Virus:Article Title: LXR/CD38 activation drives cholesterol-induced macrophage senescence and neurodegeneration via NAD + depletion.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit polyclonal anti-Iba1 Wako Cat#019-19741; RRID:AB_839504 Rat monoclonal anti-F4/80 abcam Cat#ab6640; RRID:AB_1140040 Sheep polyclonal anti-CD38 R&D Systems Cat#AF4947; RRID:AB_1241945 Rabbit polyclonal anti-Ki67 abcam Cat#abcam15580; RRID;AB_443209 Phalloidin-iFluor 647 abcam Cat#ab176759 Alexa Fluor 647 donkey anti-rabbit IgG Jackson ImmunoResearch Cat#711-605-152 Alexa Fluor 647 donkey anti-rat IgG Jackson ImmunoResearch Cat# 712-605-153 Alexa Fluor 488 donkey anti-sheep IgG Jackson ImmunoResearch Cat#713-545-147 Goat polyclonal antibody to Biotin (FITC) abcam Cat#ab6550 Bacterial and virus strains pCMV6-XL6 OriGene Technologies Cat#PCMV6XL6 pCMV6-AC-CD38-GFP OriGene Technologies Cat#MG204265 Chemicals, peptides, and recombinant proteins DMEM gibco Cat#11965-084 L-glutamate gibco Cat#25030-081 Penicillin/streptomycin (P/S) gibco Cat#15140-122 Accutase Sigma-Aldrich Cat#A6964 Cholesterol Sigma-Aldrich Cat#C4951 DNase Sigma-Aldrich Cat#D4527 DNA digestion buffer ZYMO RESEARCH Cat#E1010-1 High Capacity cDNA Reverse Transcription Kit Applied biosystems Cat#4368813 TaqMan Fast Advanced Master Mix Applied biosystems Cat#4444554 Nicotinamide-2,4,5,6-d4 C/D/N Isotopes Cat#D-3457 Lipofectamine RNAiMAX transfection reagent Thermo Fisher Scientific Cat#13778150 Lipofectamine 3000 transfection reagent Thermo Fisher Scientific Cat#L3000-008 Opti-MEM gibco Cat#31895-070 FK866 Chem Cruz Cat#sc-205325A DMEM, high glucose Sigma-Aldrich Cat#D1145 b-nicotinamide mononucleotide Sigma-Aldrich Cat#N3501 GW3965 Sigma-Aldrich Cat#G6295 78c MedChemExpress Cat#HY-123999 AP-20187 APExBIO Cat#B1274 Dasatinib Sigma-Aldrich Cat#SML2589 Quercetin Sigma-Aldrich Cat#Q4951 Seahorse XF DMEM Medium Agilent Technologies Cat#103575-100 Seahorse XF Cell Mito Stress Test kit Agilent Technologies Cat#103015-100 Seahorse XF24 V7 PS Cell Culture Microplate Agilent Technologies Cat#100777-004 Co-detection blocker Advanced Cell Diagnostics Cat#323170 Co-detection antibody diluent Advanced Cell Diagnostics Cat#323160 RNAscope probe Mm-Cdkn1a Advanced Cell Diagnostics Cat#408551 RNAscope probe Mm-Cdkn2a Advanced Cell Diagnostics Cat411011 RNAscope 2.5 HD detection reagents- red Advanced Cell Diagnostics Cat#322360 (Continued on next page) Cell Reports --, 114102, --, 2024 21 .. REAGENT or RESOURCE SOURCE IDENTIFIER SenTraGor Cell Senescence Reagent Cayman chemical Cat#35568 Critical commercial assays PierceTM BCA Protein Assay Kit Thermo Scientific Cat#23225 NBD Cholesterol Staining Dye Kit abcam Cat#ab269448 Senescence b-Galactosidase staining kit Cell Signaling Cat#9860 SPiDER b -galactosidase staining kit DOJINDO Cat#SG02 Lysosome intracellular activity assay kit abcam Cat#ab234622 TaqMan array standard plates Thermo Scientific Cat#4391524 Click-iTTM plus TUNEL Assay kits for in situ apoptosis eetection Invitrogen Cat#C10618 Fluorescent cell linker kit for general cell membrane labeling Sigma-Aldrich Cat# PKH26, PKH67 Deposited data The lipidomics data of BMDMs from Abca1/g1 -m/-m and Abca1/g1 f/f This study Mendeley Data: https://doi.org/10.17632/ gd4mprzbvh.1 The RNA sequence data for BMDMs from Abca1/g1 -m/-m and Abca1/g1 f/f This study GEO: GSE234507 The lipidomics data of retina isolated from young and old mice This study Mendeley Data: https://doi.org/10.17632/ j9gv8x9td7.1 The RNA sequence data for retinal pigment epithelium/choroid tissue of Abca1/g1 -m/-m and INK-ATTAC- Abca1/g1 -m/-m This study GEO: GSE234641 Experimental models: Organisms/strains Mouse: C57BL/6J The Jackson Laboratory RRID: IMSR_JAX:000664 Mouse: Abca1fl Abcg1fl: B6.CgAbca1tm1Jp Abcg1tm1Tall/J The Jackson Laboratory RRID: IMSR_JAX:021067 Mouse: LysM Cre: B6.129P2Lyz2tm1(cre)Ifo/J The Jackson Laboratory RRID: IMSR_JAX:004781 Mouse: INK-ATTAC Unity Biotechnology N/A Mouse: Cx3cr1 CreERT2: B6.129P2(Cg)-Cx3cr1tm2.1(cre/ERT2)Litt/ WganJ The Jackson Laboratory RRID: IMSR_JAX:021160 Mouse: Tmem119 Cre ERT2: C57BL/6-Tmem119em1(cre/ERT2)Gfng/J The Jackson Laboratory RRID: IMSR_JAX:031820 Oligonucleotides Primers for qPCR, see Table S1 Thermo Scientific N/A AllStars Negative Control siRNA QIAGEN Cat#1027281 siRNA targeting Nr1h3 (NM_013839) QIAGEN Cat#SI02740339 siRNA targeting Nr1h2 (NM_009473) QIAGEN Cat#SI00185241 siRNA targeting Cd38 (NM_007646) QIAGEN Cat#SI02666398 Software and algorithms GraphPad Prism GraphPad Software https://www.graphpad.com/scientific- software/prism/ LipidSig N/A http://chenglab.cmu.edu.tw/lipidsig/ CellProfiler https://cellprofiler.org MassHunter Quantitative Analysis Agilent Technologies https://www.agilent.com/en/product/ software-informatics/mass-spectrometrysoftware/ FlowJo BD Biosciences https://www.flowjo.com/solutions/flowjo ImageJ National Institutes of Health https://imagej.nih.gov/ij/download.html Sample Size Calculator ClinCalc https://clincalc.com/stats/samplesize. aspx.
Recombinant:Article Title: LXR/CD38 activation drives cholesterol-induced macrophage senescence and neurodegeneration via NAD + depletion.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit polyclonal anti-Iba1 Wako Cat#019-19741; RRID:AB_839504 Rat monoclonal anti-F4/80 abcam Cat#ab6640; RRID:AB_1140040 Sheep polyclonal anti-CD38 R&D Systems Cat#AF4947; RRID:AB_1241945 Rabbit polyclonal anti-Ki67 abcam Cat#abcam15580; RRID;AB_443209 Phalloidin-iFluor 647 abcam Cat#ab176759 Alexa Fluor 647 donkey anti-rabbit IgG Jackson ImmunoResearch Cat#711-605-152 Alexa Fluor 647 donkey anti-rat IgG Jackson ImmunoResearch Cat# 712-605-153 Alexa Fluor 488 donkey anti-sheep IgG Jackson ImmunoResearch Cat#713-545-147 Goat polyclonal antibody to Biotin (FITC) abcam Cat#ab6550 Bacterial and virus strains pCMV6-XL6 OriGene Technologies Cat#PCMV6XL6 pCMV6-AC-CD38-GFP OriGene Technologies Cat#MG204265 Chemicals, peptides, and recombinant proteins DMEM gibco Cat#11965-084 L-glutamate gibco Cat#25030-081 Penicillin/streptomycin (P/S) gibco Cat#15140-122 Accutase Sigma-Aldrich Cat#A6964 Cholesterol Sigma-Aldrich Cat#C4951 DNase Sigma-Aldrich Cat#D4527 DNA digestion buffer ZYMO RESEARCH Cat#E1010-1 High Capacity cDNA Reverse Transcription Kit Applied biosystems Cat#4368813 TaqMan Fast Advanced Master Mix Applied biosystems Cat#4444554 Nicotinamide-2,4,5,6-d4 C/D/N Isotopes Cat#D-3457 Lipofectamine RNAiMAX transfection reagent Thermo Fisher Scientific Cat#13778150 Lipofectamine 3000 transfection reagent Thermo Fisher Scientific Cat#L3000-008 Opti-MEM gibco Cat#31895-070 FK866 Chem Cruz Cat#sc-205325A DMEM, high glucose Sigma-Aldrich Cat#D1145 b-nicotinamide mononucleotide Sigma-Aldrich Cat#N3501 GW3965 Sigma-Aldrich Cat#G6295 78c MedChemExpress Cat#HY-123999 AP-20187 APExBIO Cat#B1274 Dasatinib Sigma-Aldrich Cat#SML2589 Quercetin Sigma-Aldrich Cat#Q4951 Seahorse XF DMEM Medium Agilent Technologies Cat#103575-100 Seahorse XF Cell Mito Stress Test kit Agilent Technologies Cat#103015-100 Seahorse XF24 V7 PS Cell Culture Microplate Agilent Technologies Cat#100777-004 Co-detection blocker Advanced Cell Diagnostics Cat#323170 Co-detection antibody diluent Advanced Cell Diagnostics Cat#323160 RNAscope probe Mm-Cdkn1a Advanced Cell Diagnostics Cat#408551 RNAscope probe Mm-Cdkn2a Advanced Cell Diagnostics Cat411011 RNAscope 2.5 HD detection reagents- red Advanced Cell Diagnostics Cat#322360 (Continued on next page) Cell Reports --, 114102, --, 2024 21 .. REAGENT or RESOURCE SOURCE IDENTIFIER SenTraGor Cell Senescence Reagent Cayman chemical Cat#35568 Critical commercial assays PierceTM BCA Protein Assay Kit Thermo Scientific Cat#23225 NBD Cholesterol Staining Dye Kit abcam Cat#ab269448 Senescence b-Galactosidase staining kit Cell Signaling Cat#9860 SPiDER b -galactosidase staining kit DOJINDO Cat#SG02 Lysosome intracellular activity assay kit abcam Cat#ab234622 TaqMan array standard plates Thermo Scientific Cat#4391524 Click-iTTM plus TUNEL Assay kits for in situ apoptosis eetection Invitrogen Cat#C10618 Fluorescent cell linker kit for general cell membrane labeling Sigma-Aldrich Cat# PKH26, PKH67 Deposited data The lipidomics data of BMDMs from Abca1/g1 -m/-m and Abca1/g1 f/f This study Mendeley Data: https://doi.org/10.17632/ gd4mprzbvh.1 The RNA sequence data for BMDMs from Abca1/g1 -m/-m and Abca1/g1 f/f This study GEO: GSE234507 The lipidomics data of retina isolated from young and old mice This study Mendeley Data: https://doi.org/10.17632/ j9gv8x9td7.1 The RNA sequence data for retinal pigment epithelium/choroid tissue of Abca1/g1 -m/-m and INK-ATTAC- Abca1/g1 -m/-m This study GEO: GSE234641 Experimental models: Organisms/strains Mouse: C57BL/6J The Jackson Laboratory RRID: IMSR_JAX:000664 Mouse: Abca1fl Abcg1fl: B6.CgAbca1tm1Jp Abcg1tm1Tall/J The Jackson Laboratory RRID: IMSR_JAX:021067 Mouse: LysM Cre: B6.129P2Lyz2tm1(cre)Ifo/J The Jackson Laboratory RRID: IMSR_JAX:004781 Mouse: INK-ATTAC Unity Biotechnology N/A Mouse: Cx3cr1 CreERT2: B6.129P2(Cg)-Cx3cr1tm2.1(cre/ERT2)Litt/ WganJ The Jackson Laboratory RRID: IMSR_JAX:021160 Mouse: Tmem119 Cre ERT2: C57BL/6-Tmem119em1(cre/ERT2)Gfng/J The Jackson Laboratory RRID: IMSR_JAX:031820 Oligonucleotides Primers for qPCR, see Table S1 Thermo Scientific N/A AllStars Negative Control siRNA QIAGEN Cat#1027281 siRNA targeting Nr1h3 (NM_013839) QIAGEN Cat#SI02740339 siRNA targeting Nr1h2 (NM_009473) QIAGEN Cat#SI00185241 siRNA targeting Cd38 (NM_007646) QIAGEN Cat#SI02666398 Software and algorithms GraphPad Prism GraphPad Software https://www.graphpad.com/scientific- software/prism/ LipidSig N/A http://chenglab.cmu.edu.tw/lipidsig/ CellProfiler https://cellprofiler.org MassHunter Quantitative Analysis Agilent Technologies https://www.agilent.com/en/product/ software-informatics/mass-spectrometrysoftware/ FlowJo BD Biosciences https://www.flowjo.com/solutions/flowjo ImageJ National Institutes of Health https://imagej.nih.gov/ij/download.html Sample Size Calculator ClinCalc https://clincalc.com/stats/samplesize. aspx.
Reverse Transcription:Article Title: LXR/CD38 activation drives cholesterol-induced macrophage senescence and neurodegeneration via NAD + depletion.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit polyclonal anti-Iba1 Wako Cat#019-19741; RRID:AB_839504 Rat monoclonal anti-F4/80 abcam Cat#ab6640; RRID:AB_1140040 Sheep polyclonal anti-CD38 R&D Systems Cat#AF4947; RRID:AB_1241945 Rabbit polyclonal anti-Ki67 abcam Cat#abcam15580; RRID;AB_443209 Phalloidin-iFluor 647 abcam Cat#ab176759 Alexa Fluor 647 donkey anti-rabbit IgG Jackson ImmunoResearch Cat#711-605-152 Alexa Fluor 647 donkey anti-rat IgG Jackson ImmunoResearch Cat# 712-605-153 Alexa Fluor 488 donkey anti-sheep IgG Jackson ImmunoResearch Cat#713-545-147 Goat polyclonal antibody to Biotin (FITC) abcam Cat#ab6550 Bacterial and virus strains pCMV6-XL6 OriGene Technologies Cat#PCMV6XL6 pCMV6-AC-CD38-GFP OriGene Technologies Cat#MG204265 Chemicals, peptides, and recombinant proteins DMEM gibco Cat#11965-084 L-glutamate gibco Cat#25030-081 Penicillin/streptomycin (P/S) gibco Cat#15140-122 Accutase Sigma-Aldrich Cat#A6964 Cholesterol Sigma-Aldrich Cat#C4951 DNase Sigma-Aldrich Cat#D4527 DNA digestion buffer ZYMO RESEARCH Cat#E1010-1 High Capacity cDNA Reverse Transcription Kit Applied biosystems Cat#4368813 TaqMan Fast Advanced Master Mix Applied biosystems Cat#4444554 Nicotinamide-2,4,5,6-d4 C/D/N Isotopes Cat#D-3457 Lipofectamine RNAiMAX transfection reagent Thermo Fisher Scientific Cat#13778150 Lipofectamine 3000 transfection reagent Thermo Fisher Scientific Cat#L3000-008 Opti-MEM gibco Cat#31895-070 FK866 Chem Cruz Cat#sc-205325A DMEM, high glucose Sigma-Aldrich Cat#D1145 b-nicotinamide mononucleotide Sigma-Aldrich Cat#N3501 GW3965 Sigma-Aldrich Cat#G6295 78c MedChemExpress Cat#HY-123999 AP-20187 APExBIO Cat#B1274 Dasatinib Sigma-Aldrich Cat#SML2589 Quercetin Sigma-Aldrich Cat#Q4951 Seahorse XF DMEM Medium Agilent Technologies Cat#103575-100 Seahorse XF Cell Mito Stress Test kit Agilent Technologies Cat#103015-100 Seahorse XF24 V7 PS Cell Culture Microplate Agilent Technologies Cat#100777-004 Co-detection blocker Advanced Cell Diagnostics Cat#323170 Co-detection antibody diluent Advanced Cell Diagnostics Cat#323160 RNAscope probe Mm-Cdkn1a Advanced Cell Diagnostics Cat#408551 RNAscope probe Mm-Cdkn2a Advanced Cell Diagnostics Cat411011 RNAscope 2.5 HD detection reagents- red Advanced Cell Diagnostics Cat#322360 (Continued on next page) Cell Reports --, 114102, --, 2024 21 .. REAGENT or RESOURCE SOURCE IDENTIFIER SenTraGor Cell Senescence Reagent Cayman chemical Cat#35568 Critical commercial assays PierceTM BCA Protein Assay Kit Thermo Scientific Cat#23225 NBD Cholesterol Staining Dye Kit abcam Cat#ab269448 Senescence b-Galactosidase staining kit Cell Signaling Cat#9860 SPiDER b -galactosidase staining kit DOJINDO Cat#SG02 Lysosome intracellular activity assay kit abcam Cat#ab234622 TaqMan array standard plates Thermo Scientific Cat#4391524 Click-iTTM plus TUNEL Assay kits for in situ apoptosis eetection Invitrogen Cat#C10618 Fluorescent cell linker kit for general cell membrane labeling Sigma-Aldrich Cat# PKH26, PKH67 Deposited data The lipidomics data of BMDMs from Abca1/g1 -m/-m and Abca1/g1 f/f This study Mendeley Data: https://doi.org/10.17632/ gd4mprzbvh.1 The RNA sequence data for BMDMs from Abca1/g1 -m/-m and Abca1/g1 f/f This study GEO: GSE234507 The lipidomics data of retina isolated from young and old mice This study Mendeley Data: https://doi.org/10.17632/ j9gv8x9td7.1 The RNA sequence data for retinal pigment epithelium/choroid tissue of Abca1/g1 -m/-m and INK-ATTAC- Abca1/g1 -m/-m This study GEO: GSE234641 Experimental models: Organisms/strains Mouse: C57BL/6J The Jackson Laboratory RRID: IMSR_JAX:000664 Mouse: Abca1fl Abcg1fl: B6.CgAbca1tm1Jp Abcg1tm1Tall/J The Jackson Laboratory RRID: IMSR_JAX:021067 Mouse: LysM Cre: B6.129P2Lyz2tm1(cre)Ifo/J The Jackson Laboratory RRID: IMSR_JAX:004781 Mouse: INK-ATTAC Unity Biotechnology N/A Mouse: Cx3cr1 CreERT2: B6.129P2(Cg)-Cx3cr1tm2.1(cre/ERT2)Litt/ WganJ The Jackson Laboratory RRID: IMSR_JAX:021160 Mouse: Tmem119 Cre ERT2: C57BL/6-Tmem119em1(cre/ERT2)Gfng/J The Jackson Laboratory RRID: IMSR_JAX:031820 Oligonucleotides Primers for qPCR, see Table S1 Thermo Scientific N/A AllStars Negative Control siRNA QIAGEN Cat#1027281 siRNA targeting Nr1h3 (NM_013839) QIAGEN Cat#SI02740339 siRNA targeting Nr1h2 (NM_009473) QIAGEN Cat#SI00185241 siRNA targeting Cd38 (NM_007646) QIAGEN Cat#SI02666398 Software and algorithms GraphPad Prism GraphPad Software https://www.graphpad.com/scientific- software/prism/ LipidSig N/A http://chenglab.cmu.edu.tw/lipidsig/ CellProfiler https://cellprofiler.org MassHunter Quantitative Analysis Agilent Technologies https://www.agilent.com/en/product/ software-informatics/mass-spectrometrysoftware/ FlowJo BD Biosciences https://www.flowjo.com/solutions/flowjo ImageJ National Institutes of Health https://imagej.nih.gov/ij/download.html Sample Size Calculator ClinCalc https://clincalc.com/stats/samplesize. aspx.
Transfection:Article Title: LXR/CD38 activation drives cholesterol-induced macrophage senescence and neurodegeneration via NAD + depletion.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit polyclonal anti-Iba1 Wako Cat#019-19741; RRID:AB_839504 Rat monoclonal anti-F4/80 abcam Cat#ab6640; RRID:AB_1140040 Sheep polyclonal anti-CD38 R&D Systems Cat#AF4947; RRID:AB_1241945 Rabbit polyclonal anti-Ki67 abcam Cat#abcam15580; RRID;AB_443209 Phalloidin-iFluor 647 abcam Cat#ab176759 Alexa Fluor 647 donkey anti-rabbit IgG Jackson ImmunoResearch Cat#711-605-152 Alexa Fluor 647 donkey anti-rat IgG Jackson ImmunoResearch Cat# 712-605-153 Alexa Fluor 488 donkey anti-sheep IgG Jackson ImmunoResearch Cat#713-545-147 Goat polyclonal antibody to Biotin (FITC) abcam Cat#ab6550 Bacterial and virus strains pCMV6-XL6 OriGene Technologies Cat#PCMV6XL6 pCMV6-AC-CD38-GFP OriGene Technologies Cat#MG204265 Chemicals, peptides, and recombinant proteins DMEM gibco Cat#11965-084 L-glutamate gibco Cat#25030-081 Penicillin/streptomycin (P/S) gibco Cat#15140-122 Accutase Sigma-Aldrich Cat#A6964 Cholesterol Sigma-Aldrich Cat#C4951 DNase Sigma-Aldrich Cat#D4527 DNA digestion buffer ZYMO RESEARCH Cat#E1010-1 High Capacity cDNA Reverse Transcription Kit Applied biosystems Cat#4368813 TaqMan Fast Advanced Master Mix Applied biosystems Cat#4444554 Nicotinamide-2,4,5,6-d4 C/D/N Isotopes Cat#D-3457 Lipofectamine RNAiMAX transfection reagent Thermo Fisher Scientific Cat#13778150 Lipofectamine 3000 transfection reagent Thermo Fisher Scientific Cat#L3000-008 Opti-MEM gibco Cat#31895-070 FK866 Chem Cruz Cat#sc-205325A DMEM, high glucose Sigma-Aldrich Cat#D1145 b-nicotinamide mononucleotide Sigma-Aldrich Cat#N3501 GW3965 Sigma-Aldrich Cat#G6295 78c MedChemExpress Cat#HY-123999 AP-20187 APExBIO Cat#B1274 Dasatinib Sigma-Aldrich Cat#SML2589 Quercetin Sigma-Aldrich Cat#Q4951 Seahorse XF DMEM Medium Agilent Technologies Cat#103575-100 Seahorse XF Cell Mito Stress Test kit Agilent Technologies Cat#103015-100 Seahorse XF24 V7 PS Cell Culture Microplate Agilent Technologies Cat#100777-004 Co-detection blocker Advanced Cell Diagnostics Cat#323170 Co-detection antibody diluent Advanced Cell Diagnostics Cat#323160 RNAscope probe Mm-Cdkn1a Advanced Cell Diagnostics Cat#408551 RNAscope probe Mm-Cdkn2a Advanced Cell Diagnostics Cat411011 RNAscope 2.5 HD detection reagents- red Advanced Cell Diagnostics Cat#322360 (Continued on next page) Cell Reports --, 114102, --, 2024 21 .. REAGENT or RESOURCE SOURCE IDENTIFIER SenTraGor Cell Senescence Reagent Cayman chemical Cat#35568 Critical commercial assays PierceTM BCA Protein Assay Kit Thermo Scientific Cat#23225 NBD Cholesterol Staining Dye Kit abcam Cat#ab269448 Senescence b-Galactosidase staining kit Cell Signaling Cat#9860 SPiDER b -galactosidase staining kit DOJINDO Cat#SG02 Lysosome intracellular activity assay kit abcam Cat#ab234622 TaqMan array standard plates Thermo Scientific Cat#4391524 Click-iTTM plus TUNEL Assay kits for in situ apoptosis eetection Invitrogen Cat#C10618 Fluorescent cell linker kit for general cell membrane labeling Sigma-Aldrich Cat# PKH26, PKH67 Deposited data The lipidomics data of BMDMs from Abca1/g1 -m/-m and Abca1/g1 f/f This study Mendeley Data: https://doi.org/10.17632/ gd4mprzbvh.1 The RNA sequence data for BMDMs from Abca1/g1 -m/-m and Abca1/g1 f/f This study GEO: GSE234507 The lipidomics data of retina isolated from young and old mice This study Mendeley Data: https://doi.org/10.17632/ j9gv8x9td7.1 The RNA sequence data for retinal pigment epithelium/choroid tissue of Abca1/g1 -m/-m and INK-ATTAC- Abca1/g1 -m/-m This study GEO: GSE234641 Experimental models: Organisms/strains Mouse: C57BL/6J The Jackson Laboratory RRID: IMSR_JAX:000664 Mouse: Abca1fl Abcg1fl: B6.CgAbca1tm1Jp Abcg1tm1Tall/J The Jackson Laboratory RRID: IMSR_JAX:021067 Mouse: LysM Cre: B6.129P2Lyz2tm1(cre)Ifo/J The Jackson Laboratory RRID: IMSR_JAX:004781 Mouse: INK-ATTAC Unity Biotechnology N/A Mouse: Cx3cr1 CreERT2: B6.129P2(Cg)-Cx3cr1tm2.1(cre/ERT2)Litt/ WganJ The Jackson Laboratory RRID: IMSR_JAX:021160 Mouse: Tmem119 Cre ERT2: C57BL/6-Tmem119em1(cre/ERT2)Gfng/J The Jackson Laboratory RRID: IMSR_JAX:031820 Oligonucleotides Primers for qPCR, see Table S1 Thermo Scientific N/A AllStars Negative Control siRNA QIAGEN Cat#1027281 siRNA targeting Nr1h3 (NM_013839) QIAGEN Cat#SI02740339 siRNA targeting Nr1h2 (NM_009473) QIAGEN Cat#SI00185241 siRNA targeting Cd38 (NM_007646) QIAGEN Cat#SI02666398 Software and algorithms GraphPad Prism GraphPad Software https://www.graphpad.com/scientific- software/prism/ LipidSig N/A http://chenglab.cmu.edu.tw/lipidsig/ CellProfiler https://cellprofiler.org MassHunter Quantitative Analysis Agilent Technologies https://www.agilent.com/en/product/ software-informatics/mass-spectrometrysoftware/ FlowJo BD Biosciences https://www.flowjo.com/solutions/flowjo ImageJ National Institutes of Health https://imagej.nih.gov/ij/download.html Sample Size Calculator ClinCalc https://clincalc.com/stats/samplesize. aspx.
Cell Culture:Article Title: LXR/CD38 activation drives cholesterol-induced macrophage senescence and neurodegeneration via NAD + depletion.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit polyclonal anti-Iba1 Wako Cat#019-19741; RRID:AB_839504 Rat monoclonal anti-F4/80 abcam Cat#ab6640; RRID:AB_1140040 Sheep polyclonal anti-CD38 R&D Systems Cat#AF4947; RRID:AB_1241945 Rabbit polyclonal anti-Ki67 abcam Cat#abcam15580; RRID;AB_443209 Phalloidin-iFluor 647 abcam Cat#ab176759 Alexa Fluor 647 donkey anti-rabbit IgG Jackson ImmunoResearch Cat#711-605-152 Alexa Fluor 647 donkey anti-rat IgG Jackson ImmunoResearch Cat# 712-605-153 Alexa Fluor 488 donkey anti-sheep IgG Jackson ImmunoResearch Cat#713-545-147 Goat polyclonal antibody to Biotin (FITC) abcam Cat#ab6550 Bacterial and virus strains pCMV6-XL6 OriGene Technologies Cat#PCMV6XL6 pCMV6-AC-CD38-GFP OriGene Technologies Cat#MG204265 Chemicals, peptides, and recombinant proteins DMEM gibco Cat#11965-084 L-glutamate gibco Cat#25030-081 Penicillin/streptomycin (P/S) gibco Cat#15140-122 Accutase Sigma-Aldrich Cat#A6964 Cholesterol Sigma-Aldrich Cat#C4951 DNase Sigma-Aldrich Cat#D4527 DNA digestion buffer ZYMO RESEARCH Cat#E1010-1 High Capacity cDNA Reverse Transcription Kit Applied biosystems Cat#4368813 TaqMan Fast Advanced Master Mix Applied biosystems Cat#4444554 Nicotinamide-2,4,5,6-d4 C/D/N Isotopes Cat#D-3457 Lipofectamine RNAiMAX transfection reagent Thermo Fisher Scientific Cat#13778150 Lipofectamine 3000 transfection reagent Thermo Fisher Scientific Cat#L3000-008 Opti-MEM gibco Cat#31895-070 FK866 Chem Cruz Cat#sc-205325A DMEM, high glucose Sigma-Aldrich Cat#D1145 b-nicotinamide mononucleotide Sigma-Aldrich Cat#N3501 GW3965 Sigma-Aldrich Cat#G6295 78c MedChemExpress Cat#HY-123999 AP-20187 APExBIO Cat#B1274 Dasatinib Sigma-Aldrich Cat#SML2589 Quercetin Sigma-Aldrich Cat#Q4951 Seahorse XF DMEM Medium Agilent Technologies Cat#103575-100 Seahorse XF Cell Mito Stress Test kit Agilent Technologies Cat#103015-100 Seahorse XF24 V7 PS Cell Culture Microplate Agilent Technologies Cat#100777-004 Co-detection blocker Advanced Cell Diagnostics Cat#323170 Co-detection antibody diluent Advanced Cell Diagnostics Cat#323160 RNAscope probe Mm-Cdkn1a Advanced Cell Diagnostics Cat#408551 RNAscope probe Mm-Cdkn2a Advanced Cell Diagnostics Cat411011 RNAscope 2.5 HD detection reagents- red Advanced Cell Diagnostics Cat#322360 (Continued on next page) Cell Reports --, 114102, --, 2024 21 .. REAGENT or RESOURCE SOURCE IDENTIFIER SenTraGor Cell Senescence Reagent Cayman chemical Cat#35568 Critical commercial assays PierceTM BCA Protein Assay Kit Thermo Scientific Cat#23225 NBD Cholesterol Staining Dye Kit abcam Cat#ab269448 Senescence b-Galactosidase staining kit Cell Signaling Cat#9860 SPiDER b -galactosidase staining kit DOJINDO Cat#SG02 Lysosome intracellular activity assay kit abcam Cat#ab234622 TaqMan array standard plates Thermo Scientific Cat#4391524 Click-iTTM plus TUNEL Assay kits for in situ apoptosis eetection Invitrogen Cat#C10618 Fluorescent cell linker kit for general cell membrane labeling Sigma-Aldrich Cat# PKH26, PKH67 Deposited data The lipidomics data of BMDMs from Abca1/g1 -m/-m and Abca1/g1 f/f This study Mendeley Data: https://doi.org/10.17632/ gd4mprzbvh.1 The RNA sequence data for BMDMs from Abca1/g1 -m/-m and Abca1/g1 f/f This study GEO: GSE234507 The lipidomics data of retina isolated from young and old mice This study Mendeley Data: https://doi.org/10.17632/ j9gv8x9td7.1 The RNA sequence data for retinal pigment epithelium/choroid tissue of Abca1/g1 -m/-m and INK-ATTAC- Abca1/g1 -m/-m This study GEO: GSE234641 Experimental models: Organisms/strains Mouse: C57BL/6J The Jackson Laboratory RRID: IMSR_JAX:000664 Mouse: Abca1fl Abcg1fl: B6.CgAbca1tm1Jp Abcg1tm1Tall/J The Jackson Laboratory RRID: IMSR_JAX:021067 Mouse: LysM Cre: B6.129P2Lyz2tm1(cre)Ifo/J The Jackson Laboratory RRID: IMSR_JAX:004781 Mouse: INK-ATTAC Unity Biotechnology N/A Mouse: Cx3cr1 CreERT2: B6.129P2(Cg)-Cx3cr1tm2.1(cre/ERT2)Litt/ WganJ The Jackson Laboratory RRID: IMSR_JAX:021160 Mouse: Tmem119 Cre ERT2: C57BL/6-Tmem119em1(cre/ERT2)Gfng/J The Jackson Laboratory RRID: IMSR_JAX:031820 Oligonucleotides Primers for qPCR, see Table S1 Thermo Scientific N/A AllStars Negative Control siRNA QIAGEN Cat#1027281 siRNA targeting Nr1h3 (NM_013839) QIAGEN Cat#SI02740339 siRNA targeting Nr1h2 (NM_009473) QIAGEN Cat#SI00185241 siRNA targeting Cd38 (NM_007646) QIAGEN Cat#SI02666398 Software and algorithms GraphPad Prism GraphPad Software https://www.graphpad.com/scientific- software/prism/ LipidSig N/A http://chenglab.cmu.edu.tw/lipidsig/ CellProfiler https://cellprofiler.org MassHunter Quantitative Analysis Agilent Technologies https://www.agilent.com/en/product/ software-informatics/mass-spectrometrysoftware/ FlowJo BD Biosciences https://www.flowjo.com/solutions/flowjo ImageJ National Institutes of Health https://imagej.nih.gov/ij/download.html Sample Size Calculator ClinCalc https://clincalc.com/stats/samplesize. aspx.
RNAscope:Article Title: LXR/CD38 activation drives cholesterol-induced macrophage senescence and neurodegeneration via NAD + depletion.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit polyclonal anti-Iba1 Wako Cat#019-19741; RRID:AB_839504 Rat monoclonal anti-F4/80 abcam Cat#ab6640; RRID:AB_1140040 Sheep polyclonal anti-CD38 R&D Systems Cat#AF4947; RRID:AB_1241945 Rabbit polyclonal anti-Ki67 abcam Cat#abcam15580; RRID;AB_443209 Phalloidin-iFluor 647 abcam Cat#ab176759 Alexa Fluor 647 donkey anti-rabbit IgG Jackson ImmunoResearch Cat#711-605-152 Alexa Fluor 647 donkey anti-rat IgG Jackson ImmunoResearch Cat# 712-605-153 Alexa Fluor 488 donkey anti-sheep IgG Jackson ImmunoResearch Cat#713-545-147 Goat polyclonal antibody to Biotin (FITC) abcam Cat#ab6550 Bacterial and virus strains pCMV6-XL6 OriGene Technologies Cat#PCMV6XL6 pCMV6-AC-CD38-GFP OriGene Technologies Cat#MG204265 Chemicals, peptides, and recombinant proteins DMEM gibco Cat#11965-084 L-glutamate gibco Cat#25030-081 Penicillin/streptomycin (P/S) gibco Cat#15140-122 Accutase Sigma-Aldrich Cat#A6964 Cholesterol Sigma-Aldrich Cat#C4951 DNase Sigma-Aldrich Cat#D4527 DNA digestion buffer ZYMO RESEARCH Cat#E1010-1 High Capacity cDNA Reverse Transcription Kit Applied biosystems Cat#4368813 TaqMan Fast Advanced Master Mix Applied biosystems Cat#4444554 Nicotinamide-2,4,5,6-d4 C/D/N Isotopes Cat#D-3457 Lipofectamine RNAiMAX transfection reagent Thermo Fisher Scientific Cat#13778150 Lipofectamine 3000 transfection reagent Thermo Fisher Scientific Cat#L3000-008 Opti-MEM gibco Cat#31895-070 FK866 Chem Cruz Cat#sc-205325A DMEM, high glucose Sigma-Aldrich Cat#D1145 b-nicotinamide mononucleotide Sigma-Aldrich Cat#N3501 GW3965 Sigma-Aldrich Cat#G6295 78c MedChemExpress Cat#HY-123999 AP-20187 APExBIO Cat#B1274 Dasatinib Sigma-Aldrich Cat#SML2589 Quercetin Sigma-Aldrich Cat#Q4951 Seahorse XF DMEM Medium Agilent Technologies Cat#103575-100 Seahorse XF Cell Mito Stress Test kit Agilent Technologies Cat#103015-100 Seahorse XF24 V7 PS Cell Culture Microplate Agilent Technologies Cat#100777-004 Co-detection blocker Advanced Cell Diagnostics Cat#323170 Co-detection antibody diluent Advanced Cell Diagnostics Cat#323160 RNAscope probe Mm-Cdkn1a Advanced Cell Diagnostics Cat#408551 RNAscope probe Mm-Cdkn2a Advanced Cell Diagnostics Cat411011 RNAscope 2.5 HD detection reagents- red Advanced Cell Diagnostics Cat#322360 (Continued on next page) Cell Reports --, 114102, --, 2024 21 .. REAGENT or RESOURCE SOURCE IDENTIFIER SenTraGor Cell Senescence Reagent Cayman chemical Cat#35568 Critical commercial assays PierceTM BCA Protein Assay Kit Thermo Scientific Cat#23225 NBD Cholesterol Staining Dye Kit abcam Cat#ab269448 Senescence b-Galactosidase staining kit Cell Signaling Cat#9860 SPiDER b -galactosidase staining kit DOJINDO Cat#SG02 Lysosome intracellular activity assay kit abcam Cat#ab234622 TaqMan array standard plates Thermo Scientific Cat#4391524 Click-iTTM plus TUNEL Assay kits for in situ apoptosis eetection Invitrogen Cat#C10618 Fluorescent cell linker kit for general cell membrane labeling Sigma-Aldrich Cat# PKH26, PKH67 Deposited data The lipidomics data of BMDMs from Abca1/g1 -m/-m and Abca1/g1 f/f This study Mendeley Data: https://doi.org/10.17632/ gd4mprzbvh.1 The RNA sequence data for BMDMs from Abca1/g1 -m/-m and Abca1/g1 f/f This study GEO: GSE234507 The lipidomics data of retina isolated from young and old mice This study Mendeley Data: https://doi.org/10.17632/ j9gv8x9td7.1 The RNA sequence data for retinal pigment epithelium/choroid tissue of Abca1/g1 -m/-m and INK-ATTAC- Abca1/g1 -m/-m This study GEO: GSE234641 Experimental models: Organisms/strains Mouse: C57BL/6J The Jackson Laboratory RRID: IMSR_JAX:000664 Mouse: Abca1fl Abcg1fl: B6.CgAbca1tm1Jp Abcg1tm1Tall/J The Jackson Laboratory RRID: IMSR_JAX:021067 Mouse: LysM Cre: B6.129P2Lyz2tm1(cre)Ifo/J The Jackson Laboratory RRID: IMSR_JAX:004781 Mouse: INK-ATTAC Unity Biotechnology N/A Mouse: Cx3cr1 CreERT2: B6.129P2(Cg)-Cx3cr1tm2.1(cre/ERT2)Litt/ WganJ The Jackson Laboratory RRID: IMSR_JAX:021160 Mouse: Tmem119 Cre ERT2: C57BL/6-Tmem119em1(cre/ERT2)Gfng/J The Jackson Laboratory RRID: IMSR_JAX:031820 Oligonucleotides Primers for qPCR, see Table S1 Thermo Scientific N/A AllStars Negative Control siRNA QIAGEN Cat#1027281 siRNA targeting Nr1h3 (NM_013839) QIAGEN Cat#SI02740339 siRNA targeting Nr1h2 (NM_009473) QIAGEN Cat#SI00185241 siRNA targeting Cd38 (NM_007646) QIAGEN Cat#SI02666398 Software and algorithms GraphPad Prism GraphPad Software https://www.graphpad.com/scientific- software/prism/ LipidSig N/A http://chenglab.cmu.edu.tw/lipidsig/ CellProfiler https://cellprofiler.org MassHunter Quantitative Analysis Agilent Technologies https://www.agilent.com/en/product/ software-informatics/mass-spectrometrysoftware/ FlowJo BD Biosciences https://www.flowjo.com/solutions/flowjo ImageJ National Institutes of Health https://imagej.nih.gov/ij/download.html Sample Size Calculator ClinCalc https://clincalc.com/stats/samplesize. aspx.
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