Single Cell:Article Title: Integrating complementary approaches reveals antigen-reactive CD4+ T cell states after SARS-CoV-2 vaccination
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Raw single-cell sequencing data – Reverse Phenotyping dataset – Part 1 In house GSE310441 Raw single-cell sequencing data – Reverse Phenotyping dataset – Part 2 In house GSE310442 Oligonucleotides hTRAC HDR genomic forward primer targeting LHA (5′-TCTCTCTCTCAGCTGG TACACGGCTGCCTTTACTCTGCCAGAG-3′) Eurofins; Müller et al. (2021) N/A hTRAC HDR genomic reverse primer targeting RHA (5′-CATCATTGACCAGAGCTCTG-3′) Eurofins; Müller et al. (2021) N/A Alt-R® CRISPR-Cas9 tracrRNA Integrated DNA Technologies Cat#1072534 hTRAC crRNA (5′-AGAGTCTCTCAGCTGGTACA-3′) Integrated DNA Technologies; Ren et al. (2017) N/A hTRBC crRNA (5′-GGAGAATGACGAGTGGACCC-3′) Integrated DNA Technologies; Schober et al. (2019) N/A Alt-R® Cas9 Electroporation Enhancer Integrated DNA Technologies Cat#10007805 Recombinant DNA HDR DNA template sequence Twist Bioscience N/A Software and algorithms FlowJo (version 10.7.2) BD Biosciences https://www.flowjo.com/ GraphPad Prism 10 software GraphPad software https://www.graphpad.com/ Affinity Designer Serif (Europe) Ltd https://www.affinity.studio/en Cellranger 10× Genomics V.6.0.2 Scanpy Wolf et al.43 Pip V.1.8.2 Scirpy Sturm et al.44 Pip V.0.10.1 HashSolo Bernstein et al.45 Pip V.1.8.2 TCRdist3 Mayer-Blackwell et al.36 Pip V.0.2.2 Gephi Gephi Consortium V.0.9.7 MUSCLE Edgar et al.46 https://ebi.ac.uk/jdispatcher/msa/muscle Logomaker Tareen et al.47 Pip V.0.8 Custom Code In house https://doi.org/10.5281/zenodo.19683785 Other MultiScreenHTS-IP, 0.45 μm, transparent, sterile Millipore Cat# MSIPS4510 4D-NucleofectorTM Core Unit Lonza Cat#AAF-1002B 4D-NucleofectorTM X Unit Lonza Cat#AAF-1002X Custom dCODE Dextramers® Immudex N/A MR1 tetramers loaded 5-OP-RU Prof. Dr. med. .. STAR★METHODS Detailed methods are provided in the online version of this paper and include the following: • KEY RESOURCES TABLE • EXPERIMENTAL MODEL AND STUDY PARTICIPANT DETAILS ○ Study design ○ Study cohort CoVa-Adapt ○ Peripheral blood mononuclear cell (PBMC) isolation • METHOD DETAILS ○ Multiparametric flow cytometry for T cells ○ IFNg Enzyme-linked immunospot (ELISpot) ○ Reverse phenotyping ○ Dextramer staining ○ Computational single-cell RNA sequencing data analysis ○ Transgenic TCR re-expression in primary human T cells ○ Transgenic TCR DNA template design ○ Double-stranded DNA production ○ T cell activation for genetic editing ○ Ribonucleoprotein production ○ Orthotopic TCR replacement (OTR) ○ Peptide-pulsing of autologous PBMCs ○ Peptide-induced activation marker expression by TCR-engineered T cells ○ MR1 tetramer staining • QUANTIFICATION AND STATISTICAL ANALYSIS SUPPLEMENTAL INFORMATION Supplemental information can be found online at https://doi.org/10.1016/j.isci.
Sequencing:Article Title: Integrating complementary approaches reveals antigen-reactive CD4+ T cell states after SARS-CoV-2 vaccination
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Raw single-cell sequencing data – Reverse Phenotyping dataset – Part 1 In house GSE310441 Raw single-cell sequencing data – Reverse Phenotyping dataset – Part 2 In house GSE310442 Oligonucleotides hTRAC HDR genomic forward primer targeting LHA (5′-TCTCTCTCTCAGCTGG TACACGGCTGCCTTTACTCTGCCAGAG-3′) Eurofins; Müller et al. (2021) N/A hTRAC HDR genomic reverse primer targeting RHA (5′-CATCATTGACCAGAGCTCTG-3′) Eurofins; Müller et al. (2021) N/A Alt-R® CRISPR-Cas9 tracrRNA Integrated DNA Technologies Cat#1072534 hTRAC crRNA (5′-AGAGTCTCTCAGCTGGTACA-3′) Integrated DNA Technologies; Ren et al. (2017) N/A hTRBC crRNA (5′-GGAGAATGACGAGTGGACCC-3′) Integrated DNA Technologies; Schober et al. (2019) N/A Alt-R® Cas9 Electroporation Enhancer Integrated DNA Technologies Cat#10007805 Recombinant DNA HDR DNA template sequence Twist Bioscience N/A Software and algorithms FlowJo (version 10.7.2) BD Biosciences https://www.flowjo.com/ GraphPad Prism 10 software GraphPad software https://www.graphpad.com/ Affinity Designer Serif (Europe) Ltd https://www.affinity.studio/en Cellranger 10× Genomics V.6.0.2 Scanpy Wolf et al.43 Pip V.1.8.2 Scirpy Sturm et al.44 Pip V.0.10.1 HashSolo Bernstein et al.45 Pip V.1.8.2 TCRdist3 Mayer-Blackwell et al.36 Pip V.0.2.2 Gephi Gephi Consortium V.0.9.7 MUSCLE Edgar et al.46 https://ebi.ac.uk/jdispatcher/msa/muscle Logomaker Tareen et al.47 Pip V.0.8 Custom Code In house https://doi.org/10.5281/zenodo.19683785 Other MultiScreenHTS-IP, 0.45 μm, transparent, sterile Millipore Cat# MSIPS4510 4D-NucleofectorTM Core Unit Lonza Cat#AAF-1002B 4D-NucleofectorTM X Unit Lonza Cat#AAF-1002X Custom dCODE Dextramers® Immudex N/A MR1 tetramers loaded 5-OP-RU Prof. Dr. med. .. STAR★METHODS Detailed methods are provided in the online version of this paper and include the following: • KEY RESOURCES TABLE • EXPERIMENTAL MODEL AND STUDY PARTICIPANT DETAILS ○ Study design ○ Study cohort CoVa-Adapt ○ Peripheral blood mononuclear cell (PBMC) isolation • METHOD DETAILS ○ Multiparametric flow cytometry for T cells ○ IFNg Enzyme-linked immunospot (ELISpot) ○ Reverse phenotyping ○ Dextramer staining ○ Computational single-cell RNA sequencing data analysis ○ Transgenic TCR re-expression in primary human T cells ○ Transgenic TCR DNA template design ○ Double-stranded DNA production ○ T cell activation for genetic editing ○ Ribonucleoprotein production ○ Orthotopic TCR replacement (OTR) ○ Peptide-pulsing of autologous PBMCs ○ Peptide-induced activation marker expression by TCR-engineered T cells ○ MR1 tetramer staining • QUANTIFICATION AND STATISTICAL ANALYSIS SUPPLEMENTAL INFORMATION Supplemental information can be found online at https://doi.org/10.1016/j.isci.
CRISPR:Article Title: Integrating complementary approaches reveals antigen-reactive CD4+ T cell states after SARS-CoV-2 vaccination
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Raw single-cell sequencing data – Reverse Phenotyping dataset – Part 1 In house GSE310441 Raw single-cell sequencing data – Reverse Phenotyping dataset – Part 2 In house GSE310442 Oligonucleotides hTRAC HDR genomic forward primer targeting LHA (5′-TCTCTCTCTCAGCTGG TACACGGCTGCCTTTACTCTGCCAGAG-3′) Eurofins; Müller et al. (2021) N/A hTRAC HDR genomic reverse primer targeting RHA (5′-CATCATTGACCAGAGCTCTG-3′) Eurofins; Müller et al. (2021) N/A Alt-R® CRISPR-Cas9 tracrRNA Integrated DNA Technologies Cat#1072534 hTRAC crRNA (5′-AGAGTCTCTCAGCTGGTACA-3′) Integrated DNA Technologies; Ren et al. (2017) N/A hTRBC crRNA (5′-GGAGAATGACGAGTGGACCC-3′) Integrated DNA Technologies; Schober et al. (2019) N/A Alt-R® Cas9 Electroporation Enhancer Integrated DNA Technologies Cat#10007805 Recombinant DNA HDR DNA template sequence Twist Bioscience N/A Software and algorithms FlowJo (version 10.7.2) BD Biosciences https://www.flowjo.com/ GraphPad Prism 10 software GraphPad software https://www.graphpad.com/ Affinity Designer Serif (Europe) Ltd https://www.affinity.studio/en Cellranger 10× Genomics V.6.0.2 Scanpy Wolf et al.43 Pip V.1.8.2 Scirpy Sturm et al.44 Pip V.0.10.1 HashSolo Bernstein et al.45 Pip V.1.8.2 TCRdist3 Mayer-Blackwell et al.36 Pip V.0.2.2 Gephi Gephi Consortium V.0.9.7 MUSCLE Edgar et al.46 https://ebi.ac.uk/jdispatcher/msa/muscle Logomaker Tareen et al.47 Pip V.0.8 Custom Code In house https://doi.org/10.5281/zenodo.19683785 Other MultiScreenHTS-IP, 0.45 μm, transparent, sterile Millipore Cat# MSIPS4510 4D-NucleofectorTM Core Unit Lonza Cat#AAF-1002B 4D-NucleofectorTM X Unit Lonza Cat#AAF-1002X Custom dCODE Dextramers® Immudex N/A MR1 tetramers loaded 5-OP-RU Prof. Dr. med. .. STAR★METHODS Detailed methods are provided in the online version of this paper and include the following: • KEY RESOURCES TABLE • EXPERIMENTAL MODEL AND STUDY PARTICIPANT DETAILS ○ Study design ○ Study cohort CoVa-Adapt ○ Peripheral blood mononuclear cell (PBMC) isolation • METHOD DETAILS ○ Multiparametric flow cytometry for T cells ○ IFNg Enzyme-linked immunospot (ELISpot) ○ Reverse phenotyping ○ Dextramer staining ○ Computational single-cell RNA sequencing data analysis ○ Transgenic TCR re-expression in primary human T cells ○ Transgenic TCR DNA template design ○ Double-stranded DNA production ○ T cell activation for genetic editing ○ Ribonucleoprotein production ○ Orthotopic TCR replacement (OTR) ○ Peptide-pulsing of autologous PBMCs ○ Peptide-induced activation marker expression by TCR-engineered T cells ○ MR1 tetramer staining • QUANTIFICATION AND STATISTICAL ANALYSIS SUPPLEMENTAL INFORMATION Supplemental information can be found online at https://doi.org/10.1016/j.isci.
Electroporation:Article Title: Integrating complementary approaches reveals antigen-reactive CD4+ T cell states after SARS-CoV-2 vaccination
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Raw single-cell sequencing data – Reverse Phenotyping dataset – Part 1 In house GSE310441 Raw single-cell sequencing data – Reverse Phenotyping dataset – Part 2 In house GSE310442 Oligonucleotides hTRAC HDR genomic forward primer targeting LHA (5′-TCTCTCTCTCAGCTGG TACACGGCTGCCTTTACTCTGCCAGAG-3′) Eurofins; Müller et al. (2021) N/A hTRAC HDR genomic reverse primer targeting RHA (5′-CATCATTGACCAGAGCTCTG-3′) Eurofins; Müller et al. (2021) N/A Alt-R® CRISPR-Cas9 tracrRNA Integrated DNA Technologies Cat#1072534 hTRAC crRNA (5′-AGAGTCTCTCAGCTGGTACA-3′) Integrated DNA Technologies; Ren et al. (2017) N/A hTRBC crRNA (5′-GGAGAATGACGAGTGGACCC-3′) Integrated DNA Technologies; Schober et al. (2019) N/A Alt-R® Cas9 Electroporation Enhancer Integrated DNA Technologies Cat#10007805 Recombinant DNA HDR DNA template sequence Twist Bioscience N/A Software and algorithms FlowJo (version 10.7.2) BD Biosciences https://www.flowjo.com/ GraphPad Prism 10 software GraphPad software https://www.graphpad.com/ Affinity Designer Serif (Europe) Ltd https://www.affinity.studio/en Cellranger 10× Genomics V.6.0.2 Scanpy Wolf et al.43 Pip V.1.8.2 Scirpy Sturm et al.44 Pip V.0.10.1 HashSolo Bernstein et al.45 Pip V.1.8.2 TCRdist3 Mayer-Blackwell et al.36 Pip V.0.2.2 Gephi Gephi Consortium V.0.9.7 MUSCLE Edgar et al.46 https://ebi.ac.uk/jdispatcher/msa/muscle Logomaker Tareen et al.47 Pip V.0.8 Custom Code In house https://doi.org/10.5281/zenodo.19683785 Other MultiScreenHTS-IP, 0.45 μm, transparent, sterile Millipore Cat# MSIPS4510 4D-NucleofectorTM Core Unit Lonza Cat#AAF-1002B 4D-NucleofectorTM X Unit Lonza Cat#AAF-1002X Custom dCODE Dextramers® Immudex N/A MR1 tetramers loaded 5-OP-RU Prof. Dr. med. .. STAR★METHODS Detailed methods are provided in the online version of this paper and include the following: • KEY RESOURCES TABLE • EXPERIMENTAL MODEL AND STUDY PARTICIPANT DETAILS ○ Study design ○ Study cohort CoVa-Adapt ○ Peripheral blood mononuclear cell (PBMC) isolation • METHOD DETAILS ○ Multiparametric flow cytometry for T cells ○ IFNg Enzyme-linked immunospot (ELISpot) ○ Reverse phenotyping ○ Dextramer staining ○ Computational single-cell RNA sequencing data analysis ○ Transgenic TCR re-expression in primary human T cells ○ Transgenic TCR DNA template design ○ Double-stranded DNA production ○ T cell activation for genetic editing ○ Ribonucleoprotein production ○ Orthotopic TCR replacement (OTR) ○ Peptide-pulsing of autologous PBMCs ○ Peptide-induced activation marker expression by TCR-engineered T cells ○ MR1 tetramer staining • QUANTIFICATION AND STATISTICAL ANALYSIS SUPPLEMENTAL INFORMATION Supplemental information can be found online at https://doi.org/10.1016/j.isci.
Recombinant:Article Title: Integrating complementary approaches reveals antigen-reactive CD4+ T cell states after SARS-CoV-2 vaccination
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Raw single-cell sequencing data – Reverse Phenotyping dataset – Part 1 In house GSE310441 Raw single-cell sequencing data – Reverse Phenotyping dataset – Part 2 In house GSE310442 Oligonucleotides hTRAC HDR genomic forward primer targeting LHA (5′-TCTCTCTCTCAGCTGG TACACGGCTGCCTTTACTCTGCCAGAG-3′) Eurofins; Müller et al. (2021) N/A hTRAC HDR genomic reverse primer targeting RHA (5′-CATCATTGACCAGAGCTCTG-3′) Eurofins; Müller et al. (2021) N/A Alt-R® CRISPR-Cas9 tracrRNA Integrated DNA Technologies Cat#1072534 hTRAC crRNA (5′-AGAGTCTCTCAGCTGGTACA-3′) Integrated DNA Technologies; Ren et al. (2017) N/A hTRBC crRNA (5′-GGAGAATGACGAGTGGACCC-3′) Integrated DNA Technologies; Schober et al. (2019) N/A Alt-R® Cas9 Electroporation Enhancer Integrated DNA Technologies Cat#10007805 Recombinant DNA HDR DNA template sequence Twist Bioscience N/A Software and algorithms FlowJo (version 10.7.2) BD Biosciences https://www.flowjo.com/ GraphPad Prism 10 software GraphPad software https://www.graphpad.com/ Affinity Designer Serif (Europe) Ltd https://www.affinity.studio/en Cellranger 10× Genomics V.6.0.2 Scanpy Wolf et al.43 Pip V.1.8.2 Scirpy Sturm et al.44 Pip V.0.10.1 HashSolo Bernstein et al.45 Pip V.1.8.2 TCRdist3 Mayer-Blackwell et al.36 Pip V.0.2.2 Gephi Gephi Consortium V.0.9.7 MUSCLE Edgar et al.46 https://ebi.ac.uk/jdispatcher/msa/muscle Logomaker Tareen et al.47 Pip V.0.8 Custom Code In house https://doi.org/10.5281/zenodo.19683785 Other MultiScreenHTS-IP, 0.45 μm, transparent, sterile Millipore Cat# MSIPS4510 4D-NucleofectorTM Core Unit Lonza Cat#AAF-1002B 4D-NucleofectorTM X Unit Lonza Cat#AAF-1002X Custom dCODE Dextramers® Immudex N/A MR1 tetramers loaded 5-OP-RU Prof. Dr. med. .. STAR★METHODS Detailed methods are provided in the online version of this paper and include the following: • KEY RESOURCES TABLE • EXPERIMENTAL MODEL AND STUDY PARTICIPANT DETAILS ○ Study design ○ Study cohort CoVa-Adapt ○ Peripheral blood mononuclear cell (PBMC) isolation • METHOD DETAILS ○ Multiparametric flow cytometry for T cells ○ IFNg Enzyme-linked immunospot (ELISpot) ○ Reverse phenotyping ○ Dextramer staining ○ Computational single-cell RNA sequencing data analysis ○ Transgenic TCR re-expression in primary human T cells ○ Transgenic TCR DNA template design ○ Double-stranded DNA production ○ T cell activation for genetic editing ○ Ribonucleoprotein production ○ Orthotopic TCR replacement (OTR) ○ Peptide-pulsing of autologous PBMCs ○ Peptide-induced activation marker expression by TCR-engineered T cells ○ MR1 tetramer staining • QUANTIFICATION AND STATISTICAL ANALYSIS SUPPLEMENTAL INFORMATION Supplemental information can be found online at https://doi.org/10.1016/j.isci.
Article Title: Disordered proteins interact with the chemical environment to tune their protective function during drying
Article Snippet: Recombinant DNA reagent , CAHS D (plasmid) , This study , NA , Cloned via Gibson assembly in pEt28b. .. Recombinant DNA reagent , AtLEA3-3 (plasmid) , Twist Bioscience , NA , Cloned in pEt28a. .. Recombinant DNA reagent , AavLEA1 (plasmid) , This study , NA , Cloned via Gibson assembly in pEt28b.
Article Title: Tracking fructose 1,6-bisphosphate dynamics in liver cancer cells using a fluorescent biosensor.
Article Snippet: .. N/A Recombinant DNA HYlight codon-optimized E. coli/H. sapiens This paper, generated by Twist Bioscience https://www.twistbioscience.com/ pQE-30 vector Qiagen https://www.qiagen.com/ko-us pCS2+ vector pCS2+HyPer7 was a gift from Vsevolod Belousov Addgene plasmid # 136466; http://n2t.net/addgene:136466; RRID:Addgene_136466 HYlight codon-optimized M. musculus Provided by John N. Koberstein Koberstein et al.5 Software and algorithms Snapgene Snapgene https://www.snapgene.com/; RRID: SCR_015052 TubeSeq Services Eurofins Genomics Eurofins Genomics https://eurofinsgenomics.eu/en/ custom-dna-sequencing/ eurofins-services/tubeseqservices/ NIS-Elements Nikon https://www.microscope. healthcare.nikon.com/products/ software/nis-elements; RRID: SCR_014329 Fiji https://doi.org/10.1038/ nmeth.2019 https://fiji.sc/; RRID: SCR_002285 GraphPad Prism GraphPad Software https://www.graphpad.com/; RRID: SCR_002798 SoftMax Pro Molecular Devices https://es.moleculardevices. com/products/microplatereaders/acquisition-andanalysis-software/softmaxpro-software; RRID: SCR_014240 Amersham ImageQuant 800 Cytiva https://www.cytivalifesciences. com/en/be/shop/proteinanalysis/molecular-imagingfor-proteins/imaging-systems/ amersham-imagequant-800systems-p-11546 Xcalibur software Thermo Scientific Cat# OPTON-30965; RRID: SCR_014593 ColabFold Milot Mirdita https://github.com/sokrypton/ ColabFold; RRID: SCR_025453 (Continued on next page) iScience 27, 111336, December 20, 2024 e3 ..
Article Title: The HIV-1 nuclear export complex reveals the role of RNA in CRM1 cargo recognition.
Article Snippet: The CRM1 variants were expressed using the Expi293 transient expression system (Thermo Fisher Scientific, US) using manufacturer supplied protocols. .. REAGENT or RESOURCE SOURCE IDENTIFIER HIV-1 Rev/RRE RNP Map This paper EMDB-70347 CRM1-RanGTP/SPN1/Nup214 Port et al.45 PDB: 5DIS HIV-1 Rev/Stem IIB mimic Jayaraman et al.20 PDB: 4PMI Experimental models: Cell lines HEK293T cells ACTT Cat# CRL-3216 N/A BHK-21 cells ACTT Cat# CCL-10 N/A Oligonucleotides Primers See Table S4 IDT N/A Recombinant DNA Gene Fragments See Table S3 IDT/Twist Biosciences N/A Software and algorithms SerialEM Mastronarde87 https://bio3d.colorado.edu/SerialEM/; RRID: SCR_019198 MotionCor2 Zheng et al.88 https://emcore.ucsf.edu/cryoem-software; RRID: SCR_016499 cryoSPARC Punjani et al.89 https://cryosparc.com; RRID: SCR_016501 RELION 2.0 Fernandez-Leiro and Scheres90 https://cam.ac.uk/relion; RRID: SCR_016274 RELION 3.0 Zivanov et al.91 https://cam.ac.uk/relion; RRID: SCR_016274 CTFFIND4 Rohou and Grigorieff92 https://elia.org/ctffind4; RRID: SCR_016732 UCSF pyem Asarnow et al.93 https://github.com/asarnow/pyem; https://doi.org/10.5281/zenodo.3576630 ChimeraX Goddard et al.94 https://www.cgl.ucsf.edu/chimerax/ download.html; RRID: SCR_015872 Rosetta Enumerative Build Das95 https://www.rosettacommons.org/home; RRID: SCR_015701 DRRAFTER Kappel96 https://www.rosettacommons.org/home; RRID: SCR_015701 COOT Casañal97 http://www2.mrc-lmb.cam.ac.uk/personal/ pemsley/coot/; RRID: SCR_014222 PHENIX Liebschner, et al.58 https://www.phenix-online.org/; RRID: SCR_014224 PHENIX Adams et al.59 https://www.phenix-online.org/; RRID: SCR_014224 EMDA Warshamanage et al.98 https://pypi.org/project/emda/ cis-TEM Grant et al.99 https://cistem.org/; RRID: SCR_016502 deepEM-hancer Sanchez-Garcia et al100 https://github.com/rsanchezgarc/deepEMhancer Prisim 8 GraphPad http://www.graphpad.com/; RRID: SCR_002798 e2 Molecular Cell 85, 3108–3122.e1–e7, August 21, 2025 gram of cell pellet. .. Lysis buffer was supplemented with Halt Protease Inhibitor (Thermo Scientific) and phenylmethylsulfonyl fluoride (PMSF) to a final concentration of 1 mM.
Software:Article Title: Integrating complementary approaches reveals antigen-reactive CD4+ T cell states after SARS-CoV-2 vaccination
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Raw single-cell sequencing data – Reverse Phenotyping dataset – Part 1 In house GSE310441 Raw single-cell sequencing data – Reverse Phenotyping dataset – Part 2 In house GSE310442 Oligonucleotides hTRAC HDR genomic forward primer targeting LHA (5′-TCTCTCTCTCAGCTGG TACACGGCTGCCTTTACTCTGCCAGAG-3′) Eurofins; Müller et al. (2021) N/A hTRAC HDR genomic reverse primer targeting RHA (5′-CATCATTGACCAGAGCTCTG-3′) Eurofins; Müller et al. (2021) N/A Alt-R® CRISPR-Cas9 tracrRNA Integrated DNA Technologies Cat#1072534 hTRAC crRNA (5′-AGAGTCTCTCAGCTGGTACA-3′) Integrated DNA Technologies; Ren et al. (2017) N/A hTRBC crRNA (5′-GGAGAATGACGAGTGGACCC-3′) Integrated DNA Technologies; Schober et al. (2019) N/A Alt-R® Cas9 Electroporation Enhancer Integrated DNA Technologies Cat#10007805 Recombinant DNA HDR DNA template sequence Twist Bioscience N/A Software and algorithms FlowJo (version 10.7.2) BD Biosciences https://www.flowjo.com/ GraphPad Prism 10 software GraphPad software https://www.graphpad.com/ Affinity Designer Serif (Europe) Ltd https://www.affinity.studio/en Cellranger 10× Genomics V.6.0.2 Scanpy Wolf et al.43 Pip V.1.8.2 Scirpy Sturm et al.44 Pip V.0.10.1 HashSolo Bernstein et al.45 Pip V.1.8.2 TCRdist3 Mayer-Blackwell et al.36 Pip V.0.2.2 Gephi Gephi Consortium V.0.9.7 MUSCLE Edgar et al.46 https://ebi.ac.uk/jdispatcher/msa/muscle Logomaker Tareen et al.47 Pip V.0.8 Custom Code In house https://doi.org/10.5281/zenodo.19683785 Other MultiScreenHTS-IP, 0.45 μm, transparent, sterile Millipore Cat# MSIPS4510 4D-NucleofectorTM Core Unit Lonza Cat#AAF-1002B 4D-NucleofectorTM X Unit Lonza Cat#AAF-1002X Custom dCODE Dextramers® Immudex N/A MR1 tetramers loaded 5-OP-RU Prof. Dr. med. .. STAR★METHODS Detailed methods are provided in the online version of this paper and include the following: • KEY RESOURCES TABLE • EXPERIMENTAL MODEL AND STUDY PARTICIPANT DETAILS ○ Study design ○ Study cohort CoVa-Adapt ○ Peripheral blood mononuclear cell (PBMC) isolation • METHOD DETAILS ○ Multiparametric flow cytometry for T cells ○ IFNg Enzyme-linked immunospot (ELISpot) ○ Reverse phenotyping ○ Dextramer staining ○ Computational single-cell RNA sequencing data analysis ○ Transgenic TCR re-expression in primary human T cells ○ Transgenic TCR DNA template design ○ Double-stranded DNA production ○ T cell activation for genetic editing ○ Ribonucleoprotein production ○ Orthotopic TCR replacement (OTR) ○ Peptide-pulsing of autologous PBMCs ○ Peptide-induced activation marker expression by TCR-engineered T cells ○ MR1 tetramer staining • QUANTIFICATION AND STATISTICAL ANALYSIS SUPPLEMENTAL INFORMATION Supplemental information can be found online at https://doi.org/10.1016/j.isci.
Article Title: Tracking fructose 1,6-bisphosphate dynamics in liver cancer cells using a fluorescent biosensor.
Article Snippet: .. N/A Recombinant DNA HYlight codon-optimized E. coli/H. sapiens This paper, generated by Twist Bioscience https://www.twistbioscience.com/ pQE-30 vector Qiagen https://www.qiagen.com/ko-us pCS2+ vector pCS2+HyPer7 was a gift from Vsevolod Belousov Addgene plasmid # 136466; http://n2t.net/addgene:136466; RRID:Addgene_136466 HYlight codon-optimized M. musculus Provided by John N. Koberstein Koberstein et al.5 Software and algorithms Snapgene Snapgene https://www.snapgene.com/; RRID: SCR_015052 TubeSeq Services Eurofins Genomics Eurofins Genomics https://eurofinsgenomics.eu/en/ custom-dna-sequencing/ eurofins-services/tubeseqservices/ NIS-Elements Nikon https://www.microscope. healthcare.nikon.com/products/ software/nis-elements; RRID: SCR_014329 Fiji https://doi.org/10.1038/ nmeth.2019 https://fiji.sc/; RRID: SCR_002285 GraphPad Prism GraphPad Software https://www.graphpad.com/; RRID: SCR_002798 SoftMax Pro Molecular Devices https://es.moleculardevices. com/products/microplatereaders/acquisition-andanalysis-software/softmaxpro-software; RRID: SCR_014240 Amersham ImageQuant 800 Cytiva https://www.cytivalifesciences. com/en/be/shop/proteinanalysis/molecular-imagingfor-proteins/imaging-systems/ amersham-imagequant-800systems-p-11546 Xcalibur software Thermo Scientific Cat# OPTON-30965; RRID: SCR_014593 ColabFold Milot Mirdita https://github.com/sokrypton/ ColabFold; RRID: SCR_025453 (Continued on next page) iScience 27, 111336, December 20, 2024 e3 ..
Article Title: The HIV-1 nuclear export complex reveals the role of RNA in CRM1 cargo recognition.
Article Snippet: The CRM1 variants were expressed using the Expi293 transient expression system (Thermo Fisher Scientific, US) using manufacturer supplied protocols. .. REAGENT or RESOURCE SOURCE IDENTIFIER HIV-1 Rev/RRE RNP Map This paper EMDB-70347 CRM1-RanGTP/SPN1/Nup214 Port et al.45 PDB: 5DIS HIV-1 Rev/Stem IIB mimic Jayaraman et al.20 PDB: 4PMI Experimental models: Cell lines HEK293T cells ACTT Cat# CRL-3216 N/A BHK-21 cells ACTT Cat# CCL-10 N/A Oligonucleotides Primers See Table S4 IDT N/A Recombinant DNA Gene Fragments See Table S3 IDT/Twist Biosciences N/A Software and algorithms SerialEM Mastronarde87 https://bio3d.colorado.edu/SerialEM/; RRID: SCR_019198 MotionCor2 Zheng et al.88 https://emcore.ucsf.edu/cryoem-software; RRID: SCR_016499 cryoSPARC Punjani et al.89 https://cryosparc.com; RRID: SCR_016501 RELION 2.0 Fernandez-Leiro and Scheres90 https://cam.ac.uk/relion; RRID: SCR_016274 RELION 3.0 Zivanov et al.91 https://cam.ac.uk/relion; RRID: SCR_016274 CTFFIND4 Rohou and Grigorieff92 https://elia.org/ctffind4; RRID: SCR_016732 UCSF pyem Asarnow et al.93 https://github.com/asarnow/pyem; https://doi.org/10.5281/zenodo.3576630 ChimeraX Goddard et al.94 https://www.cgl.ucsf.edu/chimerax/ download.html; RRID: SCR_015872 Rosetta Enumerative Build Das95 https://www.rosettacommons.org/home; RRID: SCR_015701 DRRAFTER Kappel96 https://www.rosettacommons.org/home; RRID: SCR_015701 COOT Casañal97 http://www2.mrc-lmb.cam.ac.uk/personal/ pemsley/coot/; RRID: SCR_014222 PHENIX Liebschner, et al.58 https://www.phenix-online.org/; RRID: SCR_014224 PHENIX Adams et al.59 https://www.phenix-online.org/; RRID: SCR_014224 EMDA Warshamanage et al.98 https://pypi.org/project/emda/ cis-TEM Grant et al.99 https://cistem.org/; RRID: SCR_016502 deepEM-hancer Sanchez-Garcia et al100 https://github.com/rsanchezgarc/deepEMhancer Prisim 8 GraphPad http://www.graphpad.com/; RRID: SCR_002798 e2 Molecular Cell 85, 3108–3122.e1–e7, August 21, 2025 gram of cell pellet. .. Lysis buffer was supplemented with Halt Protease Inhibitor (Thermo Scientific) and phenylmethylsulfonyl fluoride (PMSF) to a final concentration of 1 mM.
Sterility:Article Title: Integrating complementary approaches reveals antigen-reactive CD4+ T cell states after SARS-CoV-2 vaccination
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Raw single-cell sequencing data – Reverse Phenotyping dataset – Part 1 In house GSE310441 Raw single-cell sequencing data – Reverse Phenotyping dataset – Part 2 In house GSE310442 Oligonucleotides hTRAC HDR genomic forward primer targeting LHA (5′-TCTCTCTCTCAGCTGG TACACGGCTGCCTTTACTCTGCCAGAG-3′) Eurofins; Müller et al. (2021) N/A hTRAC HDR genomic reverse primer targeting RHA (5′-CATCATTGACCAGAGCTCTG-3′) Eurofins; Müller et al. (2021) N/A Alt-R® CRISPR-Cas9 tracrRNA Integrated DNA Technologies Cat#1072534 hTRAC crRNA (5′-AGAGTCTCTCAGCTGGTACA-3′) Integrated DNA Technologies; Ren et al. (2017) N/A hTRBC crRNA (5′-GGAGAATGACGAGTGGACCC-3′) Integrated DNA Technologies; Schober et al. (2019) N/A Alt-R® Cas9 Electroporation Enhancer Integrated DNA Technologies Cat#10007805 Recombinant DNA HDR DNA template sequence Twist Bioscience N/A Software and algorithms FlowJo (version 10.7.2) BD Biosciences https://www.flowjo.com/ GraphPad Prism 10 software GraphPad software https://www.graphpad.com/ Affinity Designer Serif (Europe) Ltd https://www.affinity.studio/en Cellranger 10× Genomics V.6.0.2 Scanpy Wolf et al.43 Pip V.1.8.2 Scirpy Sturm et al.44 Pip V.0.10.1 HashSolo Bernstein et al.45 Pip V.1.8.2 TCRdist3 Mayer-Blackwell et al.36 Pip V.0.2.2 Gephi Gephi Consortium V.0.9.7 MUSCLE Edgar et al.46 https://ebi.ac.uk/jdispatcher/msa/muscle Logomaker Tareen et al.47 Pip V.0.8 Custom Code In house https://doi.org/10.5281/zenodo.19683785 Other MultiScreenHTS-IP, 0.45 μm, transparent, sterile Millipore Cat# MSIPS4510 4D-NucleofectorTM Core Unit Lonza Cat#AAF-1002B 4D-NucleofectorTM X Unit Lonza Cat#AAF-1002X Custom dCODE Dextramers® Immudex N/A MR1 tetramers loaded 5-OP-RU Prof. Dr. med. .. STAR★METHODS Detailed methods are provided in the online version of this paper and include the following: • KEY RESOURCES TABLE • EXPERIMENTAL MODEL AND STUDY PARTICIPANT DETAILS ○ Study design ○ Study cohort CoVa-Adapt ○ Peripheral blood mononuclear cell (PBMC) isolation • METHOD DETAILS ○ Multiparametric flow cytometry for T cells ○ IFNg Enzyme-linked immunospot (ELISpot) ○ Reverse phenotyping ○ Dextramer staining ○ Computational single-cell RNA sequencing data analysis ○ Transgenic TCR re-expression in primary human T cells ○ Transgenic TCR DNA template design ○ Double-stranded DNA production ○ T cell activation for genetic editing ○ Ribonucleoprotein production ○ Orthotopic TCR replacement (OTR) ○ Peptide-pulsing of autologous PBMCs ○ Peptide-induced activation marker expression by TCR-engineered T cells ○ MR1 tetramer staining • QUANTIFICATION AND STATISTICAL ANALYSIS SUPPLEMENTAL INFORMATION Supplemental information can be found online at https://doi.org/10.1016/j.isci.
Plasmid Preparation:Article Title: Disordered proteins interact with the chemical environment to tune their protective function during drying
Article Snippet: Recombinant DNA reagent , CAHS D (plasmid) , This study , NA , Cloned via Gibson assembly in pEt28b. .. Recombinant DNA reagent , AtLEA3-3 (plasmid) , Twist Bioscience , NA , Cloned in pEt28a. .. Recombinant DNA reagent , AavLEA1 (plasmid) , This study , NA , Cloned via Gibson assembly in pEt28b.
Article Title: Tracking fructose 1,6-bisphosphate dynamics in liver cancer cells using a fluorescent biosensor.
Article Snippet: .. N/A Recombinant DNA HYlight codon-optimized E. coli/H. sapiens This paper, generated by Twist Bioscience https://www.twistbioscience.com/ pQE-30 vector Qiagen https://www.qiagen.com/ko-us pCS2+ vector pCS2+HyPer7 was a gift from Vsevolod Belousov Addgene plasmid # 136466; http://n2t.net/addgene:136466; RRID:Addgene_136466 HYlight codon-optimized M. musculus Provided by John N. Koberstein Koberstein et al.5 Software and algorithms Snapgene Snapgene https://www.snapgene.com/; RRID: SCR_015052 TubeSeq Services Eurofins Genomics Eurofins Genomics https://eurofinsgenomics.eu/en/ custom-dna-sequencing/ eurofins-services/tubeseqservices/ NIS-Elements Nikon https://www.microscope. healthcare.nikon.com/products/ software/nis-elements; RRID: SCR_014329 Fiji https://doi.org/10.1038/ nmeth.2019 https://fiji.sc/; RRID: SCR_002285 GraphPad Prism GraphPad Software https://www.graphpad.com/; RRID: SCR_002798 SoftMax Pro Molecular Devices https://es.moleculardevices. com/products/microplatereaders/acquisition-andanalysis-software/softmaxpro-software; RRID: SCR_014240 Amersham ImageQuant 800 Cytiva https://www.cytivalifesciences. com/en/be/shop/proteinanalysis/molecular-imagingfor-proteins/imaging-systems/ amersham-imagequant-800systems-p-11546 Xcalibur software Thermo Scientific Cat# OPTON-30965; RRID: SCR_014593 ColabFold Milot Mirdita https://github.com/sokrypton/ ColabFold; RRID: SCR_025453 (Continued on next page) iScience 27, 111336, December 20, 2024 e3 ..
Clone Assay:Article Title: Disordered proteins interact with the chemical environment to tune their protective function during drying
Article Snippet: Recombinant DNA reagent , CAHS D (plasmid) , This study , NA , Cloned via Gibson assembly in pEt28b. .. Recombinant DNA reagent , AtLEA3-3 (plasmid) , Twist Bioscience , NA , Cloned in pEt28a. .. Recombinant DNA reagent , AavLEA1 (plasmid) , This study , NA , Cloned via Gibson assembly in pEt28b.
Generated:Article Title: Tracking fructose 1,6-bisphosphate dynamics in liver cancer cells using a fluorescent biosensor.
Article Snippet: .. N/A Recombinant DNA HYlight codon-optimized E. coli/H. sapiens This paper, generated by Twist Bioscience https://www.twistbioscience.com/ pQE-30 vector Qiagen https://www.qiagen.com/ko-us pCS2+ vector pCS2+HyPer7 was a gift from Vsevolod Belousov Addgene plasmid # 136466; http://n2t.net/addgene:136466; RRID:Addgene_136466 HYlight codon-optimized M. musculus Provided by John N. Koberstein Koberstein et al.5 Software and algorithms Snapgene Snapgene https://www.snapgene.com/; RRID: SCR_015052 TubeSeq Services Eurofins Genomics Eurofins Genomics https://eurofinsgenomics.eu/en/ custom-dna-sequencing/ eurofins-services/tubeseqservices/ NIS-Elements Nikon https://www.microscope. healthcare.nikon.com/products/ software/nis-elements; RRID: SCR_014329 Fiji https://doi.org/10.1038/ nmeth.2019 https://fiji.sc/; RRID: SCR_002285 GraphPad Prism GraphPad Software https://www.graphpad.com/; RRID: SCR_002798 SoftMax Pro Molecular Devices https://es.moleculardevices. com/products/microplatereaders/acquisition-andanalysis-software/softmaxpro-software; RRID: SCR_014240 Amersham ImageQuant 800 Cytiva https://www.cytivalifesciences. com/en/be/shop/proteinanalysis/molecular-imagingfor-proteins/imaging-systems/ amersham-imagequant-800systems-p-11546 Xcalibur software Thermo Scientific Cat# OPTON-30965; RRID: SCR_014593 ColabFold Milot Mirdita https://github.com/sokrypton/ ColabFold; RRID: SCR_025453 (Continued on next page) iScience 27, 111336, December 20, 2024 e3 ..
Virus:Article Title: Genomic Surveillance of Endemic Human Coronaviruses in Côte d'Ivoire Using Targeted Hybrid-Capture Sequencing.
Article Snippet: Target enrichment was performed by solution-based hybrid capture using the Twist Respiratory Virus Research (RVR) Panel (103067, Twist Bioscience). .. Target enrichment was performed by solution-based hybrid capture using the Twist Respiratory Virus Research (RVR) Panel (103067, Twist Bioscience). .. Enriched libraries were purified, quantified, and validated using the Qubit HS Assay before sequencing on the Illumina iSeq 100 platform (Illumina, San Diego, CA, USA) using the iSeq 100 i1 Reagent v2 300-cycle kit in paired-end mode (2 × 150 bp).
Article Title: Transdisciplinary Epidemiology in Schools: Integrating Molecular Environmental and Social Surveillance Through Community Science
Article Snippet: .. To target respiratory viruses, the Twist Bioscience Respiratory Virus Panel (Twist Bioscience, 103067) was used for hybrid capture, following the version 1 protocol of the Twist Hybridization and Wash Kit. .. Final enriched libraries were sequenced on an Illumina NovaSeq 6000 System in paired-end mode with 100 bp read length.
Hybridization:Article Title: Transdisciplinary Epidemiology in Schools: Integrating Molecular Environmental and Social Surveillance Through Community Science
Article Snippet: .. To target respiratory viruses, the Twist Bioscience Respiratory Virus Panel (Twist Bioscience, 103067) was used for hybrid capture, following the version 1 protocol of the Twist Hybridization and Wash Kit. .. Final enriched libraries were sequenced on an Illumina NovaSeq 6000 System in paired-end mode with 100 bp read length.
other:Article Title: Intact protein barcoding enables one-shot identification of CRISPRi strains and their metabolic state.
Article Snippet: The ubiquitin coding sequence, T7 terminator and RBS were first amplified from the plasmid Ubiquitin WT19 (Cat#12647, Addgene) and added to pgRNA-bacteria7 using Golden gate cloning.20 The promotor J23100 was amplified from a gene fragment that was REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains YYdCas9: BW25993 intC:tetRdcas9-aadA lacY:ypet-cat Lawson et al.3 N/A MegaX DH10B T1R ElectrocompTM: F- mcrA D(mrr-hsdRMS-mcrBC), F80lacZDM15 DlacX74 recA1 endA1 araD139 D(ara, leu)7697 galU galK l- rpsL nupG tonA Invitrogen Cat# C640003 Chemicals, peptides, and recombinant proteins Anydrotetracylcine Roth Cat#1035708-25MG Carbenicillin Roth Cat#6344.3–25 MG Ammonium carbonate Honeywell Cat#10361-29-2 Isopropanol, Rotisolv R99.95%, Ultra LC-MS Roth Cat#0733.1 HP-921 and purine in API-TOF Reference Mass Solution Kit Agilent G1969-85001 Deposited data FI-MS data This paper https://doi.org/10.5281/ zenodo.11563885 and MassIVE: MSV000096254 Oligonucleotides Oligonucleotides are listed in Table S5 Twist Bioscience N/A Recombinant DNA Ubiquitin WT Brzovic et al.19 Addgene #12647 pgRNA-bacteria Qi et al.7 Addgene #44251 Software and algorithms MATLAB R2021a mathworks.com N/A FLASHDeconv 2.0 BETA+ https://openms.de/applications/ flashdeconv N/A MSConvert https://proteowizard.sourceforge.io N/A e1 Cell Reports Methods 4, 100908, December 16, 2024 OPEN ACCESS ordered from Twist Bioscience (San Francisco, USA) and was added to the pgRNA using IVA cloning,21 forming pgRNA-ubiquitin.
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