Transformation Assay:
Plasmid Preparation:Article Title: A “Function-First” Approach to Identify Regulatory T cell–Targeting Antibodies for Immunotherapy
Article Snippet: All constructs were cloned into the pcDNA3.1/-(neo) expression vector (Invitrogen, cat. #V795-20) and the sequences of the fusion constructs can be found in Supplementary Table S4. .. Bespoke primers were designed (SeqBuilder v14, Lasergene DNASTAR; sequences available in Supplementary Table S5) to induce point mutations, and plasmid DNA was mutated using the Agilent QuikChange II XL Site-Directed Mutagenesis Kit (Agilent, cat. #200522). ..
Mutagenesis:Article Title: A “Function-First” Approach to Identify Regulatory T cell–Targeting Antibodies for Immunotherapy
Article Snippet: All constructs were cloned into the pcDNA3.1/-(neo) expression vector (Invitrogen, cat. #V795-20) and the sequences of the fusion constructs can be found in Supplementary Table S4. .. Bespoke primers were designed (SeqBuilder v14, Lasergene DNASTAR; sequences available in Supplementary Table S5) to induce point mutations, and plasmid DNA was mutated using the Agilent QuikChange II XL Site-Directed Mutagenesis Kit (Agilent, cat. #200522). ..
Software:Article Title: Hyperreactive B cells instruct their elimination by T cells to curb autoinflammation and lymphomagenesis.
Article Snippet: Wildtype C57BL/6J and C57BL/6-Prf1tm1Sdz/J (Perf1-/-)79 mice are from the Jackson Laboratory. .. REAGENT or RESOURCE SOURCE IDENTIFIER GSEA v4.1.0 Broad Institute, Inc., MIT; Subramanian et al.94 http://www.gsea-msigdb.org ImageJ v1.51 National Institutes of Health (NIH) https://imagej.nih.gov R (v 4.2.1 or v 3.4.4) The R Foundation https://www.r-project.org Lasergene DNASTAR https://www.dnastar.com/ software/lasergene Geneious Prime Dotmatics https://www.geneious.com Photoshop Adobe https://www.adobe.com/ products/photoshop ImageScope (v12.4.3.4008) Leica Biosystems https://www.leicabiosystems.com Python (v.3.9.7) Python Software Foundation Python (v.3.9.7) Scanpy toolkit (v 1.8.2) Python Software Foundation https://pypi.org/project/scanpy Seaborn data visualization (v.0.11.2) Python Software Foundation https://pypi.org/project/seaborn/ bbknn package (v 1.5.1) Python Software Foundation https://pypi.org/project/bbknn Leiden algorithm (v 0.8.8) Python Software Foundation https://pypi.org/project/leidenalg CellRanger ( v 6.0.0) 10x Genomics https://support.10xgenomics.com LIMMA Bioconductor; Ritchie et al.92 https://doi.org/10.1093/nar/gkv007 ROAST Wu et al.93 https://rdrr.io/bioc/limma/man/roast.html Drop-seq (v1.12) Macosko et al.83 https://github.com/broadinstitute/ Drop-seq/releases affy package (v 3.16) Bioconductor; Gautier et al.95 https://www.bioconductor.org/ packages/release/bioc/html/affy.html Gene annotation Release M25 (GRCm38.p6) and Genome sequence Gencode Consortium https://www.gencodegenes.org/ mouse/release_M18.html Other Anti-mouse Gzmk AF568 PrimeFlow Probe Thermo Fisher AssayID: VB10-3285985-PF; Cat#: PF-210 Anti-mouse Gzmb AF568 PrimeFlow Probe Thermo Fisher AssayID: VB10-3282422-PF; Cat#: PF-204 Anti-mouse Perforin1 AF568 PrimeFlow Probe Thermo Fisher AssayID: VB10-3287008-PF; Cat#: PF-210 Microvette 500 Sarstedt Cat#: 20.1343.100 MicroWell 96-Well Plates (V-Bottom, conical) Nunc Cat#: 249570 Cell Strainer with 35mm nylon mesh Corning Cat#: 352235 MaxiSorp 96-Well Flat Bottom ELISA plates Nunc Cat#: 44-2404-21 Agencourt AMPure XP magnetic beads Beckman Coulter Cat#: 10453438 Multiscreen HTS 96 HV Filter Plate Millipore Cat#: MSHVN4B10 e7 Immunity 58, 1–19.e1–e15, January 14, 2025 All the mice used in this project were housed in a specific pathogen-free (SPF) or specific and opportunistic pathogen free (SOPF) condition, according to the legislation of the European Union and the Region of Upper Bavaria. .. Mice were bred and housed in mouse facilities in the Max-Planck institute of Biochemistry, Charles River Calco (Italy), in the Center for Preclinical Research of the MRI (Zentrum f€ur Pr€aklinisches Forschung (ZPF), Munich) and mouse facility at the Faculty of Medicine, University of Rijeka, Croatia.
Sequencing:Article Title: Hyperreactive B cells instruct their elimination by T cells to curb autoinflammation and lymphomagenesis.
Article Snippet: Wildtype C57BL/6J and C57BL/6-Prf1tm1Sdz/J (Perf1-/-)79 mice are from the Jackson Laboratory. .. REAGENT or RESOURCE SOURCE IDENTIFIER GSEA v4.1.0 Broad Institute, Inc., MIT; Subramanian et al.94 http://www.gsea-msigdb.org ImageJ v1.51 National Institutes of Health (NIH) https://imagej.nih.gov R (v 4.2.1 or v 3.4.4) The R Foundation https://www.r-project.org Lasergene DNASTAR https://www.dnastar.com/ software/lasergene Geneious Prime Dotmatics https://www.geneious.com Photoshop Adobe https://www.adobe.com/ products/photoshop ImageScope (v12.4.3.4008) Leica Biosystems https://www.leicabiosystems.com Python (v.3.9.7) Python Software Foundation Python (v.3.9.7) Scanpy toolkit (v 1.8.2) Python Software Foundation https://pypi.org/project/scanpy Seaborn data visualization (v.0.11.2) Python Software Foundation https://pypi.org/project/seaborn/ bbknn package (v 1.5.1) Python Software Foundation https://pypi.org/project/bbknn Leiden algorithm (v 0.8.8) Python Software Foundation https://pypi.org/project/leidenalg CellRanger ( v 6.0.0) 10x Genomics https://support.10xgenomics.com LIMMA Bioconductor; Ritchie et al.92 https://doi.org/10.1093/nar/gkv007 ROAST Wu et al.93 https://rdrr.io/bioc/limma/man/roast.html Drop-seq (v1.12) Macosko et al.83 https://github.com/broadinstitute/ Drop-seq/releases affy package (v 3.16) Bioconductor; Gautier et al.95 https://www.bioconductor.org/ packages/release/bioc/html/affy.html Gene annotation Release M25 (GRCm38.p6) and Genome sequence Gencode Consortium https://www.gencodegenes.org/ mouse/release_M18.html Other Anti-mouse Gzmk AF568 PrimeFlow Probe Thermo Fisher AssayID: VB10-3285985-PF; Cat#: PF-210 Anti-mouse Gzmb AF568 PrimeFlow Probe Thermo Fisher AssayID: VB10-3282422-PF; Cat#: PF-204 Anti-mouse Perforin1 AF568 PrimeFlow Probe Thermo Fisher AssayID: VB10-3287008-PF; Cat#: PF-210 Microvette 500 Sarstedt Cat#: 20.1343.100 MicroWell 96-Well Plates (V-Bottom, conical) Nunc Cat#: 249570 Cell Strainer with 35mm nylon mesh Corning Cat#: 352235 MaxiSorp 96-Well Flat Bottom ELISA plates Nunc Cat#: 44-2404-21 Agencourt AMPure XP magnetic beads Beckman Coulter Cat#: 10453438 Multiscreen HTS 96 HV Filter Plate Millipore Cat#: MSHVN4B10 e7 Immunity 58, 1–19.e1–e15, January 14, 2025 All the mice used in this project were housed in a specific pathogen-free (SPF) or specific and opportunistic pathogen free (SOPF) condition, according to the legislation of the European Union and the Region of Upper Bavaria. .. Mice were bred and housed in mouse facilities in the Max-Planck institute of Biochemistry, Charles River Calco (Italy), in the Center for Preclinical Research of the MRI (Zentrum f€ur Pr€aklinisches Forschung (ZPF), Munich) and mouse facility at the Faculty of Medicine, University of Rijeka, Croatia.
Enzyme-linked Immunosorbent Assay:Article Title: Hyperreactive B cells instruct their elimination by T cells to curb autoinflammation and lymphomagenesis.
Article Snippet: Wildtype C57BL/6J and C57BL/6-Prf1tm1Sdz/J (Perf1-/-)79 mice are from the Jackson Laboratory. .. REAGENT or RESOURCE SOURCE IDENTIFIER GSEA v4.1.0 Broad Institute, Inc., MIT; Subramanian et al.94 http://www.gsea-msigdb.org ImageJ v1.51 National Institutes of Health (NIH) https://imagej.nih.gov R (v 4.2.1 or v 3.4.4) The R Foundation https://www.r-project.org Lasergene DNASTAR https://www.dnastar.com/ software/lasergene Geneious Prime Dotmatics https://www.geneious.com Photoshop Adobe https://www.adobe.com/ products/photoshop ImageScope (v12.4.3.4008) Leica Biosystems https://www.leicabiosystems.com Python (v.3.9.7) Python Software Foundation Python (v.3.9.7) Scanpy toolkit (v 1.8.2) Python Software Foundation https://pypi.org/project/scanpy Seaborn data visualization (v.0.11.2) Python Software Foundation https://pypi.org/project/seaborn/ bbknn package (v 1.5.1) Python Software Foundation https://pypi.org/project/bbknn Leiden algorithm (v 0.8.8) Python Software Foundation https://pypi.org/project/leidenalg CellRanger ( v 6.0.0) 10x Genomics https://support.10xgenomics.com LIMMA Bioconductor; Ritchie et al.92 https://doi.org/10.1093/nar/gkv007 ROAST Wu et al.93 https://rdrr.io/bioc/limma/man/roast.html Drop-seq (v1.12) Macosko et al.83 https://github.com/broadinstitute/ Drop-seq/releases affy package (v 3.16) Bioconductor; Gautier et al.95 https://www.bioconductor.org/ packages/release/bioc/html/affy.html Gene annotation Release M25 (GRCm38.p6) and Genome sequence Gencode Consortium https://www.gencodegenes.org/ mouse/release_M18.html Other Anti-mouse Gzmk AF568 PrimeFlow Probe Thermo Fisher AssayID: VB10-3285985-PF; Cat#: PF-210 Anti-mouse Gzmb AF568 PrimeFlow Probe Thermo Fisher AssayID: VB10-3282422-PF; Cat#: PF-204 Anti-mouse Perforin1 AF568 PrimeFlow Probe Thermo Fisher AssayID: VB10-3287008-PF; Cat#: PF-210 Microvette 500 Sarstedt Cat#: 20.1343.100 MicroWell 96-Well Plates (V-Bottom, conical) Nunc Cat#: 249570 Cell Strainer with 35mm nylon mesh Corning Cat#: 352235 MaxiSorp 96-Well Flat Bottom ELISA plates Nunc Cat#: 44-2404-21 Agencourt AMPure XP magnetic beads Beckman Coulter Cat#: 10453438 Multiscreen HTS 96 HV Filter Plate Millipore Cat#: MSHVN4B10 e7 Immunity 58, 1–19.e1–e15, January 14, 2025 All the mice used in this project were housed in a specific pathogen-free (SPF) or specific and opportunistic pathogen free (SOPF) condition, according to the legislation of the European Union and the Region of Upper Bavaria. .. Mice were bred and housed in mouse facilities in the Max-Planck institute of Biochemistry, Charles River Calco (Italy), in the Center for Preclinical Research of the MRI (Zentrum f€ur Pr€aklinisches Forschung (ZPF), Munich) and mouse facility at the Faculty of Medicine, University of Rijeka, Croatia.
Magnetic Beads:Article Title: Hyperreactive B cells instruct their elimination by T cells to curb autoinflammation and lymphomagenesis.
Article Snippet: Wildtype C57BL/6J and C57BL/6-Prf1tm1Sdz/J (Perf1-/-)79 mice are from the Jackson Laboratory. .. REAGENT or RESOURCE SOURCE IDENTIFIER GSEA v4.1.0 Broad Institute, Inc., MIT; Subramanian et al.94 http://www.gsea-msigdb.org ImageJ v1.51 National Institutes of Health (NIH) https://imagej.nih.gov R (v 4.2.1 or v 3.4.4) The R Foundation https://www.r-project.org Lasergene DNASTAR https://www.dnastar.com/ software/lasergene Geneious Prime Dotmatics https://www.geneious.com Photoshop Adobe https://www.adobe.com/ products/photoshop ImageScope (v12.4.3.4008) Leica Biosystems https://www.leicabiosystems.com Python (v.3.9.7) Python Software Foundation Python (v.3.9.7) Scanpy toolkit (v 1.8.2) Python Software Foundation https://pypi.org/project/scanpy Seaborn data visualization (v.0.11.2) Python Software Foundation https://pypi.org/project/seaborn/ bbknn package (v 1.5.1) Python Software Foundation https://pypi.org/project/bbknn Leiden algorithm (v 0.8.8) Python Software Foundation https://pypi.org/project/leidenalg CellRanger ( v 6.0.0) 10x Genomics https://support.10xgenomics.com LIMMA Bioconductor; Ritchie et al.92 https://doi.org/10.1093/nar/gkv007 ROAST Wu et al.93 https://rdrr.io/bioc/limma/man/roast.html Drop-seq (v1.12) Macosko et al.83 https://github.com/broadinstitute/ Drop-seq/releases affy package (v 3.16) Bioconductor; Gautier et al.95 https://www.bioconductor.org/ packages/release/bioc/html/affy.html Gene annotation Release M25 (GRCm38.p6) and Genome sequence Gencode Consortium https://www.gencodegenes.org/ mouse/release_M18.html Other Anti-mouse Gzmk AF568 PrimeFlow Probe Thermo Fisher AssayID: VB10-3285985-PF; Cat#: PF-210 Anti-mouse Gzmb AF568 PrimeFlow Probe Thermo Fisher AssayID: VB10-3282422-PF; Cat#: PF-204 Anti-mouse Perforin1 AF568 PrimeFlow Probe Thermo Fisher AssayID: VB10-3287008-PF; Cat#: PF-210 Microvette 500 Sarstedt Cat#: 20.1343.100 MicroWell 96-Well Plates (V-Bottom, conical) Nunc Cat#: 249570 Cell Strainer with 35mm nylon mesh Corning Cat#: 352235 MaxiSorp 96-Well Flat Bottom ELISA plates Nunc Cat#: 44-2404-21 Agencourt AMPure XP magnetic beads Beckman Coulter Cat#: 10453438 Multiscreen HTS 96 HV Filter Plate Millipore Cat#: MSHVN4B10 e7 Immunity 58, 1–19.e1–e15, January 14, 2025 All the mice used in this project were housed in a specific pathogen-free (SPF) or specific and opportunistic pathogen free (SOPF) condition, according to the legislation of the European Union and the Region of Upper Bavaria. .. Mice were bred and housed in mouse facilities in the Max-Planck institute of Biochemistry, Charles River Calco (Italy), in the Center for Preclinical Research of the MRI (Zentrum f€ur Pr€aklinisches Forschung (ZPF), Munich) and mouse facility at the Faculty of Medicine, University of Rijeka, Croatia.
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