Plasmid Preparation:Article Title: Metabolic control of innate immune activation in TET2-mutant clonal hematopoiesis.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER psPAX2 Addgene Plasmid #12260 pInducer21 Addgene; Meerbrey et al.57 Plasmid #46948 SFFV gRNA expression vectors Addgene Plasmids #169941 and #169940 pAAV-MCS Cell Biolabs Cat#VPK-411 pAAV-AAVS1 targeting vector for HDR Waarts et al.55; Loke and Kim et al.18 pAAV-TET2 targeting vector for HDR Waarts et al.55; Loke and Kim et al.18 CROPseq-guide-puro Datlinger et al.58 Plasmid #86708 Software and algorithms MAGeCK v0.5.9.2 Li et al.59 https://sourceforge.net/projects/mageck/ R v3.6.1 R Project https://cran.r-project.org/ Prism v7.0 GraphPad https://www.graphpad.com/ STAR aligner v2.7.2b Dobin et al.60 https://github.com/alexdobin/STAR RSEM v1.3.1 Li and Dewey61 https://github.com/deweylab/RSEM/releases DESeq2 v1.50.2 Love et al.62 https://bioconductor.posit.co/packages/ 3.19/bioc/html/DESeq2.html Cell Ranger v9.0.1 10x Genomics https://www.10xgenomics.com/ Seurat v3 Stuart et al.63 https://cran.r-project.org/package=Seurat Bowtie2 v2.3.5 Langmead and Salzberg64 https://github.com/BenLangmead/bowtie2 Picard v2.19.0 Broad Institute https://broadinstitute.github.io/picard/ MACS2 v2.1.1 Zhang et al.65 https://pypi.org/project/MACS2/ deepTools v3.4.3 Ramı́rez et al.66 https://deeptools.readthedocs.io/ CellProfiler v4.2.8 Broad Institute https://cellprofiler.org MaxQuant v1.6.2.6 Cox and Mann67 https://maxquant.org/ TraceFinder Thermo Fisher Scientific https://www.thermofisher.com/us/en/ home/industrial/mass-spectrometry/liquidchromatography-mass-spectrometry-lcms/lc-ms-software/lc-ms-data-acquisitionsoftware/tracefinder-software.html Progenesis QI Nonlinear Dynamics https://www.nonlinear.com/progenesis/qi/download/ MZmine v3.10 Schmid et al.68 https://github.com/CSi-Studio/mzmine3 MetaboAnalyst v6.0 Pang et al.69 https://www.metaboanalyst.ca/ Other High-fat, high-cholesterol diet Teklad TD.96121 Sony MA900 cell sorter Sony Biotechnology Model MA900 Covaris E220 sonicator Covaris E220 Illumina NextSeq 550 Illumina NextSeq 550 Illumina NovaSeq (SP) Illumina NovaSeq SP Streptavidin magnetic beads Thermo Fisher Scientific Cat#88817 ll OPEN ACCESS Article e3 Cell Chemical Biology 33, 1–15.e1–e9, February 19, 2026 diet; Teklad) 4 weeks after transplantation. .. He is an equity holder and SAB member for Avilar Therapeutics, Photys Therapeutics, and Ajax Therapeutics and an equity holder in Lighthorse Therapeutics, CPD4, Inc and Anvia Therapeutics.
Expressing:Article Title: Metabolic control of innate immune activation in TET2-mutant clonal hematopoiesis.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER psPAX2 Addgene Plasmid #12260 pInducer21 Addgene; Meerbrey et al.57 Plasmid #46948 SFFV gRNA expression vectors Addgene Plasmids #169941 and #169940 pAAV-MCS Cell Biolabs Cat#VPK-411 pAAV-AAVS1 targeting vector for HDR Waarts et al.55; Loke and Kim et al.18 pAAV-TET2 targeting vector for HDR Waarts et al.55; Loke and Kim et al.18 CROPseq-guide-puro Datlinger et al.58 Plasmid #86708 Software and algorithms MAGeCK v0.5.9.2 Li et al.59 https://sourceforge.net/projects/mageck/ R v3.6.1 R Project https://cran.r-project.org/ Prism v7.0 GraphPad https://www.graphpad.com/ STAR aligner v2.7.2b Dobin et al.60 https://github.com/alexdobin/STAR RSEM v1.3.1 Li and Dewey61 https://github.com/deweylab/RSEM/releases DESeq2 v1.50.2 Love et al.62 https://bioconductor.posit.co/packages/ 3.19/bioc/html/DESeq2.html Cell Ranger v9.0.1 10x Genomics https://www.10xgenomics.com/ Seurat v3 Stuart et al.63 https://cran.r-project.org/package=Seurat Bowtie2 v2.3.5 Langmead and Salzberg64 https://github.com/BenLangmead/bowtie2 Picard v2.19.0 Broad Institute https://broadinstitute.github.io/picard/ MACS2 v2.1.1 Zhang et al.65 https://pypi.org/project/MACS2/ deepTools v3.4.3 Ramı́rez et al.66 https://deeptools.readthedocs.io/ CellProfiler v4.2.8 Broad Institute https://cellprofiler.org MaxQuant v1.6.2.6 Cox and Mann67 https://maxquant.org/ TraceFinder Thermo Fisher Scientific https://www.thermofisher.com/us/en/ home/industrial/mass-spectrometry/liquidchromatography-mass-spectrometry-lcms/lc-ms-software/lc-ms-data-acquisitionsoftware/tracefinder-software.html Progenesis QI Nonlinear Dynamics https://www.nonlinear.com/progenesis/qi/download/ MZmine v3.10 Schmid et al.68 https://github.com/CSi-Studio/mzmine3 MetaboAnalyst v6.0 Pang et al.69 https://www.metaboanalyst.ca/ Other High-fat, high-cholesterol diet Teklad TD.96121 Sony MA900 cell sorter Sony Biotechnology Model MA900 Covaris E220 sonicator Covaris E220 Illumina NextSeq 550 Illumina NextSeq 550 Illumina NovaSeq (SP) Illumina NovaSeq SP Streptavidin magnetic beads Thermo Fisher Scientific Cat#88817 ll OPEN ACCESS Article e3 Cell Chemical Biology 33, 1–15.e1–e9, February 19, 2026 diet; Teklad) 4 weeks after transplantation. .. He is an equity holder and SAB member for Avilar Therapeutics, Photys Therapeutics, and Ajax Therapeutics and an equity holder in Lighthorse Therapeutics, CPD4, Inc and Anvia Therapeutics.
Software:Article Title: Metabolic control of innate immune activation in TET2-mutant clonal hematopoiesis.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER psPAX2 Addgene Plasmid #12260 pInducer21 Addgene; Meerbrey et al.57 Plasmid #46948 SFFV gRNA expression vectors Addgene Plasmids #169941 and #169940 pAAV-MCS Cell Biolabs Cat#VPK-411 pAAV-AAVS1 targeting vector for HDR Waarts et al.55; Loke and Kim et al.18 pAAV-TET2 targeting vector for HDR Waarts et al.55; Loke and Kim et al.18 CROPseq-guide-puro Datlinger et al.58 Plasmid #86708 Software and algorithms MAGeCK v0.5.9.2 Li et al.59 https://sourceforge.net/projects/mageck/ R v3.6.1 R Project https://cran.r-project.org/ Prism v7.0 GraphPad https://www.graphpad.com/ STAR aligner v2.7.2b Dobin et al.60 https://github.com/alexdobin/STAR RSEM v1.3.1 Li and Dewey61 https://github.com/deweylab/RSEM/releases DESeq2 v1.50.2 Love et al.62 https://bioconductor.posit.co/packages/ 3.19/bioc/html/DESeq2.html Cell Ranger v9.0.1 10x Genomics https://www.10xgenomics.com/ Seurat v3 Stuart et al.63 https://cran.r-project.org/package=Seurat Bowtie2 v2.3.5 Langmead and Salzberg64 https://github.com/BenLangmead/bowtie2 Picard v2.19.0 Broad Institute https://broadinstitute.github.io/picard/ MACS2 v2.1.1 Zhang et al.65 https://pypi.org/project/MACS2/ deepTools v3.4.3 Ramı́rez et al.66 https://deeptools.readthedocs.io/ CellProfiler v4.2.8 Broad Institute https://cellprofiler.org MaxQuant v1.6.2.6 Cox and Mann67 https://maxquant.org/ TraceFinder Thermo Fisher Scientific https://www.thermofisher.com/us/en/ home/industrial/mass-spectrometry/liquidchromatography-mass-spectrometry-lcms/lc-ms-software/lc-ms-data-acquisitionsoftware/tracefinder-software.html Progenesis QI Nonlinear Dynamics https://www.nonlinear.com/progenesis/qi/download/ MZmine v3.10 Schmid et al.68 https://github.com/CSi-Studio/mzmine3 MetaboAnalyst v6.0 Pang et al.69 https://www.metaboanalyst.ca/ Other High-fat, high-cholesterol diet Teklad TD.96121 Sony MA900 cell sorter Sony Biotechnology Model MA900 Covaris E220 sonicator Covaris E220 Illumina NextSeq 550 Illumina NextSeq 550 Illumina NovaSeq (SP) Illumina NovaSeq SP Streptavidin magnetic beads Thermo Fisher Scientific Cat#88817 ll OPEN ACCESS Article e3 Cell Chemical Biology 33, 1–15.e1–e9, February 19, 2026 diet; Teklad) 4 weeks after transplantation. .. He is an equity holder and SAB member for Avilar Therapeutics, Photys Therapeutics, and Ajax Therapeutics and an equity holder in Lighthorse Therapeutics, CPD4, Inc and Anvia Therapeutics.
Magnetic Beads:Article Title: Metabolic control of innate immune activation in TET2-mutant clonal hematopoiesis.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER psPAX2 Addgene Plasmid #12260 pInducer21 Addgene; Meerbrey et al.57 Plasmid #46948 SFFV gRNA expression vectors Addgene Plasmids #169941 and #169940 pAAV-MCS Cell Biolabs Cat#VPK-411 pAAV-AAVS1 targeting vector for HDR Waarts et al.55; Loke and Kim et al.18 pAAV-TET2 targeting vector for HDR Waarts et al.55; Loke and Kim et al.18 CROPseq-guide-puro Datlinger et al.58 Plasmid #86708 Software and algorithms MAGeCK v0.5.9.2 Li et al.59 https://sourceforge.net/projects/mageck/ R v3.6.1 R Project https://cran.r-project.org/ Prism v7.0 GraphPad https://www.graphpad.com/ STAR aligner v2.7.2b Dobin et al.60 https://github.com/alexdobin/STAR RSEM v1.3.1 Li and Dewey61 https://github.com/deweylab/RSEM/releases DESeq2 v1.50.2 Love et al.62 https://bioconductor.posit.co/packages/ 3.19/bioc/html/DESeq2.html Cell Ranger v9.0.1 10x Genomics https://www.10xgenomics.com/ Seurat v3 Stuart et al.63 https://cran.r-project.org/package=Seurat Bowtie2 v2.3.5 Langmead and Salzberg64 https://github.com/BenLangmead/bowtie2 Picard v2.19.0 Broad Institute https://broadinstitute.github.io/picard/ MACS2 v2.1.1 Zhang et al.65 https://pypi.org/project/MACS2/ deepTools v3.4.3 Ramı́rez et al.66 https://deeptools.readthedocs.io/ CellProfiler v4.2.8 Broad Institute https://cellprofiler.org MaxQuant v1.6.2.6 Cox and Mann67 https://maxquant.org/ TraceFinder Thermo Fisher Scientific https://www.thermofisher.com/us/en/ home/industrial/mass-spectrometry/liquidchromatography-mass-spectrometry-lcms/lc-ms-software/lc-ms-data-acquisitionsoftware/tracefinder-software.html Progenesis QI Nonlinear Dynamics https://www.nonlinear.com/progenesis/qi/download/ MZmine v3.10 Schmid et al.68 https://github.com/CSi-Studio/mzmine3 MetaboAnalyst v6.0 Pang et al.69 https://www.metaboanalyst.ca/ Other High-fat, high-cholesterol diet Teklad TD.96121 Sony MA900 cell sorter Sony Biotechnology Model MA900 Covaris E220 sonicator Covaris E220 Illumina NextSeq 550 Illumina NextSeq 550 Illumina NovaSeq (SP) Illumina NovaSeq SP Streptavidin magnetic beads Thermo Fisher Scientific Cat#88817 ll OPEN ACCESS Article e3 Cell Chemical Biology 33, 1–15.e1–e9, February 19, 2026 diet; Teklad) 4 weeks after transplantation. .. He is an equity holder and SAB member for Avilar Therapeutics, Photys Therapeutics, and Ajax Therapeutics and an equity holder in Lighthorse Therapeutics, CPD4, Inc and Anvia Therapeutics.
Transplantation Assay:Article Title: Metabolic control of innate immune activation in TET2-mutant clonal hematopoiesis.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER psPAX2 Addgene Plasmid #12260 pInducer21 Addgene; Meerbrey et al.57 Plasmid #46948 SFFV gRNA expression vectors Addgene Plasmids #169941 and #169940 pAAV-MCS Cell Biolabs Cat#VPK-411 pAAV-AAVS1 targeting vector for HDR Waarts et al.55; Loke and Kim et al.18 pAAV-TET2 targeting vector for HDR Waarts et al.55; Loke and Kim et al.18 CROPseq-guide-puro Datlinger et al.58 Plasmid #86708 Software and algorithms MAGeCK v0.5.9.2 Li et al.59 https://sourceforge.net/projects/mageck/ R v3.6.1 R Project https://cran.r-project.org/ Prism v7.0 GraphPad https://www.graphpad.com/ STAR aligner v2.7.2b Dobin et al.60 https://github.com/alexdobin/STAR RSEM v1.3.1 Li and Dewey61 https://github.com/deweylab/RSEM/releases DESeq2 v1.50.2 Love et al.62 https://bioconductor.posit.co/packages/ 3.19/bioc/html/DESeq2.html Cell Ranger v9.0.1 10x Genomics https://www.10xgenomics.com/ Seurat v3 Stuart et al.63 https://cran.r-project.org/package=Seurat Bowtie2 v2.3.5 Langmead and Salzberg64 https://github.com/BenLangmead/bowtie2 Picard v2.19.0 Broad Institute https://broadinstitute.github.io/picard/ MACS2 v2.1.1 Zhang et al.65 https://pypi.org/project/MACS2/ deepTools v3.4.3 Ramı́rez et al.66 https://deeptools.readthedocs.io/ CellProfiler v4.2.8 Broad Institute https://cellprofiler.org MaxQuant v1.6.2.6 Cox and Mann67 https://maxquant.org/ TraceFinder Thermo Fisher Scientific https://www.thermofisher.com/us/en/ home/industrial/mass-spectrometry/liquidchromatography-mass-spectrometry-lcms/lc-ms-software/lc-ms-data-acquisitionsoftware/tracefinder-software.html Progenesis QI Nonlinear Dynamics https://www.nonlinear.com/progenesis/qi/download/ MZmine v3.10 Schmid et al.68 https://github.com/CSi-Studio/mzmine3 MetaboAnalyst v6.0 Pang et al.69 https://www.metaboanalyst.ca/ Other High-fat, high-cholesterol diet Teklad TD.96121 Sony MA900 cell sorter Sony Biotechnology Model MA900 Covaris E220 sonicator Covaris E220 Illumina NextSeq 550 Illumina NextSeq 550 Illumina NovaSeq (SP) Illumina NovaSeq SP Streptavidin magnetic beads Thermo Fisher Scientific Cat#88817 ll OPEN ACCESS Article e3 Cell Chemical Biology 33, 1–15.e1–e9, February 19, 2026 diet; Teklad) 4 weeks after transplantation. .. He is an equity holder and SAB member for Avilar Therapeutics, Photys Therapeutics, and Ajax Therapeutics and an equity holder in Lighthorse Therapeutics, CPD4, Inc and Anvia Therapeutics.
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