informer. com/5.0/ ImageJ NIH https://imagej.nih.gov/ij/

    Recombinant:

    Article Title: Hormone-induced enhancer assembly requires an optimal level of hormone receptor multivalent interactions.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER CircLigase ssDNA Ligase Epicentre Cat# CL4111K Ape1 New England BioLabs Cat# M0282S Phusion High-Fidelity DNA Polymerase New England BioLabs Cat# M0530L Gibson Assembly Master Mix New England BioLabs Cat# E2611L Proteinase K, recombinant, PCR Grade Roche Cat# 3115879001 RNase Sigma-Aldrich Cat# R6513 TRIzol LS Reagent Life Technologies Cat# 10296028 T4 PNK New England BioLabs Cat# M0201S DNase I Life Technologies Cat# AM2222 Benzonase Nuclease EMD Millipore Cat# 70746 MyOne Streptavidin T1 Dynabeads Life Technologies Cat# 65602 Nanolink Streptavidin Magnetic beads Solulink Cat# M-1002-010 AcTEV Protease Life Technologies Cat# 12575015 PEG8000 Sigma-Aldrich Cat# 89510 BioRad protein assay BioRAD Cat# 5000001 Critical commercial assays pCR 8/GW/TOPO TA Cloning Kit Life Technologies Cat# K250020 Gateway LR Clonase II Enzyme mix Life Technologies Cat# 11791100 Dual-Glo Luciferase Assay System Promega Cat# E2940 Antifade mountant with DAPI Life Technologies Cat# P36931 RNeasy Mini Kit Qiagen Cat# 74106 iScript Select cDNA Synthesis Kit BioRAD Cat# 1708897 SsoAdvanced Universal SYBR Green Supermix BioRAD Cat# 1725275 QIAquick spin columns Qiagen Cat# 28115 KAPA Hyper Prep kit Kapa Biosystems Cat# KK8504 Nextera DNA Library Prep Kit Illumina Cat# FC-121-1030 Deposited data Raw and processed sequencing data for ChIP-seq This paper GEO: GSE215161 Raw and processed sequencing data for ATAC-seq This paper GEO: GSE215160 Raw and processed sequencing data for GRO-seq This paper GEO: GSE215162 AR ChIP-seq Malinen et al.39 GEO: GSE83860 H3K27ac ChIP-seq Hazelett et al.40 GEO: GSE51621 Experimental models: Cell lines Human: LNCaP ATCC Cat# CRL-1740 Human: U2OS ATCC Cat# HTB-96 Human: SH-SY5Y ATCC Cat# CRL-2266 Human: HEK293T ATCC Cat# CRL-3216 Human: U2OS 2-6-3 Janicki et al.51 N/A Human: LNCaP-pInducer20-AR stable lines for wildtype and mutants This paper N/A Human: LNCaP-TetR stable line This paper N/A Human: LNCaP-TetR-BioID-AR stable lines for wt, DIDR, and pQ69 This paper N/A Human: LNCaP-BirA-TetR stable line This paper N/A (Continued on next page) e2 Molecular Cell 83, 3438–3456.e1–e12, October 5, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER Human: LNCaP-BirA-TetR-BLRP-AR stable lines for wt, DIDR, and pQ69 This paper N/A Oligonucleotides Primers or oligos for qPCR and GRO-seq see method details This paper N/A Recombinant DNA shAR Sigma-Aldrich TRCN0000003718 shControl Sigma-Aldrich SHC002 shControl Sigma-Aldrich SHC202 pET-His-GFP-gw This paper N/A pET-His-GFP-ARNTD for wildtype and mutants This paper N/A pEGFP-C3-gw This paper N/A pEGFP-C3-AR for wildtype and mutants This paper N/A pCRY2PHR-mCherryN1 Addgene Plasmid ID: #26866 pCRY2PHR-mCherry-gw This paper N/A pCRY2PHR-mCherry-AR for NTD andDIDR This paper N/A eYFP-gw-LacI This paper N/A eYFP-AR-LacI for wt, DIDR, 7FS, and pQ69 This paper N/A mCherry-gw This paper N/A mCherry-AR for wt, DIDR, and 7FS This paper N/A mCherry-MED1 This paper N/A pHalo-gw-NLS This paper N/A pHalo-ARNTDwt-NLS This paper N/A pHalo-ARNTDpQ69-NLS This paper N/A pInducer20 Addgene Plasmid ID: #44012 pInducer20-AR for wildtype and mutants This paper N/A pCMV-Renilla-3XARE-TATA-luciferase This paper N/A pRetroX-mycBioID-MCS This paper N/A pRetroX-mycBioID-AR for wt, DIDR, and pQ69 This paper N/A pRetroX-BLRP-MCS This paper N/A pRetroX-BLRP-AR for wt, DIDR, and pQ69 This paper N/A pCL-Ampho Novus Biologicals Cat# NBP2-29541 pMD2.G Addgene Plasmid ID: #12259 psPAX2 Addgene Plasmid ID: #12260 Software and algorithms SLIMfast Teves et al.72 https://doi.org/10.7554/eLife.22280.022 ImageJ Macros script and MATLAB code for quantifying protein binding residence times from SPT data Chong et al.13 https://doi.org/10.5281/zenodo.8292534 Bowtie v1.1.2 Langmead et al.73 http://bowtie-bio.sourceforge.net/ index.shtml MACS2 v2.1.1.20160309 Zhang et al.74 https://github.com/taoliu/MACS ChIPseeker v1.10.3 Yu et al.75 https://bioconductor.org/packages/ release/bioc/html/ChIPseeker.html Integrative Genomics Viewer (IGV) Robinson et al.76 https://software.broadinstitute.org/ software/igv/ MaxQuant software v1.5.5.1 Max-Planck-Institute of Biochemistry https://www.biochem.mpg.de/227318/ MaxQuant (Continued on next page) Molecular Cell 83, 3438–3456.e1–e12, October 5, 2023 e3 .. REAGENT or RESOURCE SOURCE IDENTIFIER Prism 5 GraphPad https://graphpad-prism.software.informer. com/5.0/ ImageJ NIH https://imagej.nih.gov/ij/

    Plasmid Preparation:

    Article Title: Hormone-induced enhancer assembly requires an optimal level of hormone receptor multivalent interactions.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER CircLigase ssDNA Ligase Epicentre Cat# CL4111K Ape1 New England BioLabs Cat# M0282S Phusion High-Fidelity DNA Polymerase New England BioLabs Cat# M0530L Gibson Assembly Master Mix New England BioLabs Cat# E2611L Proteinase K, recombinant, PCR Grade Roche Cat# 3115879001 RNase Sigma-Aldrich Cat# R6513 TRIzol LS Reagent Life Technologies Cat# 10296028 T4 PNK New England BioLabs Cat# M0201S DNase I Life Technologies Cat# AM2222 Benzonase Nuclease EMD Millipore Cat# 70746 MyOne Streptavidin T1 Dynabeads Life Technologies Cat# 65602 Nanolink Streptavidin Magnetic beads Solulink Cat# M-1002-010 AcTEV Protease Life Technologies Cat# 12575015 PEG8000 Sigma-Aldrich Cat# 89510 BioRad protein assay BioRAD Cat# 5000001 Critical commercial assays pCR 8/GW/TOPO TA Cloning Kit Life Technologies Cat# K250020 Gateway LR Clonase II Enzyme mix Life Technologies Cat# 11791100 Dual-Glo Luciferase Assay System Promega Cat# E2940 Antifade mountant with DAPI Life Technologies Cat# P36931 RNeasy Mini Kit Qiagen Cat# 74106 iScript Select cDNA Synthesis Kit BioRAD Cat# 1708897 SsoAdvanced Universal SYBR Green Supermix BioRAD Cat# 1725275 QIAquick spin columns Qiagen Cat# 28115 KAPA Hyper Prep kit Kapa Biosystems Cat# KK8504 Nextera DNA Library Prep Kit Illumina Cat# FC-121-1030 Deposited data Raw and processed sequencing data for ChIP-seq This paper GEO: GSE215161 Raw and processed sequencing data for ATAC-seq This paper GEO: GSE215160 Raw and processed sequencing data for GRO-seq This paper GEO: GSE215162 AR ChIP-seq Malinen et al.39 GEO: GSE83860 H3K27ac ChIP-seq Hazelett et al.40 GEO: GSE51621 Experimental models: Cell lines Human: LNCaP ATCC Cat# CRL-1740 Human: U2OS ATCC Cat# HTB-96 Human: SH-SY5Y ATCC Cat# CRL-2266 Human: HEK293T ATCC Cat# CRL-3216 Human: U2OS 2-6-3 Janicki et al.51 N/A Human: LNCaP-pInducer20-AR stable lines for wildtype and mutants This paper N/A Human: LNCaP-TetR stable line This paper N/A Human: LNCaP-TetR-BioID-AR stable lines for wt, DIDR, and pQ69 This paper N/A Human: LNCaP-BirA-TetR stable line This paper N/A (Continued on next page) e2 Molecular Cell 83, 3438–3456.e1–e12, October 5, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER Human: LNCaP-BirA-TetR-BLRP-AR stable lines for wt, DIDR, and pQ69 This paper N/A Oligonucleotides Primers or oligos for qPCR and GRO-seq see method details This paper N/A Recombinant DNA shAR Sigma-Aldrich TRCN0000003718 shControl Sigma-Aldrich SHC002 shControl Sigma-Aldrich SHC202 pET-His-GFP-gw This paper N/A pET-His-GFP-ARNTD for wildtype and mutants This paper N/A pEGFP-C3-gw This paper N/A pEGFP-C3-AR for wildtype and mutants This paper N/A pCRY2PHR-mCherryN1 Addgene Plasmid ID: #26866 pCRY2PHR-mCherry-gw This paper N/A pCRY2PHR-mCherry-AR for NTD andDIDR This paper N/A eYFP-gw-LacI This paper N/A eYFP-AR-LacI for wt, DIDR, 7FS, and pQ69 This paper N/A mCherry-gw This paper N/A mCherry-AR for wt, DIDR, and 7FS This paper N/A mCherry-MED1 This paper N/A pHalo-gw-NLS This paper N/A pHalo-ARNTDwt-NLS This paper N/A pHalo-ARNTDpQ69-NLS This paper N/A pInducer20 Addgene Plasmid ID: #44012 pInducer20-AR for wildtype and mutants This paper N/A pCMV-Renilla-3XARE-TATA-luciferase This paper N/A pRetroX-mycBioID-MCS This paper N/A pRetroX-mycBioID-AR for wt, DIDR, and pQ69 This paper N/A pRetroX-BLRP-MCS This paper N/A pRetroX-BLRP-AR for wt, DIDR, and pQ69 This paper N/A pCL-Ampho Novus Biologicals Cat# NBP2-29541 pMD2.G Addgene Plasmid ID: #12259 psPAX2 Addgene Plasmid ID: #12260 Software and algorithms SLIMfast Teves et al.72 https://doi.org/10.7554/eLife.22280.022 ImageJ Macros script and MATLAB code for quantifying protein binding residence times from SPT data Chong et al.13 https://doi.org/10.5281/zenodo.8292534 Bowtie v1.1.2 Langmead et al.73 http://bowtie-bio.sourceforge.net/ index.shtml MACS2 v2.1.1.20160309 Zhang et al.74 https://github.com/taoliu/MACS ChIPseeker v1.10.3 Yu et al.75 https://bioconductor.org/packages/ release/bioc/html/ChIPseeker.html Integrative Genomics Viewer (IGV) Robinson et al.76 https://software.broadinstitute.org/ software/igv/ MaxQuant software v1.5.5.1 Max-Planck-Institute of Biochemistry https://www.biochem.mpg.de/227318/ MaxQuant (Continued on next page) Molecular Cell 83, 3438–3456.e1–e12, October 5, 2023 e3 .. REAGENT or RESOURCE SOURCE IDENTIFIER Prism 5 GraphPad https://graphpad-prism.software.informer. com/5.0/ ImageJ NIH https://imagej.nih.gov/ij/

    Article Title: Sequence-directed concentration of G protein-coupled receptors in COPII vesicles
    Article Snippet: GPCR plasmids in PRESTO-Tango kits were from Addgene (#1000000068) as described. .. The 3HA-tagged human AT2R and its ExE-AxA mutant in pcDNA3.1 vectors, GFP-tagged Sec24 in pEGFP-C3 vectors and the RUSH plasmids of α 2A -AR, β 2 -AR and D2R were generated as described previously., , To generate the RUSH plasmid Str-KDEL_SBP-EGFP-VSVG, VSVG without signal peptide was amplified by PCR using primers , digested with Fsel and Xbal enzymes and then ligated to the plasmid Str-KDEL_SBP-EGFP-Ecadherin (Addgene #65286) which was digested with the same enzymes to release ecadherin. ..

    Article Title: Regulation of interferon alpha production by the MAGUK-family protein CASK under H5N1 infection
    Article Snippet: RNA FISH confocal images were analyzed for nucleus/cytoplasmic ratio using MetaMorph software. .. CASK coding sequence were constructed into pEGFP-N vector (Addgene, 6085-1) in EcoRI site to make N-terminal EGFP fusion CASK. .. Constitutively active HCK(Y499F) were constructed into pCDNA4-V5/His-A vector (Addgene, V86120) in EcoRI site by site-directed mutagenesis.

    Article Title: RTP801 mediates transneuronal toxicity in culture via extracellular vesicles
    Article Snippet: .. HEK293 cells were transfected with pEGFP‐C3 or pEGFP‐RTP801‐C3 and rat primary cortical cultures with a pCMS‐eGFP plasmid (Addgene). .. Transfections were done using Lipofectamine 2000 (Thermo Fisher Scientific) following the manufacturer's protocol.

    Article Title: Development of peptide‐18‐targeted nanoliposome formulations with an alternative stealth coating copolymer for targeting breast cancer <scp>AU565</scp> cell line
    Article Snippet: Cholesterol and L-α-Phosphatidylcholine were purchased from Sigma. .. PEtOx-DOPE and P18-PEtOx-DOPE were synthesized at Tübitak MAM Laboratories, Turkey. pDNA (pEGFP-C3 plasmid; Addgene) was prepared at Yeditepe Laboratories, Turkey (DOI: 10.1080/21691401. ..

    Article Title: PERK recruits E-Syt1 at ER–mitochondria contacts for mitochondrial lipid transport and respiration
    Article Snippet: Cells were routinely checked for mycoplasma contaminations using the Plasmotest kit (Invivogen) according to the manufacturer’s instructions. .. PERK.K622A.9E10.pCDNA myc tagged (21815; Addgene plasmid), PERK.WT.9E10.pCDNA myc tagged (21814; Addgene plasmid), eGFP-E-Syt1 (66830; Addgene plasmid) p-eGFP-C3 empty vector plasmid (2489; Addgene plasmid) and pmCherry-C1 empty vector plasmid (3552; Addgene plasmid) were obtained from Addgene. mCherry-E-Syt1, eGFP-E-Syt1-ΔDE, eGFP-E-Syt1-ΔSMP, and mCherry-E-Syt1-ΔCDE were a kind gift from Pietro De Camilli lab ( ). ..

    Software:

    Article Title: Hormone-induced enhancer assembly requires an optimal level of hormone receptor multivalent interactions.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER CircLigase ssDNA Ligase Epicentre Cat# CL4111K Ape1 New England BioLabs Cat# M0282S Phusion High-Fidelity DNA Polymerase New England BioLabs Cat# M0530L Gibson Assembly Master Mix New England BioLabs Cat# E2611L Proteinase K, recombinant, PCR Grade Roche Cat# 3115879001 RNase Sigma-Aldrich Cat# R6513 TRIzol LS Reagent Life Technologies Cat# 10296028 T4 PNK New England BioLabs Cat# M0201S DNase I Life Technologies Cat# AM2222 Benzonase Nuclease EMD Millipore Cat# 70746 MyOne Streptavidin T1 Dynabeads Life Technologies Cat# 65602 Nanolink Streptavidin Magnetic beads Solulink Cat# M-1002-010 AcTEV Protease Life Technologies Cat# 12575015 PEG8000 Sigma-Aldrich Cat# 89510 BioRad protein assay BioRAD Cat# 5000001 Critical commercial assays pCR 8/GW/TOPO TA Cloning Kit Life Technologies Cat# K250020 Gateway LR Clonase II Enzyme mix Life Technologies Cat# 11791100 Dual-Glo Luciferase Assay System Promega Cat# E2940 Antifade mountant with DAPI Life Technologies Cat# P36931 RNeasy Mini Kit Qiagen Cat# 74106 iScript Select cDNA Synthesis Kit BioRAD Cat# 1708897 SsoAdvanced Universal SYBR Green Supermix BioRAD Cat# 1725275 QIAquick spin columns Qiagen Cat# 28115 KAPA Hyper Prep kit Kapa Biosystems Cat# KK8504 Nextera DNA Library Prep Kit Illumina Cat# FC-121-1030 Deposited data Raw and processed sequencing data for ChIP-seq This paper GEO: GSE215161 Raw and processed sequencing data for ATAC-seq This paper GEO: GSE215160 Raw and processed sequencing data for GRO-seq This paper GEO: GSE215162 AR ChIP-seq Malinen et al.39 GEO: GSE83860 H3K27ac ChIP-seq Hazelett et al.40 GEO: GSE51621 Experimental models: Cell lines Human: LNCaP ATCC Cat# CRL-1740 Human: U2OS ATCC Cat# HTB-96 Human: SH-SY5Y ATCC Cat# CRL-2266 Human: HEK293T ATCC Cat# CRL-3216 Human: U2OS 2-6-3 Janicki et al.51 N/A Human: LNCaP-pInducer20-AR stable lines for wildtype and mutants This paper N/A Human: LNCaP-TetR stable line This paper N/A Human: LNCaP-TetR-BioID-AR stable lines for wt, DIDR, and pQ69 This paper N/A Human: LNCaP-BirA-TetR stable line This paper N/A (Continued on next page) e2 Molecular Cell 83, 3438–3456.e1–e12, October 5, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER Human: LNCaP-BirA-TetR-BLRP-AR stable lines for wt, DIDR, and pQ69 This paper N/A Oligonucleotides Primers or oligos for qPCR and GRO-seq see method details This paper N/A Recombinant DNA shAR Sigma-Aldrich TRCN0000003718 shControl Sigma-Aldrich SHC002 shControl Sigma-Aldrich SHC202 pET-His-GFP-gw This paper N/A pET-His-GFP-ARNTD for wildtype and mutants This paper N/A pEGFP-C3-gw This paper N/A pEGFP-C3-AR for wildtype and mutants This paper N/A pCRY2PHR-mCherryN1 Addgene Plasmid ID: #26866 pCRY2PHR-mCherry-gw This paper N/A pCRY2PHR-mCherry-AR for NTD andDIDR This paper N/A eYFP-gw-LacI This paper N/A eYFP-AR-LacI for wt, DIDR, 7FS, and pQ69 This paper N/A mCherry-gw This paper N/A mCherry-AR for wt, DIDR, and 7FS This paper N/A mCherry-MED1 This paper N/A pHalo-gw-NLS This paper N/A pHalo-ARNTDwt-NLS This paper N/A pHalo-ARNTDpQ69-NLS This paper N/A pInducer20 Addgene Plasmid ID: #44012 pInducer20-AR for wildtype and mutants This paper N/A pCMV-Renilla-3XARE-TATA-luciferase This paper N/A pRetroX-mycBioID-MCS This paper N/A pRetroX-mycBioID-AR for wt, DIDR, and pQ69 This paper N/A pRetroX-BLRP-MCS This paper N/A pRetroX-BLRP-AR for wt, DIDR, and pQ69 This paper N/A pCL-Ampho Novus Biologicals Cat# NBP2-29541 pMD2.G Addgene Plasmid ID: #12259 psPAX2 Addgene Plasmid ID: #12260 Software and algorithms SLIMfast Teves et al.72 https://doi.org/10.7554/eLife.22280.022 ImageJ Macros script and MATLAB code for quantifying protein binding residence times from SPT data Chong et al.13 https://doi.org/10.5281/zenodo.8292534 Bowtie v1.1.2 Langmead et al.73 http://bowtie-bio.sourceforge.net/ index.shtml MACS2 v2.1.1.20160309 Zhang et al.74 https://github.com/taoliu/MACS ChIPseeker v1.10.3 Yu et al.75 https://bioconductor.org/packages/ release/bioc/html/ChIPseeker.html Integrative Genomics Viewer (IGV) Robinson et al.76 https://software.broadinstitute.org/ software/igv/ MaxQuant software v1.5.5.1 Max-Planck-Institute of Biochemistry https://www.biochem.mpg.de/227318/ MaxQuant (Continued on next page) Molecular Cell 83, 3438–3456.e1–e12, October 5, 2023 e3 .. REAGENT or RESOURCE SOURCE IDENTIFIER Prism 5 GraphPad https://graphpad-prism.software.informer. com/5.0/ ImageJ NIH https://imagej.nih.gov/ij/

    Protein Binding:

    Article Title: Hormone-induced enhancer assembly requires an optimal level of hormone receptor multivalent interactions.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER CircLigase ssDNA Ligase Epicentre Cat# CL4111K Ape1 New England BioLabs Cat# M0282S Phusion High-Fidelity DNA Polymerase New England BioLabs Cat# M0530L Gibson Assembly Master Mix New England BioLabs Cat# E2611L Proteinase K, recombinant, PCR Grade Roche Cat# 3115879001 RNase Sigma-Aldrich Cat# R6513 TRIzol LS Reagent Life Technologies Cat# 10296028 T4 PNK New England BioLabs Cat# M0201S DNase I Life Technologies Cat# AM2222 Benzonase Nuclease EMD Millipore Cat# 70746 MyOne Streptavidin T1 Dynabeads Life Technologies Cat# 65602 Nanolink Streptavidin Magnetic beads Solulink Cat# M-1002-010 AcTEV Protease Life Technologies Cat# 12575015 PEG8000 Sigma-Aldrich Cat# 89510 BioRad protein assay BioRAD Cat# 5000001 Critical commercial assays pCR 8/GW/TOPO TA Cloning Kit Life Technologies Cat# K250020 Gateway LR Clonase II Enzyme mix Life Technologies Cat# 11791100 Dual-Glo Luciferase Assay System Promega Cat# E2940 Antifade mountant with DAPI Life Technologies Cat# P36931 RNeasy Mini Kit Qiagen Cat# 74106 iScript Select cDNA Synthesis Kit BioRAD Cat# 1708897 SsoAdvanced Universal SYBR Green Supermix BioRAD Cat# 1725275 QIAquick spin columns Qiagen Cat# 28115 KAPA Hyper Prep kit Kapa Biosystems Cat# KK8504 Nextera DNA Library Prep Kit Illumina Cat# FC-121-1030 Deposited data Raw and processed sequencing data for ChIP-seq This paper GEO: GSE215161 Raw and processed sequencing data for ATAC-seq This paper GEO: GSE215160 Raw and processed sequencing data for GRO-seq This paper GEO: GSE215162 AR ChIP-seq Malinen et al.39 GEO: GSE83860 H3K27ac ChIP-seq Hazelett et al.40 GEO: GSE51621 Experimental models: Cell lines Human: LNCaP ATCC Cat# CRL-1740 Human: U2OS ATCC Cat# HTB-96 Human: SH-SY5Y ATCC Cat# CRL-2266 Human: HEK293T ATCC Cat# CRL-3216 Human: U2OS 2-6-3 Janicki et al.51 N/A Human: LNCaP-pInducer20-AR stable lines for wildtype and mutants This paper N/A Human: LNCaP-TetR stable line This paper N/A Human: LNCaP-TetR-BioID-AR stable lines for wt, DIDR, and pQ69 This paper N/A Human: LNCaP-BirA-TetR stable line This paper N/A (Continued on next page) e2 Molecular Cell 83, 3438–3456.e1–e12, October 5, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER Human: LNCaP-BirA-TetR-BLRP-AR stable lines for wt, DIDR, and pQ69 This paper N/A Oligonucleotides Primers or oligos for qPCR and GRO-seq see method details This paper N/A Recombinant DNA shAR Sigma-Aldrich TRCN0000003718 shControl Sigma-Aldrich SHC002 shControl Sigma-Aldrich SHC202 pET-His-GFP-gw This paper N/A pET-His-GFP-ARNTD for wildtype and mutants This paper N/A pEGFP-C3-gw This paper N/A pEGFP-C3-AR for wildtype and mutants This paper N/A pCRY2PHR-mCherryN1 Addgene Plasmid ID: #26866 pCRY2PHR-mCherry-gw This paper N/A pCRY2PHR-mCherry-AR for NTD andDIDR This paper N/A eYFP-gw-LacI This paper N/A eYFP-AR-LacI for wt, DIDR, 7FS, and pQ69 This paper N/A mCherry-gw This paper N/A mCherry-AR for wt, DIDR, and 7FS This paper N/A mCherry-MED1 This paper N/A pHalo-gw-NLS This paper N/A pHalo-ARNTDwt-NLS This paper N/A pHalo-ARNTDpQ69-NLS This paper N/A pInducer20 Addgene Plasmid ID: #44012 pInducer20-AR for wildtype and mutants This paper N/A pCMV-Renilla-3XARE-TATA-luciferase This paper N/A pRetroX-mycBioID-MCS This paper N/A pRetroX-mycBioID-AR for wt, DIDR, and pQ69 This paper N/A pRetroX-BLRP-MCS This paper N/A pRetroX-BLRP-AR for wt, DIDR, and pQ69 This paper N/A pCL-Ampho Novus Biologicals Cat# NBP2-29541 pMD2.G Addgene Plasmid ID: #12259 psPAX2 Addgene Plasmid ID: #12260 Software and algorithms SLIMfast Teves et al.72 https://doi.org/10.7554/eLife.22280.022 ImageJ Macros script and MATLAB code for quantifying protein binding residence times from SPT data Chong et al.13 https://doi.org/10.5281/zenodo.8292534 Bowtie v1.1.2 Langmead et al.73 http://bowtie-bio.sourceforge.net/ index.shtml MACS2 v2.1.1.20160309 Zhang et al.74 https://github.com/taoliu/MACS ChIPseeker v1.10.3 Yu et al.75 https://bioconductor.org/packages/ release/bioc/html/ChIPseeker.html Integrative Genomics Viewer (IGV) Robinson et al.76 https://software.broadinstitute.org/ software/igv/ MaxQuant software v1.5.5.1 Max-Planck-Institute of Biochemistry https://www.biochem.mpg.de/227318/ MaxQuant (Continued on next page) Molecular Cell 83, 3438–3456.e1–e12, October 5, 2023 e3 .. REAGENT or RESOURCE SOURCE IDENTIFIER Prism 5 GraphPad https://graphpad-prism.software.informer. com/5.0/ ImageJ NIH https://imagej.nih.gov/ij/

    Single-particle Tracking:

    Article Title: Hormone-induced enhancer assembly requires an optimal level of hormone receptor multivalent interactions.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER CircLigase ssDNA Ligase Epicentre Cat# CL4111K Ape1 New England BioLabs Cat# M0282S Phusion High-Fidelity DNA Polymerase New England BioLabs Cat# M0530L Gibson Assembly Master Mix New England BioLabs Cat# E2611L Proteinase K, recombinant, PCR Grade Roche Cat# 3115879001 RNase Sigma-Aldrich Cat# R6513 TRIzol LS Reagent Life Technologies Cat# 10296028 T4 PNK New England BioLabs Cat# M0201S DNase I Life Technologies Cat# AM2222 Benzonase Nuclease EMD Millipore Cat# 70746 MyOne Streptavidin T1 Dynabeads Life Technologies Cat# 65602 Nanolink Streptavidin Magnetic beads Solulink Cat# M-1002-010 AcTEV Protease Life Technologies Cat# 12575015 PEG8000 Sigma-Aldrich Cat# 89510 BioRad protein assay BioRAD Cat# 5000001 Critical commercial assays pCR 8/GW/TOPO TA Cloning Kit Life Technologies Cat# K250020 Gateway LR Clonase II Enzyme mix Life Technologies Cat# 11791100 Dual-Glo Luciferase Assay System Promega Cat# E2940 Antifade mountant with DAPI Life Technologies Cat# P36931 RNeasy Mini Kit Qiagen Cat# 74106 iScript Select cDNA Synthesis Kit BioRAD Cat# 1708897 SsoAdvanced Universal SYBR Green Supermix BioRAD Cat# 1725275 QIAquick spin columns Qiagen Cat# 28115 KAPA Hyper Prep kit Kapa Biosystems Cat# KK8504 Nextera DNA Library Prep Kit Illumina Cat# FC-121-1030 Deposited data Raw and processed sequencing data for ChIP-seq This paper GEO: GSE215161 Raw and processed sequencing data for ATAC-seq This paper GEO: GSE215160 Raw and processed sequencing data for GRO-seq This paper GEO: GSE215162 AR ChIP-seq Malinen et al.39 GEO: GSE83860 H3K27ac ChIP-seq Hazelett et al.40 GEO: GSE51621 Experimental models: Cell lines Human: LNCaP ATCC Cat# CRL-1740 Human: U2OS ATCC Cat# HTB-96 Human: SH-SY5Y ATCC Cat# CRL-2266 Human: HEK293T ATCC Cat# CRL-3216 Human: U2OS 2-6-3 Janicki et al.51 N/A Human: LNCaP-pInducer20-AR stable lines for wildtype and mutants This paper N/A Human: LNCaP-TetR stable line This paper N/A Human: LNCaP-TetR-BioID-AR stable lines for wt, DIDR, and pQ69 This paper N/A Human: LNCaP-BirA-TetR stable line This paper N/A (Continued on next page) e2 Molecular Cell 83, 3438–3456.e1–e12, October 5, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER Human: LNCaP-BirA-TetR-BLRP-AR stable lines for wt, DIDR, and pQ69 This paper N/A Oligonucleotides Primers or oligos for qPCR and GRO-seq see method details This paper N/A Recombinant DNA shAR Sigma-Aldrich TRCN0000003718 shControl Sigma-Aldrich SHC002 shControl Sigma-Aldrich SHC202 pET-His-GFP-gw This paper N/A pET-His-GFP-ARNTD for wildtype and mutants This paper N/A pEGFP-C3-gw This paper N/A pEGFP-C3-AR for wildtype and mutants This paper N/A pCRY2PHR-mCherryN1 Addgene Plasmid ID: #26866 pCRY2PHR-mCherry-gw This paper N/A pCRY2PHR-mCherry-AR for NTD andDIDR This paper N/A eYFP-gw-LacI This paper N/A eYFP-AR-LacI for wt, DIDR, 7FS, and pQ69 This paper N/A mCherry-gw This paper N/A mCherry-AR for wt, DIDR, and 7FS This paper N/A mCherry-MED1 This paper N/A pHalo-gw-NLS This paper N/A pHalo-ARNTDwt-NLS This paper N/A pHalo-ARNTDpQ69-NLS This paper N/A pInducer20 Addgene Plasmid ID: #44012 pInducer20-AR for wildtype and mutants This paper N/A pCMV-Renilla-3XARE-TATA-luciferase This paper N/A pRetroX-mycBioID-MCS This paper N/A pRetroX-mycBioID-AR for wt, DIDR, and pQ69 This paper N/A pRetroX-BLRP-MCS This paper N/A pRetroX-BLRP-AR for wt, DIDR, and pQ69 This paper N/A pCL-Ampho Novus Biologicals Cat# NBP2-29541 pMD2.G Addgene Plasmid ID: #12259 psPAX2 Addgene Plasmid ID: #12260 Software and algorithms SLIMfast Teves et al.72 https://doi.org/10.7554/eLife.22280.022 ImageJ Macros script and MATLAB code for quantifying protein binding residence times from SPT data Chong et al.13 https://doi.org/10.5281/zenodo.8292534 Bowtie v1.1.2 Langmead et al.73 http://bowtie-bio.sourceforge.net/ index.shtml MACS2 v2.1.1.20160309 Zhang et al.74 https://github.com/taoliu/MACS ChIPseeker v1.10.3 Yu et al.75 https://bioconductor.org/packages/ release/bioc/html/ChIPseeker.html Integrative Genomics Viewer (IGV) Robinson et al.76 https://software.broadinstitute.org/ software/igv/ MaxQuant software v1.5.5.1 Max-Planck-Institute of Biochemistry https://www.biochem.mpg.de/227318/ MaxQuant (Continued on next page) Molecular Cell 83, 3438–3456.e1–e12, October 5, 2023 e3 .. REAGENT or RESOURCE SOURCE IDENTIFIER Prism 5 GraphPad https://graphpad-prism.software.informer. com/5.0/ ImageJ NIH https://imagej.nih.gov/ij/

    Mutagenesis:

    Article Title: Sequence-directed concentration of G protein-coupled receptors in COPII vesicles
    Article Snippet: GPCR plasmids in PRESTO-Tango kits were from Addgene (#1000000068) as described. .. The 3HA-tagged human AT2R and its ExE-AxA mutant in pcDNA3.1 vectors, GFP-tagged Sec24 in pEGFP-C3 vectors and the RUSH plasmids of α 2A -AR, β 2 -AR and D2R were generated as described previously., , To generate the RUSH plasmid Str-KDEL_SBP-EGFP-VSVG, VSVG without signal peptide was amplified by PCR using primers , digested with Fsel and Xbal enzymes and then ligated to the plasmid Str-KDEL_SBP-EGFP-Ecadherin (Addgene #65286) which was digested with the same enzymes to release ecadherin. ..

    Generated:

    Article Title: Sequence-directed concentration of G protein-coupled receptors in COPII vesicles
    Article Snippet: GPCR plasmids in PRESTO-Tango kits were from Addgene (#1000000068) as described. .. The 3HA-tagged human AT2R and its ExE-AxA mutant in pcDNA3.1 vectors, GFP-tagged Sec24 in pEGFP-C3 vectors and the RUSH plasmids of α 2A -AR, β 2 -AR and D2R were generated as described previously., , To generate the RUSH plasmid Str-KDEL_SBP-EGFP-VSVG, VSVG without signal peptide was amplified by PCR using primers , digested with Fsel and Xbal enzymes and then ligated to the plasmid Str-KDEL_SBP-EGFP-Ecadherin (Addgene #65286) which was digested with the same enzymes to release ecadherin. ..

    Amplification:

    Article Title: Sequence-directed concentration of G protein-coupled receptors in COPII vesicles
    Article Snippet: GPCR plasmids in PRESTO-Tango kits were from Addgene (#1000000068) as described. .. The 3HA-tagged human AT2R and its ExE-AxA mutant in pcDNA3.1 vectors, GFP-tagged Sec24 in pEGFP-C3 vectors and the RUSH plasmids of α 2A -AR, β 2 -AR and D2R were generated as described previously., , To generate the RUSH plasmid Str-KDEL_SBP-EGFP-VSVG, VSVG without signal peptide was amplified by PCR using primers , digested with Fsel and Xbal enzymes and then ligated to the plasmid Str-KDEL_SBP-EGFP-Ecadherin (Addgene #65286) which was digested with the same enzymes to release ecadherin. ..

    Polymerase Chain Reaction:

    Article Title: Sequence-directed concentration of G protein-coupled receptors in COPII vesicles
    Article Snippet: GPCR plasmids in PRESTO-Tango kits were from Addgene (#1000000068) as described. .. The 3HA-tagged human AT2R and its ExE-AxA mutant in pcDNA3.1 vectors, GFP-tagged Sec24 in pEGFP-C3 vectors and the RUSH plasmids of α 2A -AR, β 2 -AR and D2R were generated as described previously., , To generate the RUSH plasmid Str-KDEL_SBP-EGFP-VSVG, VSVG without signal peptide was amplified by PCR using primers , digested with Fsel and Xbal enzymes and then ligated to the plasmid Str-KDEL_SBP-EGFP-Ecadherin (Addgene #65286) which was digested with the same enzymes to release ecadherin. ..

    Sequencing:

    Article Title: Regulation of interferon alpha production by the MAGUK-family protein CASK under H5N1 infection
    Article Snippet: RNA FISH confocal images were analyzed for nucleus/cytoplasmic ratio using MetaMorph software. .. CASK coding sequence were constructed into pEGFP-N vector (Addgene, 6085-1) in EcoRI site to make N-terminal EGFP fusion CASK. .. Constitutively active HCK(Y499F) were constructed into pCDNA4-V5/His-A vector (Addgene, V86120) in EcoRI site by site-directed mutagenesis.

    Construct:

    Article Title: Regulation of interferon alpha production by the MAGUK-family protein CASK under H5N1 infection
    Article Snippet: RNA FISH confocal images were analyzed for nucleus/cytoplasmic ratio using MetaMorph software. .. CASK coding sequence were constructed into pEGFP-N vector (Addgene, 6085-1) in EcoRI site to make N-terminal EGFP fusion CASK. .. Constitutively active HCK(Y499F) were constructed into pCDNA4-V5/His-A vector (Addgene, V86120) in EcoRI site by site-directed mutagenesis.

    Transfection:

    Article Title: RTP801 mediates transneuronal toxicity in culture via extracellular vesicles
    Article Snippet: .. HEK293 cells were transfected with pEGFP‐C3 or pEGFP‐RTP801‐C3 and rat primary cortical cultures with a pCMS‐eGFP plasmid (Addgene). .. Transfections were done using Lipofectamine 2000 (Thermo Fisher Scientific) following the manufacturer's protocol.

    Synthesized:

    Article Title: Development of peptide‐18‐targeted nanoliposome formulations with an alternative stealth coating copolymer for targeting breast cancer <scp>AU565</scp> cell line
    Article Snippet: Cholesterol and L-α-Phosphatidylcholine were purchased from Sigma. .. PEtOx-DOPE and P18-PEtOx-DOPE were synthesized at Tübitak MAM Laboratories, Turkey. pDNA (pEGFP-C3 plasmid; Addgene) was prepared at Yeditepe Laboratories, Turkey (DOI: 10.1080/21691401. ..

    other:

    Article Title: Spastin locally amplifies microtubule dynamics to pattern the axon for presynaptic cargo delivery.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER BDNF PeproTech Cat# 450-02 NT-3 PeproTech Cat# 450-03 GDNF PeproTech Cat# 450-10 Lipofectamine Stem Transfection Reagent Thermo Fisher Cat# STEM00003 Halt Protease and Phosphatase Inhibitor Cocktail Thermo Fisher Cat# 78442 ViralBoost Alstem Cat# VB100 Lentivirus Precipitation Solution Alstem Cat# VC100 Puromycin Takara Cat# 631305 Hibernate A Medium Brain Bits Cat# HA100 SNAP-Cell 647-SiR New England BioLabs Cat# S9102S SynaptoRed C2 Biotium Cat# 70027 D-AP5 Thomas Scientific Cat# 14539–5 ADVASEP-7 Biotium Cat# 70029 CNQX Thomas Scientific Cat# 14618–5 EveryBlot Blocking Buffer BIO-RAD Cat# 12010020 LI-COR Revert 700 Total Protein Stain LI-COR Cat# 926–11021 Critical commercial assays BCA Protein Assay Kit Thermo Fisher Cat# 23225 Plasmid Maxi Kit QIAGEN Cat# 12163 Experimental models: Cell lines Human: NGN2 iPSCs M. Ward (National Institutes of Health)31 N/A Human: HEK293T ATCC Cat# CRL-3216; RRID:CVCL_0063 Experimental models: Organisms/strains Rat: primary rat astrocytes/glia isolated from postnatal day 1 rat brains (Sprague Dawley) Charles River Laboratories RRID: RGD_737891 Oligonucleotides Spastin-specific sgRNA guide: GACCGACGGGAACCAAGCGA Horlbeck et al.39 N/A Non-targeting sgRNA guide: GTGCCAGCTTGTGGTGTCGT Horlbeck et al.39 N/A pCRISPRia-vs2 sequencing forward oligo: ggcttggatttctataacttcg This paper N/A pCRISPRia-vs2 sequencing reverse oligo: ctactgcacttatatacggttc This paper N/A Recombinant DNA Plasmid: pCRISPRia-vs2 Addgene Cat# 84832 Plasmid: pCRISPRia-vs2-Spastin Modified from pCRISPRia-vs2 N/A Plasmid: pCRISPRia-vs2-NT Modified from pCRISPRia-vs2 N/A Plasmid: pCMV-Vsv-g Addgene Cat# #8454 Plasmid: psPAX2 (HIV pol+gag) Addgene Cat# 12260 Plasmid: pCI-mScarlet Addgene Cat# 85042 Plasmid: pC1-mScarlet-Syp Modified from pCI-mScarlet N/A Plasmid: pCIG2-GFP-MACF43 Aiken et al.51 N/A Plasmid: pEGFP-C3-Syb Addgene Cat# 42308 Plasmid: pmScarlet-Syb Modified from pEGFP-C3-Syb N/A Plasmid: pCIG2-mScarlet-SybIRES-GFP-MACF43 Modified from pCIG2-GFP-MACF43 N/A Plasmid: pCIG2-SNAP-M87 Modified from pCIG2-GFP-MACF43 N/A Plasmid: pSNAPf New England Biolabs Cat# N9183S Plasmid: pCMV-Tag/WT M87 Addgene Cat# 89322 (Continued on next page) e2 Current Biology 34, 1–18.e1–e8, April 22, 2024 Article



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