Recombinant:
Article Title: The HIV-1 nuclear export complex reveals the role of RNA in CRM1 cargo recognition.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal ANTI-FLAG Sigma-Aldrich F1804; RRID: AB_262044 Mouse monoclonal ANTI-GAPDH Proteintech 600004-1-lg; RRID: AB_2107436 Mouse monoclonal ANTI-α-Tubulin Sigma-Aldrich T5168; RRID: AB_477579 Rabbit Monoclonal ANTI-CRM1 Thermo Fisher Scientific 703569; RRID:AB_2784588 Mouse Monoclonal HRP-conjugated ANTI-Flag Invitrogen MA1-91878-HRP; RRID: AB_2537626 Bacterial and virus strains StellarTM Competent Cells Takara 636763 BL21(DE3) Competent New England Biolabs C2527H BL21(DE3)pLysS Invitrogen C606010 Chemicals, peptides, and recombinant proteins Q5® High-Fidelity 2X Master Mix New England Biosciences M0492S In-Fusion® Snap Assembly Master Mix Takara Bio Inc. 638947 PhusionTM High-Fidelity DNA Polymerase New England Biosciences M0530S Gibson Assembly® Master Mix New England Biosciences E2611 Fisher BioReagentsTM 2XYT Broth Fisher Scientific BP97432 SYBRTM Gold Nucleic Acid Gel Stain InvitrogenTM S11494 FreeStyleTM 293 Expression System InvitrogenTM K900001 FreeStyleTM 293 Expression Medium InvitrogenTM 12338018 Expi293TM Expression System Kit Thermo Fisher Scientific A14635 DMEM/High Glucose Cytvia SH30022.01 Fetal Bovine Serum (Adherent HEK Cells) Gibco A52568-01 Penicillin Streptomycin Gibco 15140–122 Lipofectamin 3000 Transfection Reagent Invitrogen L3000008 PolyJetTM In Vitro DNA Transfection Reagent SignaGen Laboratories SL100688 Promoter-Driven Control NanoLuc® Luciferase Vector (pNL1.1.TK) Promega N1501 Passive Lysis 5x Buffer Promega E1941 Nano-Glo® Dual-Luciferase® Reporter Assay System Promega N1610 HaltTM Protease Inhibitor Cocktail (100X) Thermo ScientificTM 78429 RosettaTM(DE3) pLysS Novagen 70956–3 Amylose Resin New England Biosciences E8021L PierceTM Bovine Serum Albumin Standard Pre-Diluted Set Thermo ScientificTM 23208 Strep-Tactin®XT 4Flow® resin IBA Lifesciences, GmbH 2-5010-025 Buffer BXT (10x) IBA Lifesciences, GmbH 2-1042-025 HisPurTM Ni-NTA Resin Thermo ScientificTM 88222 HIV-1 Rev HXB3 wild type Daugherty et al.22 N/A HIV-1 Rev HXB3 L60R Daugherty et al.22 N/A RanQ69L Booth et al.54 N/A Deposited data HIV-1 NEC Map This paper EMDB-42494 HIV-1 NEC Model This paper PDB: 8URJ (Continued on next page) Molecular Cell 85, 3108–3122.e1–e7, August 21, 2025 e1 .. Full-length, codon optimized human CRM1 was cloned into a modified pFastBac vector containing a mammalian cytomegalovirus (CMV) promoter between the BamHI and NotI restriction sites.101–103 The construct was assembled using G-blocks (IDT, US) and Gibson Assembly (Table S1; New England Biosciences, US).
Article Title: Comprehensive benchmarking of genome editing quantification methods for plant applications
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains DH5a Escherichia coli strain In-house N/A GV3101 Agrobacterium tumefaciens strain In-house N/A Chemicals, peptides, and recombinant proteins Q5 High Fidelity DNA Polymerase New England Biolabs M0491S Q5 High Fidelity PCR Master Mix New England Biolabs M0492S GoTaq Green PCR Master Mix Promega M7122 Rapid ligation buffer Promega C6711 T4 DNA ligase Promega M1801 T7 Endonuclease 1 New England Biolabs M0302S Exonuclease 1 New England Biolabs M0568S Shrimp Alkaline Phosphatase New England Biolabs M0371S Droplet generation oil for probe BioRad 1863005 ddPCR droplet reader oil BioRad 1863004 BsaI-HFv2 New England Biolabs R3733S NcoI-HF New England Biolabs R3193S BcoDI New England Biolabs R0542S BsrDI New England Biolabs R0574S BglII New England Biolabs R0144S MfeI-HF New England Biolabs R3589S RsaI New England Biolabs R0167S BsrDI New England Biolabs R0574S HpaI New England Biolabs R0105S BstNI New England Biolabs R0168S NuSieve GTGTM agarose Lonza Bioscience 50084 Critical commercial assays QX200 ddPCR Supermix for probe (no dUTP) BioRad 1863023 High Sensitivity D1000 ScreenTape Agilent 5067-5584 Deposited data Raw targeted amplicon sequencing This paper https://doi.org/10.5281/zenodo.15043050 Experimental models: Organisms/strains LAB wildtype Nicotiana benthamiana plants In-house N/A Oligonucleotides PCR primers and their sequences are reported in the Tables S4–S7. .. Sigma-Aldrich or Integrated DNA Technologies (This paper) N/A sgRNA spacer oligonucleotides and their sequences are reported in the Tables S1 and S2 Sigma-Aldrich or Integrated DNA Technologies (This paper) N/A FAM-labelled PCR primer with sequence reported in Table S6 Sigma-Aldrich (This paper) N/A Custom FAM or HEX labelled probes with sequences reported in Table S7 Integrated DNA Technologies (This paper) N/A Recombinant DNA pIZZA-BYR-SpCas9 Gong et al.56 N/A pBYR2eFa-U6-sgRNA Gong et al.56 N/A (Continued on next page) e1 iScience 28, 112350, June 20, 2025
Article Title: Tat-fimbriae ("tafi"): An unusual type of haloarchaeal surface structure depending on the twin-arginine translocation pathway.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit polyclonal anti-HAH_0240 This paper N/A Anti-6X His tag antibody Abcam Cat # ab14923; RRID: AB_443105 Goat anti-rabbit IgG conjugated with alkaline phosphatase Merck Cat # A3687; RRID: AB_258103 Bacterial and virus strains Bacterial and archaeal strains are listed in Table S5 N/A Chemicals, peptides, and recombinant proteins BamHI-HF NEB R3136S EcoRI-HF NEB R3101S KpnI-HF NEB R3142S NdeI NEB R0111S PstI NEB R0140S Q5 High-Fidelity DNA Polymerase NEB M0491S SphI NEB R0182S DNase I Thermo scientific EN0521 BCIP/NBT Color Development Substrate Promega S3771 IPTG Thermo scientific R0392 L-Tryptophan Merck T0254 BactoTM Casamino Acids Thermo scientific 223050 Brilliant Blue G Merck B0770 Schiff’s fuchsin-sulfite reagent Merck S5133 DNA Ladder 1 kb Evrogen NL001 PageRulerTM Prestained Protein Ladder, 10 to 180 kDa Thermo scientific 26616 5-Fluoroorotic Acid (5-FOA) Thermo scientific R0811 Uracil Merck U0750 Proteinase K AppliChem A4392 Trypsin Merck T4799 Polyethylene glycol (PEG) 6000 Panreac 203-473-3 Critical commercial assays GeneJET Plasmid Miniprep Kit Thermo scientific K0502 QIAquick PCR Purification Kit Qiagen 28104 Amicon Ultra Centrifugal Filter, 3 kDa MWCO Merck UFC9003 Oligonucleotides See Table S6 for cloning primers This work N/A Recombinant DNA See Table S5 This work N/A Software and algorithms ImageJ National Institutes of Health N/A Software used for protein structure prediction AlphaFold2 https://alphafold.ebi.ac.uk Software used for protein structure alignment Dali server http://ekhidna2.biocenter.helsinki.fi/dali/ Other Immobilon -PSQ PVDF Membrane Merck ISEQ00010 Poros MS/M 10/100 column Applied Biosystems N/A iScience 28, 111793, February 21, 2025 e1 ..
Article Title: Low-input RNA-seq suggests metabolic specialization underlying morphological heterogeneity in a gut commensal bacterium.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains Bacteroides thetaiotaomicron VPI-5842 DSM 2079 Phocaeicola vulgatus DSM 1447 Bacteroides uniformis DSM 6597 Campylobacter jejuni NTC1168 Provided by Cynthia Sharma CSS-5295 Salmonella enterica serovar Typhimurium DSM 24522 Clostridioides difficile 630 Provided by Franziska Faber DSM27543 E. coli S17-1 lambda pir ATCC BAA-2428 See Table S4 for strains generated in this study This paper N/A Chemicals, peptides, and recombinant proteins Anhydrotetracycline VWR J66688.MA BamHI Thermo Fischer Scientific FD0054 Cas9 nuclease New England Biolabs MO386T Cefoxitin Carl Roth 4156.2 dCTPs Invitrogen 10217016 Deepvent DNA polymerase New England Biolabs M0259L DNaseI Thermo Fischer Scientific EN0521 dNTPs New England Biolabs N0447L IPTG AppliChem A4773,0005 Lysozyme (single cell) Epicentre R1804M Lysozyme (FISH) Thermo Fischer Scientific 90082 NheI Thermo Fischer Scientific FD0974 Nuclease Free Water Ambion AM9916 Paraformaldehyde Carl Roth 0335.1 Phusion DNA polymerase Biozym 332530 L Proteinase K New England Biolabs P8107S Recombinant RNase Inhibitor Takara 2313A RNAlater Qiagen 76104 RNsseH New England Biolabs M0297L RNAseIf New England Biolabs M0243S SSC buffer (20X) Invitrogen AM9763 SuperScript IV Reverse Transcriptase Thermo Fischer Scientific 18090010 T4 DNA Polymerase New England Biolabs M0203L Terminal Transferase New England Biolabs M0315S XbaI Thermo Fisher Scientific FD0684 XhoI Thermo Fisher Scientific FD0694 10X lysis buffer Takara 635013 Critical commercial assays Agilent High Sensitivity DNA Kit Agilent 5067–4626 Ampure XP beads Beckman Coulter A63881 HCR-FISH Molecular Instruments N/A KAPA HiFi HotStart ReadyMix Roche sequencing store KK2602/SKU:7958935001 MEGAscript T7 transcription Kit (Ambion) Thermo Fisher Scientific AMB13345 Monarch RNA Cleanupt Kit NEB T2050S NEBuilder HiFi DNA Assembly Mix New England Biolabs E2621L (Continued on next page) 14 Cell Reports 44, 115844, June 24, 2025 .. Animal experiments were performed at the Helmholtz Center for Infection Research, Braunschweig, Germany, according to the National Animal Protection Law (Tierschutzgesetz [TierSchG] and Animal Experiment Regulations [Tierschutz-Versuchstierverordnung [TierSchVersV]), following the recommendations of the Federation of European Laboratory Animal Science Association (FELASA).
Molecular Weight:
Marker:
Chromosome Transmission Fidelity Colony Color Assay:
Purification:
Article Title: Tat-fimbriae ("tafi"): An unusual type of haloarchaeal surface structure depending on the twin-arginine translocation pathway.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit polyclonal anti-HAH_0240 This paper N/A Anti-6X His tag antibody Abcam Cat # ab14923; RRID: AB_443105 Goat anti-rabbit IgG conjugated with alkaline phosphatase Merck Cat # A3687; RRID: AB_258103 Bacterial and virus strains Bacterial and archaeal strains are listed in Table S5 N/A Chemicals, peptides, and recombinant proteins BamHI-HF NEB R3136S EcoRI-HF NEB R3101S KpnI-HF NEB R3142S NdeI NEB R0111S PstI NEB R0140S Q5 High-Fidelity DNA Polymerase NEB M0491S SphI NEB R0182S DNase I Thermo scientific EN0521 BCIP/NBT Color Development Substrate Promega S3771 IPTG Thermo scientific R0392 L-Tryptophan Merck T0254 BactoTM Casamino Acids Thermo scientific 223050 Brilliant Blue G Merck B0770 Schiff’s fuchsin-sulfite reagent Merck S5133 DNA Ladder 1 kb Evrogen NL001 PageRulerTM Prestained Protein Ladder, 10 to 180 kDa Thermo scientific 26616 5-Fluoroorotic Acid (5-FOA) Thermo scientific R0811 Uracil Merck U0750 Proteinase K AppliChem A4392 Trypsin Merck T4799 Polyethylene glycol (PEG) 6000 Panreac 203-473-3 Critical commercial assays GeneJET Plasmid Miniprep Kit Thermo scientific K0502 QIAquick PCR Purification Kit Qiagen 28104 Amicon Ultra Centrifugal Filter, 3 kDa MWCO Merck UFC9003 Oligonucleotides See Table S6 for cloning primers This work N/A Recombinant DNA See Table S5 This work N/A Software and algorithms ImageJ National Institutes of Health N/A Software used for protein structure prediction AlphaFold2 https://alphafold.ebi.ac.uk Software used for protein structure alignment Dali server http://ekhidna2.biocenter.helsinki.fi/dali/ Other Immobilon -PSQ PVDF Membrane Merck ISEQ00010 Poros MS/M 10/100 column Applied Biosystems N/A iScience 28, 111793, February 21, 2025 e1 ..
Western Blot:
Activity Assay:
Colorimetric Assay:
Virus:Article Title: The HIV-1 nuclear export complex reveals the role of RNA in CRM1 cargo recognition.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal ANTI-FLAG Sigma-Aldrich F1804; RRID: AB_262044 Mouse monoclonal ANTI-GAPDH Proteintech 600004-1-lg; RRID: AB_2107436 Mouse monoclonal ANTI-α-Tubulin Sigma-Aldrich T5168; RRID: AB_477579 Rabbit Monoclonal ANTI-CRM1 Thermo Fisher Scientific 703569; RRID:AB_2784588 Mouse Monoclonal HRP-conjugated ANTI-Flag Invitrogen MA1-91878-HRP; RRID: AB_2537626 Bacterial and virus strains StellarTM Competent Cells Takara 636763 BL21(DE3) Competent New England Biolabs C2527H BL21(DE3)pLysS Invitrogen C606010 Chemicals, peptides, and recombinant proteins Q5® High-Fidelity 2X Master Mix New England Biosciences M0492S In-Fusion® Snap Assembly Master Mix Takara Bio Inc. 638947 PhusionTM High-Fidelity DNA Polymerase New England Biosciences M0530S Gibson Assembly® Master Mix New England Biosciences E2611 Fisher BioReagentsTM 2XYT Broth Fisher Scientific BP97432 SYBRTM Gold Nucleic Acid Gel Stain InvitrogenTM S11494 FreeStyleTM 293 Expression System InvitrogenTM K900001 FreeStyleTM 293 Expression Medium InvitrogenTM 12338018 Expi293TM Expression System Kit Thermo Fisher Scientific A14635 DMEM/High Glucose Cytvia SH30022.01 Fetal Bovine Serum (Adherent HEK Cells) Gibco A52568-01 Penicillin Streptomycin Gibco 15140–122 Lipofectamin 3000 Transfection Reagent Invitrogen L3000008 PolyJetTM In Vitro DNA Transfection Reagent SignaGen Laboratories SL100688 Promoter-Driven Control NanoLuc® Luciferase Vector (pNL1.1.TK) Promega N1501 Passive Lysis 5x Buffer Promega E1941 Nano-Glo® Dual-Luciferase® Reporter Assay System Promega N1610 HaltTM Protease Inhibitor Cocktail (100X) Thermo ScientificTM 78429 RosettaTM(DE3) pLysS Novagen 70956–3 Amylose Resin New England Biosciences E8021L PierceTM Bovine Serum Albumin Standard Pre-Diluted Set Thermo ScientificTM 23208 Strep-Tactin®XT 4Flow® resin IBA Lifesciences, GmbH 2-5010-025 Buffer BXT (10x) IBA Lifesciences, GmbH 2-1042-025 HisPurTM Ni-NTA Resin Thermo ScientificTM 88222 HIV-1 Rev HXB3 wild type Daugherty et al.22 N/A HIV-1 Rev HXB3 L60R Daugherty et al.22 N/A RanQ69L Booth et al.54 N/A Deposited data HIV-1 NEC Map This paper EMDB-42494 HIV-1 NEC Model This paper PDB: 8URJ (Continued on next page) Molecular Cell 85, 3108–3122.e1–e7, August 21, 2025 e1 .. Full-length, codon optimized human CRM1 was cloned into a modified pFastBac vector containing a mammalian cytomegalovirus (CMV) promoter between the BamHI and NotI restriction sites.101–103 The construct was assembled using G-blocks (IDT, US) and Gibson Assembly (Table S1; New England Biosciences, US).
Article Title: Comprehensive benchmarking of genome editing quantification methods for plant applications
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains DH5a Escherichia coli strain In-house N/A GV3101 Agrobacterium tumefaciens strain In-house N/A Chemicals, peptides, and recombinant proteins Q5 High Fidelity DNA Polymerase New England Biolabs M0491S Q5 High Fidelity PCR Master Mix New England Biolabs M0492S GoTaq Green PCR Master Mix Promega M7122 Rapid ligation buffer Promega C6711 T4 DNA ligase Promega M1801 T7 Endonuclease 1 New England Biolabs M0302S Exonuclease 1 New England Biolabs M0568S Shrimp Alkaline Phosphatase New England Biolabs M0371S Droplet generation oil for probe BioRad 1863005 ddPCR droplet reader oil BioRad 1863004 BsaI-HFv2 New England Biolabs R3733S NcoI-HF New England Biolabs R3193S BcoDI New England Biolabs R0542S BsrDI New England Biolabs R0574S BglII New England Biolabs R0144S MfeI-HF New England Biolabs R3589S RsaI New England Biolabs R0167S BsrDI New England Biolabs R0574S HpaI New England Biolabs R0105S BstNI New England Biolabs R0168S NuSieve GTGTM agarose Lonza Bioscience 50084 Critical commercial assays QX200 ddPCR Supermix for probe (no dUTP) BioRad 1863023 High Sensitivity D1000 ScreenTape Agilent 5067-5584 Deposited data Raw targeted amplicon sequencing This paper https://doi.org/10.5281/zenodo.15043050 Experimental models: Organisms/strains LAB wildtype Nicotiana benthamiana plants In-house N/A Oligonucleotides PCR primers and their sequences are reported in the Tables S4–S7. .. Sigma-Aldrich or Integrated DNA Technologies (This paper) N/A sgRNA spacer oligonucleotides and their sequences are reported in the Tables S1 and S2 Sigma-Aldrich or Integrated DNA Technologies (This paper) N/A FAM-labelled PCR primer with sequence reported in Table S6 Sigma-Aldrich (This paper) N/A Custom FAM or HEX labelled probes with sequences reported in Table S7 Integrated DNA Technologies (This paper) N/A Recombinant DNA pIZZA-BYR-SpCas9 Gong et al.56 N/A pBYR2eFa-U6-sgRNA Gong et al.56 N/A (Continued on next page) e1 iScience 28, 112350, June 20, 2025
Article Title: Tat-fimbriae ("tafi"): An unusual type of haloarchaeal surface structure depending on the twin-arginine translocation pathway.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit polyclonal anti-HAH_0240 This paper N/A Anti-6X His tag antibody Abcam Cat # ab14923; RRID: AB_443105 Goat anti-rabbit IgG conjugated with alkaline phosphatase Merck Cat # A3687; RRID: AB_258103 Bacterial and virus strains Bacterial and archaeal strains are listed in Table S5 N/A Chemicals, peptides, and recombinant proteins BamHI-HF NEB R3136S EcoRI-HF NEB R3101S KpnI-HF NEB R3142S NdeI NEB R0111S PstI NEB R0140S Q5 High-Fidelity DNA Polymerase NEB M0491S SphI NEB R0182S DNase I Thermo scientific EN0521 BCIP/NBT Color Development Substrate Promega S3771 IPTG Thermo scientific R0392 L-Tryptophan Merck T0254 BactoTM Casamino Acids Thermo scientific 223050 Brilliant Blue G Merck B0770 Schiff’s fuchsin-sulfite reagent Merck S5133 DNA Ladder 1 kb Evrogen NL001 PageRulerTM Prestained Protein Ladder, 10 to 180 kDa Thermo scientific 26616 5-Fluoroorotic Acid (5-FOA) Thermo scientific R0811 Uracil Merck U0750 Proteinase K AppliChem A4392 Trypsin Merck T4799 Polyethylene glycol (PEG) 6000 Panreac 203-473-3 Critical commercial assays GeneJET Plasmid Miniprep Kit Thermo scientific K0502 QIAquick PCR Purification Kit Qiagen 28104 Amicon Ultra Centrifugal Filter, 3 kDa MWCO Merck UFC9003 Oligonucleotides See Table S6 for cloning primers This work N/A Recombinant DNA See Table S5 This work N/A Software and algorithms ImageJ National Institutes of Health N/A Software used for protein structure prediction AlphaFold2 https://alphafold.ebi.ac.uk Software used for protein structure alignment Dali server http://ekhidna2.biocenter.helsinki.fi/dali/ Other Immobilon -PSQ PVDF Membrane Merck ISEQ00010 Poros MS/M 10/100 column Applied Biosystems N/A iScience 28, 111793, February 21, 2025 e1 ..
Article Title: Low-input RNA-seq suggests metabolic specialization underlying morphological heterogeneity in a gut commensal bacterium.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains Bacteroides thetaiotaomicron VPI-5842 DSM 2079 Phocaeicola vulgatus DSM 1447 Bacteroides uniformis DSM 6597 Campylobacter jejuni NTC1168 Provided by Cynthia Sharma CSS-5295 Salmonella enterica serovar Typhimurium DSM 24522 Clostridioides difficile 630 Provided by Franziska Faber DSM27543 E. coli S17-1 lambda pir ATCC BAA-2428 See Table S4 for strains generated in this study This paper N/A Chemicals, peptides, and recombinant proteins Anhydrotetracycline VWR J66688.MA BamHI Thermo Fischer Scientific FD0054 Cas9 nuclease New England Biolabs MO386T Cefoxitin Carl Roth 4156.2 dCTPs Invitrogen 10217016 Deepvent DNA polymerase New England Biolabs M0259L DNaseI Thermo Fischer Scientific EN0521 dNTPs New England Biolabs N0447L IPTG AppliChem A4773,0005 Lysozyme (single cell) Epicentre R1804M Lysozyme (FISH) Thermo Fischer Scientific 90082 NheI Thermo Fischer Scientific FD0974 Nuclease Free Water Ambion AM9916 Paraformaldehyde Carl Roth 0335.1 Phusion DNA polymerase Biozym 332530 L Proteinase K New England Biolabs P8107S Recombinant RNase Inhibitor Takara 2313A RNAlater Qiagen 76104 RNsseH New England Biolabs M0297L RNAseIf New England Biolabs M0243S SSC buffer (20X) Invitrogen AM9763 SuperScript IV Reverse Transcriptase Thermo Fischer Scientific 18090010 T4 DNA Polymerase New England Biolabs M0203L Terminal Transferase New England Biolabs M0315S XbaI Thermo Fisher Scientific FD0684 XhoI Thermo Fisher Scientific FD0694 10X lysis buffer Takara 635013 Critical commercial assays Agilent High Sensitivity DNA Kit Agilent 5067–4626 Ampure XP beads Beckman Coulter A63881 HCR-FISH Molecular Instruments N/A KAPA HiFi HotStart ReadyMix Roche sequencing store KK2602/SKU:7958935001 MEGAscript T7 transcription Kit (Ambion) Thermo Fisher Scientific AMB13345 Monarch RNA Cleanupt Kit NEB T2050S NEBuilder HiFi DNA Assembly Mix New England Biolabs E2621L (Continued on next page) 14 Cell Reports 44, 115844, June 24, 2025 .. Animal experiments were performed at the Helmholtz Center for Infection Research, Braunschweig, Germany, according to the National Animal Protection Law (Tierschutzgesetz [TierSchG] and Animal Experiment Regulations [Tierschutz-Versuchstierverordnung [TierSchVersV]), following the recommendations of the Federation of European Laboratory Animal Science Association (FELASA).
Staining:Article Title: The HIV-1 nuclear export complex reveals the role of RNA in CRM1 cargo recognition.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal ANTI-FLAG Sigma-Aldrich F1804; RRID: AB_262044 Mouse monoclonal ANTI-GAPDH Proteintech 600004-1-lg; RRID: AB_2107436 Mouse monoclonal ANTI-α-Tubulin Sigma-Aldrich T5168; RRID: AB_477579 Rabbit Monoclonal ANTI-CRM1 Thermo Fisher Scientific 703569; RRID:AB_2784588 Mouse Monoclonal HRP-conjugated ANTI-Flag Invitrogen MA1-91878-HRP; RRID: AB_2537626 Bacterial and virus strains StellarTM Competent Cells Takara 636763 BL21(DE3) Competent New England Biolabs C2527H BL21(DE3)pLysS Invitrogen C606010 Chemicals, peptides, and recombinant proteins Q5® High-Fidelity 2X Master Mix New England Biosciences M0492S In-Fusion® Snap Assembly Master Mix Takara Bio Inc. 638947 PhusionTM High-Fidelity DNA Polymerase New England Biosciences M0530S Gibson Assembly® Master Mix New England Biosciences E2611 Fisher BioReagentsTM 2XYT Broth Fisher Scientific BP97432 SYBRTM Gold Nucleic Acid Gel Stain InvitrogenTM S11494 FreeStyleTM 293 Expression System InvitrogenTM K900001 FreeStyleTM 293 Expression Medium InvitrogenTM 12338018 Expi293TM Expression System Kit Thermo Fisher Scientific A14635 DMEM/High Glucose Cytvia SH30022.01 Fetal Bovine Serum (Adherent HEK Cells) Gibco A52568-01 Penicillin Streptomycin Gibco 15140–122 Lipofectamin 3000 Transfection Reagent Invitrogen L3000008 PolyJetTM In Vitro DNA Transfection Reagent SignaGen Laboratories SL100688 Promoter-Driven Control NanoLuc® Luciferase Vector (pNL1.1.TK) Promega N1501 Passive Lysis 5x Buffer Promega E1941 Nano-Glo® Dual-Luciferase® Reporter Assay System Promega N1610 HaltTM Protease Inhibitor Cocktail (100X) Thermo ScientificTM 78429 RosettaTM(DE3) pLysS Novagen 70956–3 Amylose Resin New England Biosciences E8021L PierceTM Bovine Serum Albumin Standard Pre-Diluted Set Thermo ScientificTM 23208 Strep-Tactin®XT 4Flow® resin IBA Lifesciences, GmbH 2-5010-025 Buffer BXT (10x) IBA Lifesciences, GmbH 2-1042-025 HisPurTM Ni-NTA Resin Thermo ScientificTM 88222 HIV-1 Rev HXB3 wild type Daugherty et al.22 N/A HIV-1 Rev HXB3 L60R Daugherty et al.22 N/A RanQ69L Booth et al.54 N/A Deposited data HIV-1 NEC Map This paper EMDB-42494 HIV-1 NEC Model This paper PDB: 8URJ (Continued on next page) Molecular Cell 85, 3108–3122.e1–e7, August 21, 2025 e1 .. Full-length, codon optimized human CRM1 was cloned into a modified pFastBac vector containing a mammalian cytomegalovirus (CMV) promoter between the BamHI and NotI restriction sites.101–103 The construct was assembled using G-blocks (IDT, US) and Gibson Assembly (Table S1; New England Biosciences, US).
Expressing:Article Title: The HIV-1 nuclear export complex reveals the role of RNA in CRM1 cargo recognition.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal ANTI-FLAG Sigma-Aldrich F1804; RRID: AB_262044 Mouse monoclonal ANTI-GAPDH Proteintech 600004-1-lg; RRID: AB_2107436 Mouse monoclonal ANTI-α-Tubulin Sigma-Aldrich T5168; RRID: AB_477579 Rabbit Monoclonal ANTI-CRM1 Thermo Fisher Scientific 703569; RRID:AB_2784588 Mouse Monoclonal HRP-conjugated ANTI-Flag Invitrogen MA1-91878-HRP; RRID: AB_2537626 Bacterial and virus strains StellarTM Competent Cells Takara 636763 BL21(DE3) Competent New England Biolabs C2527H BL21(DE3)pLysS Invitrogen C606010 Chemicals, peptides, and recombinant proteins Q5® High-Fidelity 2X Master Mix New England Biosciences M0492S In-Fusion® Snap Assembly Master Mix Takara Bio Inc. 638947 PhusionTM High-Fidelity DNA Polymerase New England Biosciences M0530S Gibson Assembly® Master Mix New England Biosciences E2611 Fisher BioReagentsTM 2XYT Broth Fisher Scientific BP97432 SYBRTM Gold Nucleic Acid Gel Stain InvitrogenTM S11494 FreeStyleTM 293 Expression System InvitrogenTM K900001 FreeStyleTM 293 Expression Medium InvitrogenTM 12338018 Expi293TM Expression System Kit Thermo Fisher Scientific A14635 DMEM/High Glucose Cytvia SH30022.01 Fetal Bovine Serum (Adherent HEK Cells) Gibco A52568-01 Penicillin Streptomycin Gibco 15140–122 Lipofectamin 3000 Transfection Reagent Invitrogen L3000008 PolyJetTM In Vitro DNA Transfection Reagent SignaGen Laboratories SL100688 Promoter-Driven Control NanoLuc® Luciferase Vector (pNL1.1.TK) Promega N1501 Passive Lysis 5x Buffer Promega E1941 Nano-Glo® Dual-Luciferase® Reporter Assay System Promega N1610 HaltTM Protease Inhibitor Cocktail (100X) Thermo ScientificTM 78429 RosettaTM(DE3) pLysS Novagen 70956–3 Amylose Resin New England Biosciences E8021L PierceTM Bovine Serum Albumin Standard Pre-Diluted Set Thermo ScientificTM 23208 Strep-Tactin®XT 4Flow® resin IBA Lifesciences, GmbH 2-5010-025 Buffer BXT (10x) IBA Lifesciences, GmbH 2-1042-025 HisPurTM Ni-NTA Resin Thermo ScientificTM 88222 HIV-1 Rev HXB3 wild type Daugherty et al.22 N/A HIV-1 Rev HXB3 L60R Daugherty et al.22 N/A RanQ69L Booth et al.54 N/A Deposited data HIV-1 NEC Map This paper EMDB-42494 HIV-1 NEC Model This paper PDB: 8URJ (Continued on next page) Molecular Cell 85, 3108–3122.e1–e7, August 21, 2025 e1 .. Full-length, codon optimized human CRM1 was cloned into a modified pFastBac vector containing a mammalian cytomegalovirus (CMV) promoter between the BamHI and NotI restriction sites.101–103 The construct was assembled using G-blocks (IDT, US) and Gibson Assembly (Table S1; New England Biosciences, US).
Transfection:Article Title: The HIV-1 nuclear export complex reveals the role of RNA in CRM1 cargo recognition.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal ANTI-FLAG Sigma-Aldrich F1804; RRID: AB_262044 Mouse monoclonal ANTI-GAPDH Proteintech 600004-1-lg; RRID: AB_2107436 Mouse monoclonal ANTI-α-Tubulin Sigma-Aldrich T5168; RRID: AB_477579 Rabbit Monoclonal ANTI-CRM1 Thermo Fisher Scientific 703569; RRID:AB_2784588 Mouse Monoclonal HRP-conjugated ANTI-Flag Invitrogen MA1-91878-HRP; RRID: AB_2537626 Bacterial and virus strains StellarTM Competent Cells Takara 636763 BL21(DE3) Competent New England Biolabs C2527H BL21(DE3)pLysS Invitrogen C606010 Chemicals, peptides, and recombinant proteins Q5® High-Fidelity 2X Master Mix New England Biosciences M0492S In-Fusion® Snap Assembly Master Mix Takara Bio Inc. 638947 PhusionTM High-Fidelity DNA Polymerase New England Biosciences M0530S Gibson Assembly® Master Mix New England Biosciences E2611 Fisher BioReagentsTM 2XYT Broth Fisher Scientific BP97432 SYBRTM Gold Nucleic Acid Gel Stain InvitrogenTM S11494 FreeStyleTM 293 Expression System InvitrogenTM K900001 FreeStyleTM 293 Expression Medium InvitrogenTM 12338018 Expi293TM Expression System Kit Thermo Fisher Scientific A14635 DMEM/High Glucose Cytvia SH30022.01 Fetal Bovine Serum (Adherent HEK Cells) Gibco A52568-01 Penicillin Streptomycin Gibco 15140–122 Lipofectamin 3000 Transfection Reagent Invitrogen L3000008 PolyJetTM In Vitro DNA Transfection Reagent SignaGen Laboratories SL100688 Promoter-Driven Control NanoLuc® Luciferase Vector (pNL1.1.TK) Promega N1501 Passive Lysis 5x Buffer Promega E1941 Nano-Glo® Dual-Luciferase® Reporter Assay System Promega N1610 HaltTM Protease Inhibitor Cocktail (100X) Thermo ScientificTM 78429 RosettaTM(DE3) pLysS Novagen 70956–3 Amylose Resin New England Biosciences E8021L PierceTM Bovine Serum Albumin Standard Pre-Diluted Set Thermo ScientificTM 23208 Strep-Tactin®XT 4Flow® resin IBA Lifesciences, GmbH 2-5010-025 Buffer BXT (10x) IBA Lifesciences, GmbH 2-1042-025 HisPurTM Ni-NTA Resin Thermo ScientificTM 88222 HIV-1 Rev HXB3 wild type Daugherty et al.22 N/A HIV-1 Rev HXB3 L60R Daugherty et al.22 N/A RanQ69L Booth et al.54 N/A Deposited data HIV-1 NEC Map This paper EMDB-42494 HIV-1 NEC Model This paper PDB: 8URJ (Continued on next page) Molecular Cell 85, 3108–3122.e1–e7, August 21, 2025 e1 .. Full-length, codon optimized human CRM1 was cloned into a modified pFastBac vector containing a mammalian cytomegalovirus (CMV) promoter between the BamHI and NotI restriction sites.101–103 The construct was assembled using G-blocks (IDT, US) and Gibson Assembly (Table S1; New England Biosciences, US).
In Vitro:Article Title: The HIV-1 nuclear export complex reveals the role of RNA in CRM1 cargo recognition.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal ANTI-FLAG Sigma-Aldrich F1804; RRID: AB_262044 Mouse monoclonal ANTI-GAPDH Proteintech 600004-1-lg; RRID: AB_2107436 Mouse monoclonal ANTI-α-Tubulin Sigma-Aldrich T5168; RRID: AB_477579 Rabbit Monoclonal ANTI-CRM1 Thermo Fisher Scientific 703569; RRID:AB_2784588 Mouse Monoclonal HRP-conjugated ANTI-Flag Invitrogen MA1-91878-HRP; RRID: AB_2537626 Bacterial and virus strains StellarTM Competent Cells Takara 636763 BL21(DE3) Competent New England Biolabs C2527H BL21(DE3)pLysS Invitrogen C606010 Chemicals, peptides, and recombinant proteins Q5® High-Fidelity 2X Master Mix New England Biosciences M0492S In-Fusion® Snap Assembly Master Mix Takara Bio Inc. 638947 PhusionTM High-Fidelity DNA Polymerase New England Biosciences M0530S Gibson Assembly® Master Mix New England Biosciences E2611 Fisher BioReagentsTM 2XYT Broth Fisher Scientific BP97432 SYBRTM Gold Nucleic Acid Gel Stain InvitrogenTM S11494 FreeStyleTM 293 Expression System InvitrogenTM K900001 FreeStyleTM 293 Expression Medium InvitrogenTM 12338018 Expi293TM Expression System Kit Thermo Fisher Scientific A14635 DMEM/High Glucose Cytvia SH30022.01 Fetal Bovine Serum (Adherent HEK Cells) Gibco A52568-01 Penicillin Streptomycin Gibco 15140–122 Lipofectamin 3000 Transfection Reagent Invitrogen L3000008 PolyJetTM In Vitro DNA Transfection Reagent SignaGen Laboratories SL100688 Promoter-Driven Control NanoLuc® Luciferase Vector (pNL1.1.TK) Promega N1501 Passive Lysis 5x Buffer Promega E1941 Nano-Glo® Dual-Luciferase® Reporter Assay System Promega N1610 HaltTM Protease Inhibitor Cocktail (100X) Thermo ScientificTM 78429 RosettaTM(DE3) pLysS Novagen 70956–3 Amylose Resin New England Biosciences E8021L PierceTM Bovine Serum Albumin Standard Pre-Diluted Set Thermo ScientificTM 23208 Strep-Tactin®XT 4Flow® resin IBA Lifesciences, GmbH 2-5010-025 Buffer BXT (10x) IBA Lifesciences, GmbH 2-1042-025 HisPurTM Ni-NTA Resin Thermo ScientificTM 88222 HIV-1 Rev HXB3 wild type Daugherty et al.22 N/A HIV-1 Rev HXB3 L60R Daugherty et al.22 N/A RanQ69L Booth et al.54 N/A Deposited data HIV-1 NEC Map This paper EMDB-42494 HIV-1 NEC Model This paper PDB: 8URJ (Continued on next page) Molecular Cell 85, 3108–3122.e1–e7, August 21, 2025 e1 .. Full-length, codon optimized human CRM1 was cloned into a modified pFastBac vector containing a mammalian cytomegalovirus (CMV) promoter between the BamHI and NotI restriction sites.101–103 The construct was assembled using G-blocks (IDT, US) and Gibson Assembly (Table S1; New England Biosciences, US).
Control:Article Title: The HIV-1 nuclear export complex reveals the role of RNA in CRM1 cargo recognition.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal ANTI-FLAG Sigma-Aldrich F1804; RRID: AB_262044 Mouse monoclonal ANTI-GAPDH Proteintech 600004-1-lg; RRID: AB_2107436 Mouse monoclonal ANTI-α-Tubulin Sigma-Aldrich T5168; RRID: AB_477579 Rabbit Monoclonal ANTI-CRM1 Thermo Fisher Scientific 703569; RRID:AB_2784588 Mouse Monoclonal HRP-conjugated ANTI-Flag Invitrogen MA1-91878-HRP; RRID: AB_2537626 Bacterial and virus strains StellarTM Competent Cells Takara 636763 BL21(DE3) Competent New England Biolabs C2527H BL21(DE3)pLysS Invitrogen C606010 Chemicals, peptides, and recombinant proteins Q5® High-Fidelity 2X Master Mix New England Biosciences M0492S In-Fusion® Snap Assembly Master Mix Takara Bio Inc. 638947 PhusionTM High-Fidelity DNA Polymerase New England Biosciences M0530S Gibson Assembly® Master Mix New England Biosciences E2611 Fisher BioReagentsTM 2XYT Broth Fisher Scientific BP97432 SYBRTM Gold Nucleic Acid Gel Stain InvitrogenTM S11494 FreeStyleTM 293 Expression System InvitrogenTM K900001 FreeStyleTM 293 Expression Medium InvitrogenTM 12338018 Expi293TM Expression System Kit Thermo Fisher Scientific A14635 DMEM/High Glucose Cytvia SH30022.01 Fetal Bovine Serum (Adherent HEK Cells) Gibco A52568-01 Penicillin Streptomycin Gibco 15140–122 Lipofectamin 3000 Transfection Reagent Invitrogen L3000008 PolyJetTM In Vitro DNA Transfection Reagent SignaGen Laboratories SL100688 Promoter-Driven Control NanoLuc® Luciferase Vector (pNL1.1.TK) Promega N1501 Passive Lysis 5x Buffer Promega E1941 Nano-Glo® Dual-Luciferase® Reporter Assay System Promega N1610 HaltTM Protease Inhibitor Cocktail (100X) Thermo ScientificTM 78429 RosettaTM(DE3) pLysS Novagen 70956–3 Amylose Resin New England Biosciences E8021L PierceTM Bovine Serum Albumin Standard Pre-Diluted Set Thermo ScientificTM 23208 Strep-Tactin®XT 4Flow® resin IBA Lifesciences, GmbH 2-5010-025 Buffer BXT (10x) IBA Lifesciences, GmbH 2-1042-025 HisPurTM Ni-NTA Resin Thermo ScientificTM 88222 HIV-1 Rev HXB3 wild type Daugherty et al.22 N/A HIV-1 Rev HXB3 L60R Daugherty et al.22 N/A RanQ69L Booth et al.54 N/A Deposited data HIV-1 NEC Map This paper EMDB-42494 HIV-1 NEC Model This paper PDB: 8URJ (Continued on next page) Molecular Cell 85, 3108–3122.e1–e7, August 21, 2025 e1 .. Full-length, codon optimized human CRM1 was cloned into a modified pFastBac vector containing a mammalian cytomegalovirus (CMV) promoter between the BamHI and NotI restriction sites.101–103 The construct was assembled using G-blocks (IDT, US) and Gibson Assembly (Table S1; New England Biosciences, US).
Luciferase:Article Title: The HIV-1 nuclear export complex reveals the role of RNA in CRM1 cargo recognition.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal ANTI-FLAG Sigma-Aldrich F1804; RRID: AB_262044 Mouse monoclonal ANTI-GAPDH Proteintech 600004-1-lg; RRID: AB_2107436 Mouse monoclonal ANTI-α-Tubulin Sigma-Aldrich T5168; RRID: AB_477579 Rabbit Monoclonal ANTI-CRM1 Thermo Fisher Scientific 703569; RRID:AB_2784588 Mouse Monoclonal HRP-conjugated ANTI-Flag Invitrogen MA1-91878-HRP; RRID: AB_2537626 Bacterial and virus strains StellarTM Competent Cells Takara 636763 BL21(DE3) Competent New England Biolabs C2527H BL21(DE3)pLysS Invitrogen C606010 Chemicals, peptides, and recombinant proteins Q5® High-Fidelity 2X Master Mix New England Biosciences M0492S In-Fusion® Snap Assembly Master Mix Takara Bio Inc. 638947 PhusionTM High-Fidelity DNA Polymerase New England Biosciences M0530S Gibson Assembly® Master Mix New England Biosciences E2611 Fisher BioReagentsTM 2XYT Broth Fisher Scientific BP97432 SYBRTM Gold Nucleic Acid Gel Stain InvitrogenTM S11494 FreeStyleTM 293 Expression System InvitrogenTM K900001 FreeStyleTM 293 Expression Medium InvitrogenTM 12338018 Expi293TM Expression System Kit Thermo Fisher Scientific A14635 DMEM/High Glucose Cytvia SH30022.01 Fetal Bovine Serum (Adherent HEK Cells) Gibco A52568-01 Penicillin Streptomycin Gibco 15140–122 Lipofectamin 3000 Transfection Reagent Invitrogen L3000008 PolyJetTM In Vitro DNA Transfection Reagent SignaGen Laboratories SL100688 Promoter-Driven Control NanoLuc® Luciferase Vector (pNL1.1.TK) Promega N1501 Passive Lysis 5x Buffer Promega E1941 Nano-Glo® Dual-Luciferase® Reporter Assay System Promega N1610 HaltTM Protease Inhibitor Cocktail (100X) Thermo ScientificTM 78429 RosettaTM(DE3) pLysS Novagen 70956–3 Amylose Resin New England Biosciences E8021L PierceTM Bovine Serum Albumin Standard Pre-Diluted Set Thermo ScientificTM 23208 Strep-Tactin®XT 4Flow® resin IBA Lifesciences, GmbH 2-5010-025 Buffer BXT (10x) IBA Lifesciences, GmbH 2-1042-025 HisPurTM Ni-NTA Resin Thermo ScientificTM 88222 HIV-1 Rev HXB3 wild type Daugherty et al.22 N/A HIV-1 Rev HXB3 L60R Daugherty et al.22 N/A RanQ69L Booth et al.54 N/A Deposited data HIV-1 NEC Map This paper EMDB-42494 HIV-1 NEC Model This paper PDB: 8URJ (Continued on next page) Molecular Cell 85, 3108–3122.e1–e7, August 21, 2025 e1 .. Full-length, codon optimized human CRM1 was cloned into a modified pFastBac vector containing a mammalian cytomegalovirus (CMV) promoter between the BamHI and NotI restriction sites.101–103 The construct was assembled using G-blocks (IDT, US) and Gibson Assembly (Table S1; New England Biosciences, US).
Lysis:Article Title: The HIV-1 nuclear export complex reveals the role of RNA in CRM1 cargo recognition.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal ANTI-FLAG Sigma-Aldrich F1804; RRID: AB_262044 Mouse monoclonal ANTI-GAPDH Proteintech 600004-1-lg; RRID: AB_2107436 Mouse monoclonal ANTI-α-Tubulin Sigma-Aldrich T5168; RRID: AB_477579 Rabbit Monoclonal ANTI-CRM1 Thermo Fisher Scientific 703569; RRID:AB_2784588 Mouse Monoclonal HRP-conjugated ANTI-Flag Invitrogen MA1-91878-HRP; RRID: AB_2537626 Bacterial and virus strains StellarTM Competent Cells Takara 636763 BL21(DE3) Competent New England Biolabs C2527H BL21(DE3)pLysS Invitrogen C606010 Chemicals, peptides, and recombinant proteins Q5® High-Fidelity 2X Master Mix New England Biosciences M0492S In-Fusion® Snap Assembly Master Mix Takara Bio Inc. 638947 PhusionTM High-Fidelity DNA Polymerase New England Biosciences M0530S Gibson Assembly® Master Mix New England Biosciences E2611 Fisher BioReagentsTM 2XYT Broth Fisher Scientific BP97432 SYBRTM Gold Nucleic Acid Gel Stain InvitrogenTM S11494 FreeStyleTM 293 Expression System InvitrogenTM K900001 FreeStyleTM 293 Expression Medium InvitrogenTM 12338018 Expi293TM Expression System Kit Thermo Fisher Scientific A14635 DMEM/High Glucose Cytvia SH30022.01 Fetal Bovine Serum (Adherent HEK Cells) Gibco A52568-01 Penicillin Streptomycin Gibco 15140–122 Lipofectamin 3000 Transfection Reagent Invitrogen L3000008 PolyJetTM In Vitro DNA Transfection Reagent SignaGen Laboratories SL100688 Promoter-Driven Control NanoLuc® Luciferase Vector (pNL1.1.TK) Promega N1501 Passive Lysis 5x Buffer Promega E1941 Nano-Glo® Dual-Luciferase® Reporter Assay System Promega N1610 HaltTM Protease Inhibitor Cocktail (100X) Thermo ScientificTM 78429 RosettaTM(DE3) pLysS Novagen 70956–3 Amylose Resin New England Biosciences E8021L PierceTM Bovine Serum Albumin Standard Pre-Diluted Set Thermo ScientificTM 23208 Strep-Tactin®XT 4Flow® resin IBA Lifesciences, GmbH 2-5010-025 Buffer BXT (10x) IBA Lifesciences, GmbH 2-1042-025 HisPurTM Ni-NTA Resin Thermo ScientificTM 88222 HIV-1 Rev HXB3 wild type Daugherty et al.22 N/A HIV-1 Rev HXB3 L60R Daugherty et al.22 N/A RanQ69L Booth et al.54 N/A Deposited data HIV-1 NEC Map This paper EMDB-42494 HIV-1 NEC Model This paper PDB: 8URJ (Continued on next page) Molecular Cell 85, 3108–3122.e1–e7, August 21, 2025 e1 .. Full-length, codon optimized human CRM1 was cloned into a modified pFastBac vector containing a mammalian cytomegalovirus (CMV) promoter between the BamHI and NotI restriction sites.101–103 The construct was assembled using G-blocks (IDT, US) and Gibson Assembly (Table S1; New England Biosciences, US).
Article Title: Low-input RNA-seq suggests metabolic specialization underlying morphological heterogeneity in a gut commensal bacterium.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains Bacteroides thetaiotaomicron VPI-5842 DSM 2079 Phocaeicola vulgatus DSM 1447 Bacteroides uniformis DSM 6597 Campylobacter jejuni NTC1168 Provided by Cynthia Sharma CSS-5295 Salmonella enterica serovar Typhimurium DSM 24522 Clostridioides difficile 630 Provided by Franziska Faber DSM27543 E. coli S17-1 lambda pir ATCC BAA-2428 See Table S4 for strains generated in this study This paper N/A Chemicals, peptides, and recombinant proteins Anhydrotetracycline VWR J66688.MA BamHI Thermo Fischer Scientific FD0054 Cas9 nuclease New England Biolabs MO386T Cefoxitin Carl Roth 4156.2 dCTPs Invitrogen 10217016 Deepvent DNA polymerase New England Biolabs M0259L DNaseI Thermo Fischer Scientific EN0521 dNTPs New England Biolabs N0447L IPTG AppliChem A4773,0005 Lysozyme (single cell) Epicentre R1804M Lysozyme (FISH) Thermo Fischer Scientific 90082 NheI Thermo Fischer Scientific FD0974 Nuclease Free Water Ambion AM9916 Paraformaldehyde Carl Roth 0335.1 Phusion DNA polymerase Biozym 332530 L Proteinase K New England Biolabs P8107S Recombinant RNase Inhibitor Takara 2313A RNAlater Qiagen 76104 RNsseH New England Biolabs M0297L RNAseIf New England Biolabs M0243S SSC buffer (20X) Invitrogen AM9763 SuperScript IV Reverse Transcriptase Thermo Fischer Scientific 18090010 T4 DNA Polymerase New England Biolabs M0203L Terminal Transferase New England Biolabs M0315S XbaI Thermo Fisher Scientific FD0684 XhoI Thermo Fisher Scientific FD0694 10X lysis buffer Takara 635013 Critical commercial assays Agilent High Sensitivity DNA Kit Agilent 5067–4626 Ampure XP beads Beckman Coulter A63881 HCR-FISH Molecular Instruments N/A KAPA HiFi HotStart ReadyMix Roche sequencing store KK2602/SKU:7958935001 MEGAscript T7 transcription Kit (Ambion) Thermo Fisher Scientific AMB13345 Monarch RNA Cleanupt Kit NEB T2050S NEBuilder HiFi DNA Assembly Mix New England Biolabs E2621L (Continued on next page) 14 Cell Reports 44, 115844, June 24, 2025 .. Animal experiments were performed at the Helmholtz Center for Infection Research, Braunschweig, Germany, according to the National Animal Protection Law (Tierschutzgesetz [TierSchG] and Animal Experiment Regulations [Tierschutz-Versuchstierverordnung [TierSchVersV]), following the recommendations of the Federation of European Laboratory Animal Science Association (FELASA).
Reporter Assay:Article Title: The HIV-1 nuclear export complex reveals the role of RNA in CRM1 cargo recognition.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal ANTI-FLAG Sigma-Aldrich F1804; RRID: AB_262044 Mouse monoclonal ANTI-GAPDH Proteintech 600004-1-lg; RRID: AB_2107436 Mouse monoclonal ANTI-α-Tubulin Sigma-Aldrich T5168; RRID: AB_477579 Rabbit Monoclonal ANTI-CRM1 Thermo Fisher Scientific 703569; RRID:AB_2784588 Mouse Monoclonal HRP-conjugated ANTI-Flag Invitrogen MA1-91878-HRP; RRID: AB_2537626 Bacterial and virus strains StellarTM Competent Cells Takara 636763 BL21(DE3) Competent New England Biolabs C2527H BL21(DE3)pLysS Invitrogen C606010 Chemicals, peptides, and recombinant proteins Q5® High-Fidelity 2X Master Mix New England Biosciences M0492S In-Fusion® Snap Assembly Master Mix Takara Bio Inc. 638947 PhusionTM High-Fidelity DNA Polymerase New England Biosciences M0530S Gibson Assembly® Master Mix New England Biosciences E2611 Fisher BioReagentsTM 2XYT Broth Fisher Scientific BP97432 SYBRTM Gold Nucleic Acid Gel Stain InvitrogenTM S11494 FreeStyleTM 293 Expression System InvitrogenTM K900001 FreeStyleTM 293 Expression Medium InvitrogenTM 12338018 Expi293TM Expression System Kit Thermo Fisher Scientific A14635 DMEM/High Glucose Cytvia SH30022.01 Fetal Bovine Serum (Adherent HEK Cells) Gibco A52568-01 Penicillin Streptomycin Gibco 15140–122 Lipofectamin 3000 Transfection Reagent Invitrogen L3000008 PolyJetTM In Vitro DNA Transfection Reagent SignaGen Laboratories SL100688 Promoter-Driven Control NanoLuc® Luciferase Vector (pNL1.1.TK) Promega N1501 Passive Lysis 5x Buffer Promega E1941 Nano-Glo® Dual-Luciferase® Reporter Assay System Promega N1610 HaltTM Protease Inhibitor Cocktail (100X) Thermo ScientificTM 78429 RosettaTM(DE3) pLysS Novagen 70956–3 Amylose Resin New England Biosciences E8021L PierceTM Bovine Serum Albumin Standard Pre-Diluted Set Thermo ScientificTM 23208 Strep-Tactin®XT 4Flow® resin IBA Lifesciences, GmbH 2-5010-025 Buffer BXT (10x) IBA Lifesciences, GmbH 2-1042-025 HisPurTM Ni-NTA Resin Thermo ScientificTM 88222 HIV-1 Rev HXB3 wild type Daugherty et al.22 N/A HIV-1 Rev HXB3 L60R Daugherty et al.22 N/A RanQ69L Booth et al.54 N/A Deposited data HIV-1 NEC Map This paper EMDB-42494 HIV-1 NEC Model This paper PDB: 8URJ (Continued on next page) Molecular Cell 85, 3108–3122.e1–e7, August 21, 2025 e1 .. Full-length, codon optimized human CRM1 was cloned into a modified pFastBac vector containing a mammalian cytomegalovirus (CMV) promoter between the BamHI and NotI restriction sites.101–103 The construct was assembled using G-blocks (IDT, US) and Gibson Assembly (Table S1; New England Biosciences, US).
Protease Inhibitor:Article Title: The HIV-1 nuclear export complex reveals the role of RNA in CRM1 cargo recognition.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal ANTI-FLAG Sigma-Aldrich F1804; RRID: AB_262044 Mouse monoclonal ANTI-GAPDH Proteintech 600004-1-lg; RRID: AB_2107436 Mouse monoclonal ANTI-α-Tubulin Sigma-Aldrich T5168; RRID: AB_477579 Rabbit Monoclonal ANTI-CRM1 Thermo Fisher Scientific 703569; RRID:AB_2784588 Mouse Monoclonal HRP-conjugated ANTI-Flag Invitrogen MA1-91878-HRP; RRID: AB_2537626 Bacterial and virus strains StellarTM Competent Cells Takara 636763 BL21(DE3) Competent New England Biolabs C2527H BL21(DE3)pLysS Invitrogen C606010 Chemicals, peptides, and recombinant proteins Q5® High-Fidelity 2X Master Mix New England Biosciences M0492S In-Fusion® Snap Assembly Master Mix Takara Bio Inc. 638947 PhusionTM High-Fidelity DNA Polymerase New England Biosciences M0530S Gibson Assembly® Master Mix New England Biosciences E2611 Fisher BioReagentsTM 2XYT Broth Fisher Scientific BP97432 SYBRTM Gold Nucleic Acid Gel Stain InvitrogenTM S11494 FreeStyleTM 293 Expression System InvitrogenTM K900001 FreeStyleTM 293 Expression Medium InvitrogenTM 12338018 Expi293TM Expression System Kit Thermo Fisher Scientific A14635 DMEM/High Glucose Cytvia SH30022.01 Fetal Bovine Serum (Adherent HEK Cells) Gibco A52568-01 Penicillin Streptomycin Gibco 15140–122 Lipofectamin 3000 Transfection Reagent Invitrogen L3000008 PolyJetTM In Vitro DNA Transfection Reagent SignaGen Laboratories SL100688 Promoter-Driven Control NanoLuc® Luciferase Vector (pNL1.1.TK) Promega N1501 Passive Lysis 5x Buffer Promega E1941 Nano-Glo® Dual-Luciferase® Reporter Assay System Promega N1610 HaltTM Protease Inhibitor Cocktail (100X) Thermo ScientificTM 78429 RosettaTM(DE3) pLysS Novagen 70956–3 Amylose Resin New England Biosciences E8021L PierceTM Bovine Serum Albumin Standard Pre-Diluted Set Thermo ScientificTM 23208 Strep-Tactin®XT 4Flow® resin IBA Lifesciences, GmbH 2-5010-025 Buffer BXT (10x) IBA Lifesciences, GmbH 2-1042-025 HisPurTM Ni-NTA Resin Thermo ScientificTM 88222 HIV-1 Rev HXB3 wild type Daugherty et al.22 N/A HIV-1 Rev HXB3 L60R Daugherty et al.22 N/A RanQ69L Booth et al.54 N/A Deposited data HIV-1 NEC Map This paper EMDB-42494 HIV-1 NEC Model This paper PDB: 8URJ (Continued on next page) Molecular Cell 85, 3108–3122.e1–e7, August 21, 2025 e1 .. Full-length, codon optimized human CRM1 was cloned into a modified pFastBac vector containing a mammalian cytomegalovirus (CMV) promoter between the BamHI and NotI restriction sites.101–103 The construct was assembled using G-blocks (IDT, US) and Gibson Assembly (Table S1; New England Biosciences, US).
Polymerase Chain Reaction:Article Title: Comprehensive benchmarking of genome editing quantification methods for plant applications
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains DH5a Escherichia coli strain In-house N/A GV3101 Agrobacterium tumefaciens strain In-house N/A Chemicals, peptides, and recombinant proteins Q5 High Fidelity DNA Polymerase New England Biolabs M0491S Q5 High Fidelity PCR Master Mix New England Biolabs M0492S GoTaq Green PCR Master Mix Promega M7122 Rapid ligation buffer Promega C6711 T4 DNA ligase Promega M1801 T7 Endonuclease 1 New England Biolabs M0302S Exonuclease 1 New England Biolabs M0568S Shrimp Alkaline Phosphatase New England Biolabs M0371S Droplet generation oil for probe BioRad 1863005 ddPCR droplet reader oil BioRad 1863004 BsaI-HFv2 New England Biolabs R3733S NcoI-HF New England Biolabs R3193S BcoDI New England Biolabs R0542S BsrDI New England Biolabs R0574S BglII New England Biolabs R0144S MfeI-HF New England Biolabs R3589S RsaI New England Biolabs R0167S BsrDI New England Biolabs R0574S HpaI New England Biolabs R0105S BstNI New England Biolabs R0168S NuSieve GTGTM agarose Lonza Bioscience 50084 Critical commercial assays QX200 ddPCR Supermix for probe (no dUTP) BioRad 1863023 High Sensitivity D1000 ScreenTape Agilent 5067-5584 Deposited data Raw targeted amplicon sequencing This paper https://doi.org/10.5281/zenodo.15043050 Experimental models: Organisms/strains LAB wildtype Nicotiana benthamiana plants In-house N/A Oligonucleotides PCR primers and their sequences are reported in the Tables S4–S7. .. Sigma-Aldrich or Integrated DNA Technologies (This paper) N/A sgRNA spacer oligonucleotides and their sequences are reported in the Tables S1 and S2 Sigma-Aldrich or Integrated DNA Technologies (This paper) N/A FAM-labelled PCR primer with sequence reported in Table S6 Sigma-Aldrich (This paper) N/A Custom FAM or HEX labelled probes with sequences reported in Table S7 Integrated DNA Technologies (This paper) N/A Recombinant DNA pIZZA-BYR-SpCas9 Gong et al.56 N/A pBYR2eFa-U6-sgRNA Gong et al.56 N/A (Continued on next page) e1 iScience 28, 112350, June 20, 2025
Article Title: Tat-fimbriae ("tafi"): An unusual type of haloarchaeal surface structure depending on the twin-arginine translocation pathway.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit polyclonal anti-HAH_0240 This paper N/A Anti-6X His tag antibody Abcam Cat # ab14923; RRID: AB_443105 Goat anti-rabbit IgG conjugated with alkaline phosphatase Merck Cat # A3687; RRID: AB_258103 Bacterial and virus strains Bacterial and archaeal strains are listed in Table S5 N/A Chemicals, peptides, and recombinant proteins BamHI-HF NEB R3136S EcoRI-HF NEB R3101S KpnI-HF NEB R3142S NdeI NEB R0111S PstI NEB R0140S Q5 High-Fidelity DNA Polymerase NEB M0491S SphI NEB R0182S DNase I Thermo scientific EN0521 BCIP/NBT Color Development Substrate Promega S3771 IPTG Thermo scientific R0392 L-Tryptophan Merck T0254 BactoTM Casamino Acids Thermo scientific 223050 Brilliant Blue G Merck B0770 Schiff’s fuchsin-sulfite reagent Merck S5133 DNA Ladder 1 kb Evrogen NL001 PageRulerTM Prestained Protein Ladder, 10 to 180 kDa Thermo scientific 26616 5-Fluoroorotic Acid (5-FOA) Thermo scientific R0811 Uracil Merck U0750 Proteinase K AppliChem A4392 Trypsin Merck T4799 Polyethylene glycol (PEG) 6000 Panreac 203-473-3 Critical commercial assays GeneJET Plasmid Miniprep Kit Thermo scientific K0502 QIAquick PCR Purification Kit Qiagen 28104 Amicon Ultra Centrifugal Filter, 3 kDa MWCO Merck UFC9003 Oligonucleotides See Table S6 for cloning primers This work N/A Recombinant DNA See Table S5 This work N/A Software and algorithms ImageJ National Institutes of Health N/A Software used for protein structure prediction AlphaFold2 https://alphafold.ebi.ac.uk Software used for protein structure alignment Dali server http://ekhidna2.biocenter.helsinki.fi/dali/ Other Immobilon -PSQ PVDF Membrane Merck ISEQ00010 Poros MS/M 10/100 column Applied Biosystems N/A iScience 28, 111793, February 21, 2025 e1 ..
Ligation:Article Title: Comprehensive benchmarking of genome editing quantification methods for plant applications
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains DH5a Escherichia coli strain In-house N/A GV3101 Agrobacterium tumefaciens strain In-house N/A Chemicals, peptides, and recombinant proteins Q5 High Fidelity DNA Polymerase New England Biolabs M0491S Q5 High Fidelity PCR Master Mix New England Biolabs M0492S GoTaq Green PCR Master Mix Promega M7122 Rapid ligation buffer Promega C6711 T4 DNA ligase Promega M1801 T7 Endonuclease 1 New England Biolabs M0302S Exonuclease 1 New England Biolabs M0568S Shrimp Alkaline Phosphatase New England Biolabs M0371S Droplet generation oil for probe BioRad 1863005 ddPCR droplet reader oil BioRad 1863004 BsaI-HFv2 New England Biolabs R3733S NcoI-HF New England Biolabs R3193S BcoDI New England Biolabs R0542S BsrDI New England Biolabs R0574S BglII New England Biolabs R0144S MfeI-HF New England Biolabs R3589S RsaI New England Biolabs R0167S BsrDI New England Biolabs R0574S HpaI New England Biolabs R0105S BstNI New England Biolabs R0168S NuSieve GTGTM agarose Lonza Bioscience 50084 Critical commercial assays QX200 ddPCR Supermix for probe (no dUTP) BioRad 1863023 High Sensitivity D1000 ScreenTape Agilent 5067-5584 Deposited data Raw targeted amplicon sequencing This paper https://doi.org/10.5281/zenodo.15043050 Experimental models: Organisms/strains LAB wildtype Nicotiana benthamiana plants In-house N/A Oligonucleotides PCR primers and their sequences are reported in the Tables S4–S7. .. Sigma-Aldrich or Integrated DNA Technologies (This paper) N/A sgRNA spacer oligonucleotides and their sequences are reported in the Tables S1 and S2 Sigma-Aldrich or Integrated DNA Technologies (This paper) N/A FAM-labelled PCR primer with sequence reported in Table S6 Sigma-Aldrich (This paper) N/A Custom FAM or HEX labelled probes with sequences reported in Table S7 Integrated DNA Technologies (This paper) N/A Recombinant DNA pIZZA-BYR-SpCas9 Gong et al.56 N/A pBYR2eFa-U6-sgRNA Gong et al.56 N/A (Continued on next page) e1 iScience 28, 112350, June 20, 2025
Amplification:Article Title: Comprehensive benchmarking of genome editing quantification methods for plant applications
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains DH5a Escherichia coli strain In-house N/A GV3101 Agrobacterium tumefaciens strain In-house N/A Chemicals, peptides, and recombinant proteins Q5 High Fidelity DNA Polymerase New England Biolabs M0491S Q5 High Fidelity PCR Master Mix New England Biolabs M0492S GoTaq Green PCR Master Mix Promega M7122 Rapid ligation buffer Promega C6711 T4 DNA ligase Promega M1801 T7 Endonuclease 1 New England Biolabs M0302S Exonuclease 1 New England Biolabs M0568S Shrimp Alkaline Phosphatase New England Biolabs M0371S Droplet generation oil for probe BioRad 1863005 ddPCR droplet reader oil BioRad 1863004 BsaI-HFv2 New England Biolabs R3733S NcoI-HF New England Biolabs R3193S BcoDI New England Biolabs R0542S BsrDI New England Biolabs R0574S BglII New England Biolabs R0144S MfeI-HF New England Biolabs R3589S RsaI New England Biolabs R0167S BsrDI New England Biolabs R0574S HpaI New England Biolabs R0105S BstNI New England Biolabs R0168S NuSieve GTGTM agarose Lonza Bioscience 50084 Critical commercial assays QX200 ddPCR Supermix for probe (no dUTP) BioRad 1863023 High Sensitivity D1000 ScreenTape Agilent 5067-5584 Deposited data Raw targeted amplicon sequencing This paper https://doi.org/10.5281/zenodo.15043050 Experimental models: Organisms/strains LAB wildtype Nicotiana benthamiana plants In-house N/A Oligonucleotides PCR primers and their sequences are reported in the Tables S4–S7. .. Sigma-Aldrich or Integrated DNA Technologies (This paper) N/A sgRNA spacer oligonucleotides and their sequences are reported in the Tables S1 and S2 Sigma-Aldrich or Integrated DNA Technologies (This paper) N/A FAM-labelled PCR primer with sequence reported in Table S6 Sigma-Aldrich (This paper) N/A Custom FAM or HEX labelled probes with sequences reported in Table S7 Integrated DNA Technologies (This paper) N/A Recombinant DNA pIZZA-BYR-SpCas9 Gong et al.56 N/A pBYR2eFa-U6-sgRNA Gong et al.56 N/A (Continued on next page) e1 iScience 28, 112350, June 20, 2025
Sequencing:Article Title: Comprehensive benchmarking of genome editing quantification methods for plant applications
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains DH5a Escherichia coli strain In-house N/A GV3101 Agrobacterium tumefaciens strain In-house N/A Chemicals, peptides, and recombinant proteins Q5 High Fidelity DNA Polymerase New England Biolabs M0491S Q5 High Fidelity PCR Master Mix New England Biolabs M0492S GoTaq Green PCR Master Mix Promega M7122 Rapid ligation buffer Promega C6711 T4 DNA ligase Promega M1801 T7 Endonuclease 1 New England Biolabs M0302S Exonuclease 1 New England Biolabs M0568S Shrimp Alkaline Phosphatase New England Biolabs M0371S Droplet generation oil for probe BioRad 1863005 ddPCR droplet reader oil BioRad 1863004 BsaI-HFv2 New England Biolabs R3733S NcoI-HF New England Biolabs R3193S BcoDI New England Biolabs R0542S BsrDI New England Biolabs R0574S BglII New England Biolabs R0144S MfeI-HF New England Biolabs R3589S RsaI New England Biolabs R0167S BsrDI New England Biolabs R0574S HpaI New England Biolabs R0105S BstNI New England Biolabs R0168S NuSieve GTGTM agarose Lonza Bioscience 50084 Critical commercial assays QX200 ddPCR Supermix for probe (no dUTP) BioRad 1863023 High Sensitivity D1000 ScreenTape Agilent 5067-5584 Deposited data Raw targeted amplicon sequencing This paper https://doi.org/10.5281/zenodo.15043050 Experimental models: Organisms/strains LAB wildtype Nicotiana benthamiana plants In-house N/A Oligonucleotides PCR primers and their sequences are reported in the Tables S4–S7. .. Sigma-Aldrich or Integrated DNA Technologies (This paper) N/A sgRNA spacer oligonucleotides and their sequences are reported in the Tables S1 and S2 Sigma-Aldrich or Integrated DNA Technologies (This paper) N/A FAM-labelled PCR primer with sequence reported in Table S6 Sigma-Aldrich (This paper) N/A Custom FAM or HEX labelled probes with sequences reported in Table S7 Integrated DNA Technologies (This paper) N/A Recombinant DNA pIZZA-BYR-SpCas9 Gong et al.56 N/A pBYR2eFa-U6-sgRNA Gong et al.56 N/A (Continued on next page) e1 iScience 28, 112350, June 20, 2025
Incubation:
Article Title: Supporting Information for DOT1L-mediated RAP80 methylation promotes BRCA1 recruitment to elicit DNA repair
Article Snippet: .. Peptides (H3K79, both methylated and unmodified as indicated in the figure) were incubated with streptavidin agarose slurry (New England Biolabs, Ipswich, MA, USA) in binding buffer (50 mM Tris–HCl pH 7.4, 150 mM NaCl, 10% Glycerol, 1 mM EDTA, 2 mM MgCl2, 0.5% NP-40) at 4°C overnight. .. Peptides (H3K79, both methylated and unmodified as indicated in the figure) were incubated with streptavidin agarose slurry (New England Biolabs, Ipswich, MA, USA) in binding buffer (50 mM Tris–HCl pH 7.4, 150 mM NaCl, 10% Glycerol, 1 mM EDTA, 2 mM MgCl2, 0.5% NP-40) at 4°C overnight.
Methylation:Article Title: Supporting Information for DOT1L-mediated RAP80 methylation promotes BRCA1 recruitment to elicit DNA repair
Article Snippet: .. Peptides (H3K79, both methylated and unmodified as indicated in the figure) were incubated with streptavidin agarose slurry (New England Biolabs, Ipswich, MA, USA) in binding buffer (50 mM Tris–HCl pH 7.4, 150 mM NaCl, 10% Glycerol, 1 mM EDTA, 2 mM MgCl2, 0.5% NP-40) at 4°C overnight. .. Peptides (H3K79, both methylated and unmodified as indicated in the figure) were incubated with streptavidin agarose slurry (New England Biolabs, Ipswich, MA, USA) in binding buffer (50 mM Tris–HCl pH 7.4, 150 mM NaCl, 10% Glycerol, 1 mM EDTA, 2 mM MgCl2, 0.5% NP-40) at 4°C overnight.
Binding Assay:Article Title: Supporting Information for DOT1L-mediated RAP80 methylation promotes BRCA1 recruitment to elicit DNA repair
Article Snippet: .. Peptides (H3K79, both methylated and unmodified as indicated in the figure) were incubated with streptavidin agarose slurry (New England Biolabs, Ipswich, MA, USA) in binding buffer (50 mM Tris–HCl pH 7.4, 150 mM NaCl, 10% Glycerol, 1 mM EDTA, 2 mM MgCl2, 0.5% NP-40) at 4°C overnight. .. Peptides (H3K79, both methylated and unmodified as indicated in the figure) were incubated with streptavidin agarose slurry (New England Biolabs, Ipswich, MA, USA) in binding buffer (50 mM Tris–HCl pH 7.4, 150 mM NaCl, 10% Glycerol, 1 mM EDTA, 2 mM MgCl2, 0.5% NP-40) at 4°C overnight.
Plasmid Preparation:Article Title: Tat-fimbriae ("tafi"): An unusual type of haloarchaeal surface structure depending on the twin-arginine translocation pathway.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit polyclonal anti-HAH_0240 This paper N/A Anti-6X His tag antibody Abcam Cat # ab14923; RRID: AB_443105 Goat anti-rabbit IgG conjugated with alkaline phosphatase Merck Cat # A3687; RRID: AB_258103 Bacterial and virus strains Bacterial and archaeal strains are listed in Table S5 N/A Chemicals, peptides, and recombinant proteins BamHI-HF NEB R3136S EcoRI-HF NEB R3101S KpnI-HF NEB R3142S NdeI NEB R0111S PstI NEB R0140S Q5 High-Fidelity DNA Polymerase NEB M0491S SphI NEB R0182S DNase I Thermo scientific EN0521 BCIP/NBT Color Development Substrate Promega S3771 IPTG Thermo scientific R0392 L-Tryptophan Merck T0254 BactoTM Casamino Acids Thermo scientific 223050 Brilliant Blue G Merck B0770 Schiff’s fuchsin-sulfite reagent Merck S5133 DNA Ladder 1 kb Evrogen NL001 PageRulerTM Prestained Protein Ladder, 10 to 180 kDa Thermo scientific 26616 5-Fluoroorotic Acid (5-FOA) Thermo scientific R0811 Uracil Merck U0750 Proteinase K AppliChem A4392 Trypsin Merck T4799 Polyethylene glycol (PEG) 6000 Panreac 203-473-3 Critical commercial assays GeneJET Plasmid Miniprep Kit Thermo scientific K0502 QIAquick PCR Purification Kit Qiagen 28104 Amicon Ultra Centrifugal Filter, 3 kDa MWCO Merck UFC9003 Oligonucleotides See Table S6 for cloning primers This work N/A Recombinant DNA See Table S5 This work N/A Software and algorithms ImageJ National Institutes of Health N/A Software used for protein structure prediction AlphaFold2 https://alphafold.ebi.ac.uk Software used for protein structure alignment Dali server http://ekhidna2.biocenter.helsinki.fi/dali/ Other Immobilon -PSQ PVDF Membrane Merck ISEQ00010 Poros MS/M 10/100 column Applied Biosystems N/A iScience 28, 111793, February 21, 2025 e1 ..
Cloning:Article Title: Tat-fimbriae ("tafi"): An unusual type of haloarchaeal surface structure depending on the twin-arginine translocation pathway.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit polyclonal anti-HAH_0240 This paper N/A Anti-6X His tag antibody Abcam Cat # ab14923; RRID: AB_443105 Goat anti-rabbit IgG conjugated with alkaline phosphatase Merck Cat # A3687; RRID: AB_258103 Bacterial and virus strains Bacterial and archaeal strains are listed in Table S5 N/A Chemicals, peptides, and recombinant proteins BamHI-HF NEB R3136S EcoRI-HF NEB R3101S KpnI-HF NEB R3142S NdeI NEB R0111S PstI NEB R0140S Q5 High-Fidelity DNA Polymerase NEB M0491S SphI NEB R0182S DNase I Thermo scientific EN0521 BCIP/NBT Color Development Substrate Promega S3771 IPTG Thermo scientific R0392 L-Tryptophan Merck T0254 BactoTM Casamino Acids Thermo scientific 223050 Brilliant Blue G Merck B0770 Schiff’s fuchsin-sulfite reagent Merck S5133 DNA Ladder 1 kb Evrogen NL001 PageRulerTM Prestained Protein Ladder, 10 to 180 kDa Thermo scientific 26616 5-Fluoroorotic Acid (5-FOA) Thermo scientific R0811 Uracil Merck U0750 Proteinase K AppliChem A4392 Trypsin Merck T4799 Polyethylene glycol (PEG) 6000 Panreac 203-473-3 Critical commercial assays GeneJET Plasmid Miniprep Kit Thermo scientific K0502 QIAquick PCR Purification Kit Qiagen 28104 Amicon Ultra Centrifugal Filter, 3 kDa MWCO Merck UFC9003 Oligonucleotides See Table S6 for cloning primers This work N/A Recombinant DNA See Table S5 This work N/A Software and algorithms ImageJ National Institutes of Health N/A Software used for protein structure prediction AlphaFold2 https://alphafold.ebi.ac.uk Software used for protein structure alignment Dali server http://ekhidna2.biocenter.helsinki.fi/dali/ Other Immobilon -PSQ PVDF Membrane Merck ISEQ00010 Poros MS/M 10/100 column Applied Biosystems N/A iScience 28, 111793, February 21, 2025 e1 ..
Software:Article Title: Tat-fimbriae ("tafi"): An unusual type of haloarchaeal surface structure depending on the twin-arginine translocation pathway.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit polyclonal anti-HAH_0240 This paper N/A Anti-6X His tag antibody Abcam Cat # ab14923; RRID: AB_443105 Goat anti-rabbit IgG conjugated with alkaline phosphatase Merck Cat # A3687; RRID: AB_258103 Bacterial and virus strains Bacterial and archaeal strains are listed in Table S5 N/A Chemicals, peptides, and recombinant proteins BamHI-HF NEB R3136S EcoRI-HF NEB R3101S KpnI-HF NEB R3142S NdeI NEB R0111S PstI NEB R0140S Q5 High-Fidelity DNA Polymerase NEB M0491S SphI NEB R0182S DNase I Thermo scientific EN0521 BCIP/NBT Color Development Substrate Promega S3771 IPTG Thermo scientific R0392 L-Tryptophan Merck T0254 BactoTM Casamino Acids Thermo scientific 223050 Brilliant Blue G Merck B0770 Schiff’s fuchsin-sulfite reagent Merck S5133 DNA Ladder 1 kb Evrogen NL001 PageRulerTM Prestained Protein Ladder, 10 to 180 kDa Thermo scientific 26616 5-Fluoroorotic Acid (5-FOA) Thermo scientific R0811 Uracil Merck U0750 Proteinase K AppliChem A4392 Trypsin Merck T4799 Polyethylene glycol (PEG) 6000 Panreac 203-473-3 Critical commercial assays GeneJET Plasmid Miniprep Kit Thermo scientific K0502 QIAquick PCR Purification Kit Qiagen 28104 Amicon Ultra Centrifugal Filter, 3 kDa MWCO Merck UFC9003 Oligonucleotides See Table S6 for cloning primers This work N/A Recombinant DNA See Table S5 This work N/A Software and algorithms ImageJ National Institutes of Health N/A Software used for protein structure prediction AlphaFold2 https://alphafold.ebi.ac.uk Software used for protein structure alignment Dali server http://ekhidna2.biocenter.helsinki.fi/dali/ Other Immobilon -PSQ PVDF Membrane Merck ISEQ00010 Poros MS/M 10/100 column Applied Biosystems N/A iScience 28, 111793, February 21, 2025 e1 ..
Membrane:Article Title: Tat-fimbriae ("tafi"): An unusual type of haloarchaeal surface structure depending on the twin-arginine translocation pathway.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit polyclonal anti-HAH_0240 This paper N/A Anti-6X His tag antibody Abcam Cat # ab14923; RRID: AB_443105 Goat anti-rabbit IgG conjugated with alkaline phosphatase Merck Cat # A3687; RRID: AB_258103 Bacterial and virus strains Bacterial and archaeal strains are listed in Table S5 N/A Chemicals, peptides, and recombinant proteins BamHI-HF NEB R3136S EcoRI-HF NEB R3101S KpnI-HF NEB R3142S NdeI NEB R0111S PstI NEB R0140S Q5 High-Fidelity DNA Polymerase NEB M0491S SphI NEB R0182S DNase I Thermo scientific EN0521 BCIP/NBT Color Development Substrate Promega S3771 IPTG Thermo scientific R0392 L-Tryptophan Merck T0254 BactoTM Casamino Acids Thermo scientific 223050 Brilliant Blue G Merck B0770 Schiff’s fuchsin-sulfite reagent Merck S5133 DNA Ladder 1 kb Evrogen NL001 PageRulerTM Prestained Protein Ladder, 10 to 180 kDa Thermo scientific 26616 5-Fluoroorotic Acid (5-FOA) Thermo scientific R0811 Uracil Merck U0750 Proteinase K AppliChem A4392 Trypsin Merck T4799 Polyethylene glycol (PEG) 6000 Panreac 203-473-3 Critical commercial assays GeneJET Plasmid Miniprep Kit Thermo scientific K0502 QIAquick PCR Purification Kit Qiagen 28104 Amicon Ultra Centrifugal Filter, 3 kDa MWCO Merck UFC9003 Oligonucleotides See Table S6 for cloning primers This work N/A Recombinant DNA See Table S5 This work N/A Software and algorithms ImageJ National Institutes of Health N/A Software used for protein structure prediction AlphaFold2 https://alphafold.ebi.ac.uk Software used for protein structure alignment Dali server http://ekhidna2.biocenter.helsinki.fi/dali/ Other Immobilon -PSQ PVDF Membrane Merck ISEQ00010 Poros MS/M 10/100 column Applied Biosystems N/A iScience 28, 111793, February 21, 2025 e1 ..
Generated:Article Title: Low-input RNA-seq suggests metabolic specialization underlying morphological heterogeneity in a gut commensal bacterium.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains Bacteroides thetaiotaomicron VPI-5842 DSM 2079 Phocaeicola vulgatus DSM 1447 Bacteroides uniformis DSM 6597 Campylobacter jejuni NTC1168 Provided by Cynthia Sharma CSS-5295 Salmonella enterica serovar Typhimurium DSM 24522 Clostridioides difficile 630 Provided by Franziska Faber DSM27543 E. coli S17-1 lambda pir ATCC BAA-2428 See Table S4 for strains generated in this study This paper N/A Chemicals, peptides, and recombinant proteins Anhydrotetracycline VWR J66688.MA BamHI Thermo Fischer Scientific FD0054 Cas9 nuclease New England Biolabs MO386T Cefoxitin Carl Roth 4156.2 dCTPs Invitrogen 10217016 Deepvent DNA polymerase New England Biolabs M0259L DNaseI Thermo Fischer Scientific EN0521 dNTPs New England Biolabs N0447L IPTG AppliChem A4773,0005 Lysozyme (single cell) Epicentre R1804M Lysozyme (FISH) Thermo Fischer Scientific 90082 NheI Thermo Fischer Scientific FD0974 Nuclease Free Water Ambion AM9916 Paraformaldehyde Carl Roth 0335.1 Phusion DNA polymerase Biozym 332530 L Proteinase K New England Biolabs P8107S Recombinant RNase Inhibitor Takara 2313A RNAlater Qiagen 76104 RNsseH New England Biolabs M0297L RNAseIf New England Biolabs M0243S SSC buffer (20X) Invitrogen AM9763 SuperScript IV Reverse Transcriptase Thermo Fischer Scientific 18090010 T4 DNA Polymerase New England Biolabs M0203L Terminal Transferase New England Biolabs M0315S XbaI Thermo Fisher Scientific FD0684 XhoI Thermo Fisher Scientific FD0694 10X lysis buffer Takara 635013 Critical commercial assays Agilent High Sensitivity DNA Kit Agilent 5067–4626 Ampure XP beads Beckman Coulter A63881 HCR-FISH Molecular Instruments N/A KAPA HiFi HotStart ReadyMix Roche sequencing store KK2602/SKU:7958935001 MEGAscript T7 transcription Kit (Ambion) Thermo Fisher Scientific AMB13345 Monarch RNA Cleanupt Kit NEB T2050S NEBuilder HiFi DNA Assembly Mix New England Biolabs E2621L (Continued on next page) 14 Cell Reports 44, 115844, June 24, 2025 .. Animal experiments were performed at the Helmholtz Center for Infection Research, Braunschweig, Germany, according to the National Animal Protection Law (Tierschutzgesetz [TierSchG] and Animal Experiment Regulations [Tierschutz-Versuchstierverordnung [TierSchVersV]), following the recommendations of the Federation of European Laboratory Animal Science Association (FELASA).
Single Cell:Article Title: Low-input RNA-seq suggests metabolic specialization underlying morphological heterogeneity in a gut commensal bacterium.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains Bacteroides thetaiotaomicron VPI-5842 DSM 2079 Phocaeicola vulgatus DSM 1447 Bacteroides uniformis DSM 6597 Campylobacter jejuni NTC1168 Provided by Cynthia Sharma CSS-5295 Salmonella enterica serovar Typhimurium DSM 24522 Clostridioides difficile 630 Provided by Franziska Faber DSM27543 E. coli S17-1 lambda pir ATCC BAA-2428 See Table S4 for strains generated in this study This paper N/A Chemicals, peptides, and recombinant proteins Anhydrotetracycline VWR J66688.MA BamHI Thermo Fischer Scientific FD0054 Cas9 nuclease New England Biolabs MO386T Cefoxitin Carl Roth 4156.2 dCTPs Invitrogen 10217016 Deepvent DNA polymerase New England Biolabs M0259L DNaseI Thermo Fischer Scientific EN0521 dNTPs New England Biolabs N0447L IPTG AppliChem A4773,0005 Lysozyme (single cell) Epicentre R1804M Lysozyme (FISH) Thermo Fischer Scientific 90082 NheI Thermo Fischer Scientific FD0974 Nuclease Free Water Ambion AM9916 Paraformaldehyde Carl Roth 0335.1 Phusion DNA polymerase Biozym 332530 L Proteinase K New England Biolabs P8107S Recombinant RNase Inhibitor Takara 2313A RNAlater Qiagen 76104 RNsseH New England Biolabs M0297L RNAseIf New England Biolabs M0243S SSC buffer (20X) Invitrogen AM9763 SuperScript IV Reverse Transcriptase Thermo Fischer Scientific 18090010 T4 DNA Polymerase New England Biolabs M0203L Terminal Transferase New England Biolabs M0315S XbaI Thermo Fisher Scientific FD0684 XhoI Thermo Fisher Scientific FD0694 10X lysis buffer Takara 635013 Critical commercial assays Agilent High Sensitivity DNA Kit Agilent 5067–4626 Ampure XP beads Beckman Coulter A63881 HCR-FISH Molecular Instruments N/A KAPA HiFi HotStart ReadyMix Roche sequencing store KK2602/SKU:7958935001 MEGAscript T7 transcription Kit (Ambion) Thermo Fisher Scientific AMB13345 Monarch RNA Cleanupt Kit NEB T2050S NEBuilder HiFi DNA Assembly Mix New England Biolabs E2621L (Continued on next page) 14 Cell Reports 44, 115844, June 24, 2025 .. Animal experiments were performed at the Helmholtz Center for Infection Research, Braunschweig, Germany, according to the National Animal Protection Law (Tierschutzgesetz [TierSchG] and Animal Experiment Regulations [Tierschutz-Versuchstierverordnung [TierSchVersV]), following the recommendations of the Federation of European Laboratory Animal Science Association (FELASA).
Fluorescence In Situ Hybridization:Article Title: Low-input RNA-seq suggests metabolic specialization underlying morphological heterogeneity in a gut commensal bacterium.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains Bacteroides thetaiotaomicron VPI-5842 DSM 2079 Phocaeicola vulgatus DSM 1447 Bacteroides uniformis DSM 6597 Campylobacter jejuni NTC1168 Provided by Cynthia Sharma CSS-5295 Salmonella enterica serovar Typhimurium DSM 24522 Clostridioides difficile 630 Provided by Franziska Faber DSM27543 E. coli S17-1 lambda pir ATCC BAA-2428 See Table S4 for strains generated in this study This paper N/A Chemicals, peptides, and recombinant proteins Anhydrotetracycline VWR J66688.MA BamHI Thermo Fischer Scientific FD0054 Cas9 nuclease New England Biolabs MO386T Cefoxitin Carl Roth 4156.2 dCTPs Invitrogen 10217016 Deepvent DNA polymerase New England Biolabs M0259L DNaseI Thermo Fischer Scientific EN0521 dNTPs New England Biolabs N0447L IPTG AppliChem A4773,0005 Lysozyme (single cell) Epicentre R1804M Lysozyme (FISH) Thermo Fischer Scientific 90082 NheI Thermo Fischer Scientific FD0974 Nuclease Free Water Ambion AM9916 Paraformaldehyde Carl Roth 0335.1 Phusion DNA polymerase Biozym 332530 L Proteinase K New England Biolabs P8107S Recombinant RNase Inhibitor Takara 2313A RNAlater Qiagen 76104 RNsseH New England Biolabs M0297L RNAseIf New England Biolabs M0243S SSC buffer (20X) Invitrogen AM9763 SuperScript IV Reverse Transcriptase Thermo Fischer Scientific 18090010 T4 DNA Polymerase New England Biolabs M0203L Terminal Transferase New England Biolabs M0315S XbaI Thermo Fisher Scientific FD0684 XhoI Thermo Fisher Scientific FD0694 10X lysis buffer Takara 635013 Critical commercial assays Agilent High Sensitivity DNA Kit Agilent 5067–4626 Ampure XP beads Beckman Coulter A63881 HCR-FISH Molecular Instruments N/A KAPA HiFi HotStart ReadyMix Roche sequencing store KK2602/SKU:7958935001 MEGAscript T7 transcription Kit (Ambion) Thermo Fisher Scientific AMB13345 Monarch RNA Cleanupt Kit NEB T2050S NEBuilder HiFi DNA Assembly Mix New England Biolabs E2621L (Continued on next page) 14 Cell Reports 44, 115844, June 24, 2025 .. Animal experiments were performed at the Helmholtz Center for Infection Research, Braunschweig, Germany, according to the National Animal Protection Law (Tierschutzgesetz [TierSchG] and Animal Experiment Regulations [Tierschutz-Versuchstierverordnung [TierSchVersV]), following the recommendations of the Federation of European Laboratory Animal Science Association (FELASA).
Reverse Transcription:Article Title: Low-input RNA-seq suggests metabolic specialization underlying morphological heterogeneity in a gut commensal bacterium.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains Bacteroides thetaiotaomicron VPI-5842 DSM 2079 Phocaeicola vulgatus DSM 1447 Bacteroides uniformis DSM 6597 Campylobacter jejuni NTC1168 Provided by Cynthia Sharma CSS-5295 Salmonella enterica serovar Typhimurium DSM 24522 Clostridioides difficile 630 Provided by Franziska Faber DSM27543 E. coli S17-1 lambda pir ATCC BAA-2428 See Table S4 for strains generated in this study This paper N/A Chemicals, peptides, and recombinant proteins Anhydrotetracycline VWR J66688.MA BamHI Thermo Fischer Scientific FD0054 Cas9 nuclease New England Biolabs MO386T Cefoxitin Carl Roth 4156.2 dCTPs Invitrogen 10217016 Deepvent DNA polymerase New England Biolabs M0259L DNaseI Thermo Fischer Scientific EN0521 dNTPs New England Biolabs N0447L IPTG AppliChem A4773,0005 Lysozyme (single cell) Epicentre R1804M Lysozyme (FISH) Thermo Fischer Scientific 90082 NheI Thermo Fischer Scientific FD0974 Nuclease Free Water Ambion AM9916 Paraformaldehyde Carl Roth 0335.1 Phusion DNA polymerase Biozym 332530 L Proteinase K New England Biolabs P8107S Recombinant RNase Inhibitor Takara 2313A RNAlater Qiagen 76104 RNsseH New England Biolabs M0297L RNAseIf New England Biolabs M0243S SSC buffer (20X) Invitrogen AM9763 SuperScript IV Reverse Transcriptase Thermo Fischer Scientific 18090010 T4 DNA Polymerase New England Biolabs M0203L Terminal Transferase New England Biolabs M0315S XbaI Thermo Fisher Scientific FD0684 XhoI Thermo Fisher Scientific FD0694 10X lysis buffer Takara 635013 Critical commercial assays Agilent High Sensitivity DNA Kit Agilent 5067–4626 Ampure XP beads Beckman Coulter A63881 HCR-FISH Molecular Instruments N/A KAPA HiFi HotStart ReadyMix Roche sequencing store KK2602/SKU:7958935001 MEGAscript T7 transcription Kit (Ambion) Thermo Fisher Scientific AMB13345 Monarch RNA Cleanupt Kit NEB T2050S NEBuilder HiFi DNA Assembly Mix New England Biolabs E2621L (Continued on next page) 14 Cell Reports 44, 115844, June 24, 2025 .. Animal experiments were performed at the Helmholtz Center for Infection Research, Braunschweig, Germany, according to the National Animal Protection Law (Tierschutzgesetz [TierSchG] and Animal Experiment Regulations [Tierschutz-Versuchstierverordnung [TierSchVersV]), following the recommendations of the Federation of European Laboratory Animal Science Association (FELASA).
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![( A ) Acute viral infection model. ( B and C ) qRT-PCR analysis (B) and immunoblots (C) of NSD2 expression in CD44 hi CD8 + T cells at different time points postinfection relative to naïve CD8 + T cells [CD44 low CD8; day (d) 0]. β-actin as the loading control. Quantifications and representative histograms were shown ( n = 5). ( D , G , and H ) Representative flow cytometry histograms of <t>GP33</t> + CD8 + T cells in spleens and lymph nodes from WT mice and Nsd2 CKO mice. Quantifications of frequency and absolute cell number at day 8 (D, n = 5 for spleen; n = 9 for lymph nodes), day 15 (G, n = 6), and day 45 (H, n = 8 for spleen; n = 9 for lymph nodes) postinfection were shown. ( E , I , and J ) Representative histograms and quantifications of GP33 + MPECs in spleens and lymph nodes from WT mice and Nsd2 CKO mice at day 8 (E, n = 5 for spleen; n = 9 for lymph nodes from WT mice; n = 6 for lymph nodes from Nsd2 CKO mice), day 15 (I, n = 5 for spleen from WT mice; n = 6 for spleen from Nsd2 CKO mice; n = 6 for lymph nodes), and day 45 (J, n = 6 for spleen; n = 5 for lymph nodes) postinfection were shown. ( F ) Quantifications of viral load in spleen, lung, and liver from WT mice and Nsd2 CKO mice at day 5 postinfection ( n = 9). Data are presented as means ± SEM pooled from two independent experiments (G and H) or from one representative experiment of at least three independent experiments [(B) to (F), (I), and (J)]. Statistical analysis was performed using one-way analysis of variance (ANOVA) [(B) and (C)] and two-tailed unpaired Student’s t test [(D) to (J)]. ns, not significant; * P < 0.05; ** P < 0.01; *** P < 0.001; **** P < 0.0001.](https://pub-med-central-images-cdn.bioz.com/pub_med_central_ids_ending_with_3679/pmc13693679/pmc13693679__sciadv.aee9670-f1.jpg)