Protease Inhibitor:Article Title: APOE4-promoted gliosis and degeneration in tauopathy are ameliorated by pharmacological inhibition of HMGB1 release.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse anti-AT8 Thermo Fisher Scientific Cat#: MN1020; RRID: AB_223647 Rat anti-CD68 Bio-Rad Cat#: MCA1957; RRID: AB_322219 Mouse anti-GAPDH Cell Signaling Cat#: 97166; RRID: AB_2756824 Mouse anti-GFAP Millipore Cat#: MAB3402; RRID: AB_94844 Rabbit anti-HMGB1 Abcam Cat#: ab18256; RRID: AB_444360 Rabbit anti-Acetyl-HMGB1 (Lys29) Thermo Fisher Scientific Cat#: PA5-120416 RRID: AB_2913988 Rabbit anti-Iba1 Wako Cat#: 019-19741; RRID: AB_839504 Rabbit anti-MBP Abcam Cat#: ab40390 RRID: AB_1141521 Goat anti-Iba1 Abcam Cat#: ab5076 RRID: AB_2224402 Guinea Pig anti-NeuN Millipore Cat#: ABN90; RRID: AB_11205592 Mouse anti-SIRT1 Abcam Cat#: ab110304 RRID: AB_10864359 Rabbit anti-S100b Abcam Cat#: ab52642; RRID: AB_882426 Rabbit anti-TUJ1 Biolegend Cat#: 802001; RRID: AB_2564645 Donkey anti-mouse Biotin-SP Jackson Immuno Research Labs Cat#: 715-065-150; RRID: AB_2307438 Donkey anti-mouse Alexa Fluor 488 Abcam Cat#: ab150105; RRID: AB_2732856 Donkey anti-rabbit Alexa Fluor 488 Abcam Cat#: ab150073; RRID: AB_2636877 Donkey anti-rat Alexa Fluor 488 Abcam Cat#: ab150153; RRID: AB_2737355 Donkey anti-mouse Alexa Fluor 594 Abcam Cat#: ab150108 RRID: AB_2732073 Donkey anti-rabbit Alexa Fluor 594 Abcam Cat#: ab150076 RRID: AB_2782993 Donkey anti-guinea pig 594 Jackson Immuno Research Labs Cat#: 706-585-148; RRID: AB_2340474 Donkey anti-mouse 647 Abcam Cat#: ab150107; RRID: AB_2890037 Donkey anti-rabbit 647 Abcam Cat#ab150075; RRID: AB_2752244 Donkey anti-guinea pig 647 Jackson Immuno Research Labs Cat#: 706-605-148; RRID: AB_2340476 Donkey anti-mouse IRDye 800CW LI-COR Cat#: 926-32212; RRID: AB_621847 Donkey anti-rabbit IRDye 680RD LI-COR Cat#: 926-68073; RRID: AB_10954442 Chemicals, peptides, and recombinant proteins Artificial CSF Harvard Apparatus Cat#: 59-7316 Biotinylated donkey anti-mouse Jackson Immuno Research Labs Cat#: 715-065-150 Benzonase Nuclease Sigma-Aldrich Cat#: E1014 (Continued on next page) 22 Cell Reports 42, 113252, October 31, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER cOmplete Protease Inhibitor Cocktail Roche Cat#: 11836145001 DAPI Thermofischer Cat#: 62248 DPX mounting medium Sigma-Aldrich Cat#: 6522 Ethyl Pyruvate Sigma-Aldrich Cat#: 8066170500 Glycyrrhizic Acid Sigma-Aldrich Cat#: 50531-50G Intercept Blocking Buffer (PBS) LI-COR Cat#: 927-70001 M.O.M. blocking buffer Vector Labs Cat#: MKB-2213-1 NewBlot IR Stripping Buffer LICOR Cat#: 928-40028 Normal Donkey Serum Jackson Immuno Research Labs Cat#: 17000121 NuPage 12% Bis-Tris gel Invitrogen Cat#: NP0343 NuPage MOPS SDS Running Buffer Novex Cat#: NP0001 Paraformaldehyde Electron Microscopy Sciences Cat#: 15710-S ProLong Gold mounting medium Vector Labs Cat#: P36930 PhosSTOP phosphatase inhibitor Roche Cat#: 04-906-845-001 RAB buffer G Biosciences Cat#: 786-91 Recombinant Human HMGB1 protein R&D Systems Cat#: 1690-HMB-050 RIPA buffer Thermo Fisher Scientific Cat#: 89900 Saline (0.9%) Fisher Scientific Cat#: Z1376 Sudan Black B Sigma-Aldrich Cat#: 199664 Critical commercial assays Avidin/Biotin blocking kit Vector Labs Cat#: SP-2001 ABC-HRP Kit, Peroxidase Vector Labs Cat#: PK-6100 DAB Substrate Kit Vector Labs Cat#: SK-4100 Chromium Next GEM Single Cell 3ʹ Library and Gel Bead kit v3.1 10x Genomics Cat#: 1000128 Mouse HMGB1 ELISA kit Novus Biologicals Cat#: NBP2-62767 V-PLEX Plus Mouse Cytokine 19-Plex kit Meso Scal Diagnostics Cat#: K15255G NE-PER nuclear and cytoplasmic extraction reagents Thermo Fisher Scientific Cat#: 78835 Deposited data Raw snRNA-seq data This paper GEO accession number: GSE242153 Processed snRNA-seq data This paper Tables S1, S2, S3, S4, S5, S6 Experimental models: Organisms/strains Mouse: APOE3-KI: Apoetm2(APOE_i3)Yhg Yadong Huang Bien-Ly et. al.49, 2012 Mouse: APOE4-KI: Apoetm3(APOE_i4)Yhg Yadong Huang Bien-Ly et. al.49, 2012 Mouse; PS19-E4 APOE4-KI crossbred to Tau-P301S (PS19 line) (Jax #008169) This paper N/A Mouse: PS19-E3 APOE3-KI crossbred to Tau-P301S (PS19 line) (Jax #008169) This paper N/A Mouse: PS19-E4/Syn1-Cre APOE4-KI crossbred to Tau P301S (PS19 line; Jax #008169) crossbred to Syn1-Cre (Jax 003966) This paper N/A Mouse: Wildtype The Jackson Laboratory Cat#: 000664 Human: Brain tissue from ROSMAP cohort Bennett et al932018 radc.rush.edu (Continued on next page) Cell Reports 42, 113252, October 31, 2023 23 OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides Software and algorithms GraphPad Prism 9 for Mac GraphPad Software https://www.graphpad.com/ scientific-software/prism/ Fiji v2.3 Schindelin et al, 2012 https://imagej.net/software/fiji/downloads Image Studio Lite v.5.2.5 LI-COR https://www.licor.com/bio/ image-studio-lite/resources Seurat v4.0.5 Hao et al94, 2021 https://satijalab.org/seurat/articles/install. html Cellranger v6.1.1 10x Genomics https://support.10xgenomics.com/ single-cell-gene-expression/software/ downloads/6.1/ glmGamPoi v1.6.0 Ahlmann-Eltze et al95, 2021 https://bioconductor.org/packages/ release/bioc/html/glmGamPoi.html lme4 v.1.1-27.1 Bates et al96, 2015 https://cran.r-project.org/web/packages/ lme4/index.html lme4 v.1.1-30 Bates et al96, 2015 https://cran.r-project.org/web/packages/ lme4/index.html R v4.1.2 R Core Team https://www.R-project.org Codes generated in this study This paper https://github.com/ADNetworksPPG/ YH_NK01_APOE4_HMGB1_paper/ Codes generated in this study This paper https://doi.org/10.5281/zenodo.8309839.
Blocking Assay:Article Title: APOE4-promoted gliosis and degeneration in tauopathy are ameliorated by pharmacological inhibition of HMGB1 release.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse anti-AT8 Thermo Fisher Scientific Cat#: MN1020; RRID: AB_223647 Rat anti-CD68 Bio-Rad Cat#: MCA1957; RRID: AB_322219 Mouse anti-GAPDH Cell Signaling Cat#: 97166; RRID: AB_2756824 Mouse anti-GFAP Millipore Cat#: MAB3402; RRID: AB_94844 Rabbit anti-HMGB1 Abcam Cat#: ab18256; RRID: AB_444360 Rabbit anti-Acetyl-HMGB1 (Lys29) Thermo Fisher Scientific Cat#: PA5-120416 RRID: AB_2913988 Rabbit anti-Iba1 Wako Cat#: 019-19741; RRID: AB_839504 Rabbit anti-MBP Abcam Cat#: ab40390 RRID: AB_1141521 Goat anti-Iba1 Abcam Cat#: ab5076 RRID: AB_2224402 Guinea Pig anti-NeuN Millipore Cat#: ABN90; RRID: AB_11205592 Mouse anti-SIRT1 Abcam Cat#: ab110304 RRID: AB_10864359 Rabbit anti-S100b Abcam Cat#: ab52642; RRID: AB_882426 Rabbit anti-TUJ1 Biolegend Cat#: 802001; RRID: AB_2564645 Donkey anti-mouse Biotin-SP Jackson Immuno Research Labs Cat#: 715-065-150; RRID: AB_2307438 Donkey anti-mouse Alexa Fluor 488 Abcam Cat#: ab150105; RRID: AB_2732856 Donkey anti-rabbit Alexa Fluor 488 Abcam Cat#: ab150073; RRID: AB_2636877 Donkey anti-rat Alexa Fluor 488 Abcam Cat#: ab150153; RRID: AB_2737355 Donkey anti-mouse Alexa Fluor 594 Abcam Cat#: ab150108 RRID: AB_2732073 Donkey anti-rabbit Alexa Fluor 594 Abcam Cat#: ab150076 RRID: AB_2782993 Donkey anti-guinea pig 594 Jackson Immuno Research Labs Cat#: 706-585-148; RRID: AB_2340474 Donkey anti-mouse 647 Abcam Cat#: ab150107; RRID: AB_2890037 Donkey anti-rabbit 647 Abcam Cat#ab150075; RRID: AB_2752244 Donkey anti-guinea pig 647 Jackson Immuno Research Labs Cat#: 706-605-148; RRID: AB_2340476 Donkey anti-mouse IRDye 800CW LI-COR Cat#: 926-32212; RRID: AB_621847 Donkey anti-rabbit IRDye 680RD LI-COR Cat#: 926-68073; RRID: AB_10954442 Chemicals, peptides, and recombinant proteins Artificial CSF Harvard Apparatus Cat#: 59-7316 Biotinylated donkey anti-mouse Jackson Immuno Research Labs Cat#: 715-065-150 Benzonase Nuclease Sigma-Aldrich Cat#: E1014 (Continued on next page) 22 Cell Reports 42, 113252, October 31, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER cOmplete Protease Inhibitor Cocktail Roche Cat#: 11836145001 DAPI Thermofischer Cat#: 62248 DPX mounting medium Sigma-Aldrich Cat#: 6522 Ethyl Pyruvate Sigma-Aldrich Cat#: 8066170500 Glycyrrhizic Acid Sigma-Aldrich Cat#: 50531-50G Intercept Blocking Buffer (PBS) LI-COR Cat#: 927-70001 M.O.M. blocking buffer Vector Labs Cat#: MKB-2213-1 NewBlot IR Stripping Buffer LICOR Cat#: 928-40028 Normal Donkey Serum Jackson Immuno Research Labs Cat#: 17000121 NuPage 12% Bis-Tris gel Invitrogen Cat#: NP0343 NuPage MOPS SDS Running Buffer Novex Cat#: NP0001 Paraformaldehyde Electron Microscopy Sciences Cat#: 15710-S ProLong Gold mounting medium Vector Labs Cat#: P36930 PhosSTOP phosphatase inhibitor Roche Cat#: 04-906-845-001 RAB buffer G Biosciences Cat#: 786-91 Recombinant Human HMGB1 protein R&D Systems Cat#: 1690-HMB-050 RIPA buffer Thermo Fisher Scientific Cat#: 89900 Saline (0.9%) Fisher Scientific Cat#: Z1376 Sudan Black B Sigma-Aldrich Cat#: 199664 Critical commercial assays Avidin/Biotin blocking kit Vector Labs Cat#: SP-2001 ABC-HRP Kit, Peroxidase Vector Labs Cat#: PK-6100 DAB Substrate Kit Vector Labs Cat#: SK-4100 Chromium Next GEM Single Cell 3ʹ Library and Gel Bead kit v3.1 10x Genomics Cat#: 1000128 Mouse HMGB1 ELISA kit Novus Biologicals Cat#: NBP2-62767 V-PLEX Plus Mouse Cytokine 19-Plex kit Meso Scal Diagnostics Cat#: K15255G NE-PER nuclear and cytoplasmic extraction reagents Thermo Fisher Scientific Cat#: 78835 Deposited data Raw snRNA-seq data This paper GEO accession number: GSE242153 Processed snRNA-seq data This paper Tables S1, S2, S3, S4, S5, S6 Experimental models: Organisms/strains Mouse: APOE3-KI: Apoetm2(APOE_i3)Yhg Yadong Huang Bien-Ly et. al.49, 2012 Mouse: APOE4-KI: Apoetm3(APOE_i4)Yhg Yadong Huang Bien-Ly et. al.49, 2012 Mouse; PS19-E4 APOE4-KI crossbred to Tau-P301S (PS19 line) (Jax #008169) This paper N/A Mouse: PS19-E3 APOE3-KI crossbred to Tau-P301S (PS19 line) (Jax #008169) This paper N/A Mouse: PS19-E4/Syn1-Cre APOE4-KI crossbred to Tau P301S (PS19 line; Jax #008169) crossbred to Syn1-Cre (Jax 003966) This paper N/A Mouse: Wildtype The Jackson Laboratory Cat#: 000664 Human: Brain tissue from ROSMAP cohort Bennett et al932018 radc.rush.edu (Continued on next page) Cell Reports 42, 113252, October 31, 2023 23 OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides Software and algorithms GraphPad Prism 9 for Mac GraphPad Software https://www.graphpad.com/ scientific-software/prism/ Fiji v2.3 Schindelin et al, 2012 https://imagej.net/software/fiji/downloads Image Studio Lite v.5.2.5 LI-COR https://www.licor.com/bio/ image-studio-lite/resources Seurat v4.0.5 Hao et al94, 2021 https://satijalab.org/seurat/articles/install. html Cellranger v6.1.1 10x Genomics https://support.10xgenomics.com/ single-cell-gene-expression/software/ downloads/6.1/ glmGamPoi v1.6.0 Ahlmann-Eltze et al95, 2021 https://bioconductor.org/packages/ release/bioc/html/glmGamPoi.html lme4 v.1.1-27.1 Bates et al96, 2015 https://cran.r-project.org/web/packages/ lme4/index.html lme4 v.1.1-30 Bates et al96, 2015 https://cran.r-project.org/web/packages/ lme4/index.html R v4.1.2 R Core Team https://www.R-project.org Codes generated in this study This paper https://github.com/ADNetworksPPG/ YH_NK01_APOE4_HMGB1_paper/ Codes generated in this study This paper https://doi.org/10.5281/zenodo.8309839.
Stripping Membranes:Article Title: APOE4-promoted gliosis and degeneration in tauopathy are ameliorated by pharmacological inhibition of HMGB1 release.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse anti-AT8 Thermo Fisher Scientific Cat#: MN1020; RRID: AB_223647 Rat anti-CD68 Bio-Rad Cat#: MCA1957; RRID: AB_322219 Mouse anti-GAPDH Cell Signaling Cat#: 97166; RRID: AB_2756824 Mouse anti-GFAP Millipore Cat#: MAB3402; RRID: AB_94844 Rabbit anti-HMGB1 Abcam Cat#: ab18256; RRID: AB_444360 Rabbit anti-Acetyl-HMGB1 (Lys29) Thermo Fisher Scientific Cat#: PA5-120416 RRID: AB_2913988 Rabbit anti-Iba1 Wako Cat#: 019-19741; RRID: AB_839504 Rabbit anti-MBP Abcam Cat#: ab40390 RRID: AB_1141521 Goat anti-Iba1 Abcam Cat#: ab5076 RRID: AB_2224402 Guinea Pig anti-NeuN Millipore Cat#: ABN90; RRID: AB_11205592 Mouse anti-SIRT1 Abcam Cat#: ab110304 RRID: AB_10864359 Rabbit anti-S100b Abcam Cat#: ab52642; RRID: AB_882426 Rabbit anti-TUJ1 Biolegend Cat#: 802001; RRID: AB_2564645 Donkey anti-mouse Biotin-SP Jackson Immuno Research Labs Cat#: 715-065-150; RRID: AB_2307438 Donkey anti-mouse Alexa Fluor 488 Abcam Cat#: ab150105; RRID: AB_2732856 Donkey anti-rabbit Alexa Fluor 488 Abcam Cat#: ab150073; RRID: AB_2636877 Donkey anti-rat Alexa Fluor 488 Abcam Cat#: ab150153; RRID: AB_2737355 Donkey anti-mouse Alexa Fluor 594 Abcam Cat#: ab150108 RRID: AB_2732073 Donkey anti-rabbit Alexa Fluor 594 Abcam Cat#: ab150076 RRID: AB_2782993 Donkey anti-guinea pig 594 Jackson Immuno Research Labs Cat#: 706-585-148; RRID: AB_2340474 Donkey anti-mouse 647 Abcam Cat#: ab150107; RRID: AB_2890037 Donkey anti-rabbit 647 Abcam Cat#ab150075; RRID: AB_2752244 Donkey anti-guinea pig 647 Jackson Immuno Research Labs Cat#: 706-605-148; RRID: AB_2340476 Donkey anti-mouse IRDye 800CW LI-COR Cat#: 926-32212; RRID: AB_621847 Donkey anti-rabbit IRDye 680RD LI-COR Cat#: 926-68073; RRID: AB_10954442 Chemicals, peptides, and recombinant proteins Artificial CSF Harvard Apparatus Cat#: 59-7316 Biotinylated donkey anti-mouse Jackson Immuno Research Labs Cat#: 715-065-150 Benzonase Nuclease Sigma-Aldrich Cat#: E1014 (Continued on next page) 22 Cell Reports 42, 113252, October 31, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER cOmplete Protease Inhibitor Cocktail Roche Cat#: 11836145001 DAPI Thermofischer Cat#: 62248 DPX mounting medium Sigma-Aldrich Cat#: 6522 Ethyl Pyruvate Sigma-Aldrich Cat#: 8066170500 Glycyrrhizic Acid Sigma-Aldrich Cat#: 50531-50G Intercept Blocking Buffer (PBS) LI-COR Cat#: 927-70001 M.O.M. blocking buffer Vector Labs Cat#: MKB-2213-1 NewBlot IR Stripping Buffer LICOR Cat#: 928-40028 Normal Donkey Serum Jackson Immuno Research Labs Cat#: 17000121 NuPage 12% Bis-Tris gel Invitrogen Cat#: NP0343 NuPage MOPS SDS Running Buffer Novex Cat#: NP0001 Paraformaldehyde Electron Microscopy Sciences Cat#: 15710-S ProLong Gold mounting medium Vector Labs Cat#: P36930 PhosSTOP phosphatase inhibitor Roche Cat#: 04-906-845-001 RAB buffer G Biosciences Cat#: 786-91 Recombinant Human HMGB1 protein R&D Systems Cat#: 1690-HMB-050 RIPA buffer Thermo Fisher Scientific Cat#: 89900 Saline (0.9%) Fisher Scientific Cat#: Z1376 Sudan Black B Sigma-Aldrich Cat#: 199664 Critical commercial assays Avidin/Biotin blocking kit Vector Labs Cat#: SP-2001 ABC-HRP Kit, Peroxidase Vector Labs Cat#: PK-6100 DAB Substrate Kit Vector Labs Cat#: SK-4100 Chromium Next GEM Single Cell 3ʹ Library and Gel Bead kit v3.1 10x Genomics Cat#: 1000128 Mouse HMGB1 ELISA kit Novus Biologicals Cat#: NBP2-62767 V-PLEX Plus Mouse Cytokine 19-Plex kit Meso Scal Diagnostics Cat#: K15255G NE-PER nuclear and cytoplasmic extraction reagents Thermo Fisher Scientific Cat#: 78835 Deposited data Raw snRNA-seq data This paper GEO accession number: GSE242153 Processed snRNA-seq data This paper Tables S1, S2, S3, S4, S5, S6 Experimental models: Organisms/strains Mouse: APOE3-KI: Apoetm2(APOE_i3)Yhg Yadong Huang Bien-Ly et. al.49, 2012 Mouse: APOE4-KI: Apoetm3(APOE_i4)Yhg Yadong Huang Bien-Ly et. al.49, 2012 Mouse; PS19-E4 APOE4-KI crossbred to Tau-P301S (PS19 line) (Jax #008169) This paper N/A Mouse: PS19-E3 APOE3-KI crossbred to Tau-P301S (PS19 line) (Jax #008169) This paper N/A Mouse: PS19-E4/Syn1-Cre APOE4-KI crossbred to Tau P301S (PS19 line; Jax #008169) crossbred to Syn1-Cre (Jax 003966) This paper N/A Mouse: Wildtype The Jackson Laboratory Cat#: 000664 Human: Brain tissue from ROSMAP cohort Bennett et al932018 radc.rush.edu (Continued on next page) Cell Reports 42, 113252, October 31, 2023 23 OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides Software and algorithms GraphPad Prism 9 for Mac GraphPad Software https://www.graphpad.com/ scientific-software/prism/ Fiji v2.3 Schindelin et al, 2012 https://imagej.net/software/fiji/downloads Image Studio Lite v.5.2.5 LI-COR https://www.licor.com/bio/ image-studio-lite/resources Seurat v4.0.5 Hao et al94, 2021 https://satijalab.org/seurat/articles/install. html Cellranger v6.1.1 10x Genomics https://support.10xgenomics.com/ single-cell-gene-expression/software/ downloads/6.1/ glmGamPoi v1.6.0 Ahlmann-Eltze et al95, 2021 https://bioconductor.org/packages/ release/bioc/html/glmGamPoi.html lme4 v.1.1-27.1 Bates et al96, 2015 https://cran.r-project.org/web/packages/ lme4/index.html lme4 v.1.1-30 Bates et al96, 2015 https://cran.r-project.org/web/packages/ lme4/index.html R v4.1.2 R Core Team https://www.R-project.org Codes generated in this study This paper https://github.com/ADNetworksPPG/ YH_NK01_APOE4_HMGB1_paper/ Codes generated in this study This paper https://doi.org/10.5281/zenodo.8309839.
Electron Microscopy:Article Title: APOE4-promoted gliosis and degeneration in tauopathy are ameliorated by pharmacological inhibition of HMGB1 release.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse anti-AT8 Thermo Fisher Scientific Cat#: MN1020; RRID: AB_223647 Rat anti-CD68 Bio-Rad Cat#: MCA1957; RRID: AB_322219 Mouse anti-GAPDH Cell Signaling Cat#: 97166; RRID: AB_2756824 Mouse anti-GFAP Millipore Cat#: MAB3402; RRID: AB_94844 Rabbit anti-HMGB1 Abcam Cat#: ab18256; RRID: AB_444360 Rabbit anti-Acetyl-HMGB1 (Lys29) Thermo Fisher Scientific Cat#: PA5-120416 RRID: AB_2913988 Rabbit anti-Iba1 Wako Cat#: 019-19741; RRID: AB_839504 Rabbit anti-MBP Abcam Cat#: ab40390 RRID: AB_1141521 Goat anti-Iba1 Abcam Cat#: ab5076 RRID: AB_2224402 Guinea Pig anti-NeuN Millipore Cat#: ABN90; RRID: AB_11205592 Mouse anti-SIRT1 Abcam Cat#: ab110304 RRID: AB_10864359 Rabbit anti-S100b Abcam Cat#: ab52642; RRID: AB_882426 Rabbit anti-TUJ1 Biolegend Cat#: 802001; RRID: AB_2564645 Donkey anti-mouse Biotin-SP Jackson Immuno Research Labs Cat#: 715-065-150; RRID: AB_2307438 Donkey anti-mouse Alexa Fluor 488 Abcam Cat#: ab150105; RRID: AB_2732856 Donkey anti-rabbit Alexa Fluor 488 Abcam Cat#: ab150073; RRID: AB_2636877 Donkey anti-rat Alexa Fluor 488 Abcam Cat#: ab150153; RRID: AB_2737355 Donkey anti-mouse Alexa Fluor 594 Abcam Cat#: ab150108 RRID: AB_2732073 Donkey anti-rabbit Alexa Fluor 594 Abcam Cat#: ab150076 RRID: AB_2782993 Donkey anti-guinea pig 594 Jackson Immuno Research Labs Cat#: 706-585-148; RRID: AB_2340474 Donkey anti-mouse 647 Abcam Cat#: ab150107; RRID: AB_2890037 Donkey anti-rabbit 647 Abcam Cat#ab150075; RRID: AB_2752244 Donkey anti-guinea pig 647 Jackson Immuno Research Labs Cat#: 706-605-148; RRID: AB_2340476 Donkey anti-mouse IRDye 800CW LI-COR Cat#: 926-32212; RRID: AB_621847 Donkey anti-rabbit IRDye 680RD LI-COR Cat#: 926-68073; RRID: AB_10954442 Chemicals, peptides, and recombinant proteins Artificial CSF Harvard Apparatus Cat#: 59-7316 Biotinylated donkey anti-mouse Jackson Immuno Research Labs Cat#: 715-065-150 Benzonase Nuclease Sigma-Aldrich Cat#: E1014 (Continued on next page) 22 Cell Reports 42, 113252, October 31, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER cOmplete Protease Inhibitor Cocktail Roche Cat#: 11836145001 DAPI Thermofischer Cat#: 62248 DPX mounting medium Sigma-Aldrich Cat#: 6522 Ethyl Pyruvate Sigma-Aldrich Cat#: 8066170500 Glycyrrhizic Acid Sigma-Aldrich Cat#: 50531-50G Intercept Blocking Buffer (PBS) LI-COR Cat#: 927-70001 M.O.M. blocking buffer Vector Labs Cat#: MKB-2213-1 NewBlot IR Stripping Buffer LICOR Cat#: 928-40028 Normal Donkey Serum Jackson Immuno Research Labs Cat#: 17000121 NuPage 12% Bis-Tris gel Invitrogen Cat#: NP0343 NuPage MOPS SDS Running Buffer Novex Cat#: NP0001 Paraformaldehyde Electron Microscopy Sciences Cat#: 15710-S ProLong Gold mounting medium Vector Labs Cat#: P36930 PhosSTOP phosphatase inhibitor Roche Cat#: 04-906-845-001 RAB buffer G Biosciences Cat#: 786-91 Recombinant Human HMGB1 protein R&D Systems Cat#: 1690-HMB-050 RIPA buffer Thermo Fisher Scientific Cat#: 89900 Saline (0.9%) Fisher Scientific Cat#: Z1376 Sudan Black B Sigma-Aldrich Cat#: 199664 Critical commercial assays Avidin/Biotin blocking kit Vector Labs Cat#: SP-2001 ABC-HRP Kit, Peroxidase Vector Labs Cat#: PK-6100 DAB Substrate Kit Vector Labs Cat#: SK-4100 Chromium Next GEM Single Cell 3ʹ Library and Gel Bead kit v3.1 10x Genomics Cat#: 1000128 Mouse HMGB1 ELISA kit Novus Biologicals Cat#: NBP2-62767 V-PLEX Plus Mouse Cytokine 19-Plex kit Meso Scal Diagnostics Cat#: K15255G NE-PER nuclear and cytoplasmic extraction reagents Thermo Fisher Scientific Cat#: 78835 Deposited data Raw snRNA-seq data This paper GEO accession number: GSE242153 Processed snRNA-seq data This paper Tables S1, S2, S3, S4, S5, S6 Experimental models: Organisms/strains Mouse: APOE3-KI: Apoetm2(APOE_i3)Yhg Yadong Huang Bien-Ly et. al.49, 2012 Mouse: APOE4-KI: Apoetm3(APOE_i4)Yhg Yadong Huang Bien-Ly et. al.49, 2012 Mouse; PS19-E4 APOE4-KI crossbred to Tau-P301S (PS19 line) (Jax #008169) This paper N/A Mouse: PS19-E3 APOE3-KI crossbred to Tau-P301S (PS19 line) (Jax #008169) This paper N/A Mouse: PS19-E4/Syn1-Cre APOE4-KI crossbred to Tau P301S (PS19 line; Jax #008169) crossbred to Syn1-Cre (Jax 003966) This paper N/A Mouse: Wildtype The Jackson Laboratory Cat#: 000664 Human: Brain tissue from ROSMAP cohort Bennett et al932018 radc.rush.edu (Continued on next page) Cell Reports 42, 113252, October 31, 2023 23 OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides Software and algorithms GraphPad Prism 9 for Mac GraphPad Software https://www.graphpad.com/ scientific-software/prism/ Fiji v2.3 Schindelin et al, 2012 https://imagej.net/software/fiji/downloads Image Studio Lite v.5.2.5 LI-COR https://www.licor.com/bio/ image-studio-lite/resources Seurat v4.0.5 Hao et al94, 2021 https://satijalab.org/seurat/articles/install. html Cellranger v6.1.1 10x Genomics https://support.10xgenomics.com/ single-cell-gene-expression/software/ downloads/6.1/ glmGamPoi v1.6.0 Ahlmann-Eltze et al95, 2021 https://bioconductor.org/packages/ release/bioc/html/glmGamPoi.html lme4 v.1.1-27.1 Bates et al96, 2015 https://cran.r-project.org/web/packages/ lme4/index.html lme4 v.1.1-30 Bates et al96, 2015 https://cran.r-project.org/web/packages/ lme4/index.html R v4.1.2 R Core Team https://www.R-project.org Codes generated in this study This paper https://github.com/ADNetworksPPG/ YH_NK01_APOE4_HMGB1_paper/ Codes generated in this study This paper https://doi.org/10.5281/zenodo.8309839.
Recombinant:Article Title: APOE4-promoted gliosis and degeneration in tauopathy are ameliorated by pharmacological inhibition of HMGB1 release.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse anti-AT8 Thermo Fisher Scientific Cat#: MN1020; RRID: AB_223647 Rat anti-CD68 Bio-Rad Cat#: MCA1957; RRID: AB_322219 Mouse anti-GAPDH Cell Signaling Cat#: 97166; RRID: AB_2756824 Mouse anti-GFAP Millipore Cat#: MAB3402; RRID: AB_94844 Rabbit anti-HMGB1 Abcam Cat#: ab18256; RRID: AB_444360 Rabbit anti-Acetyl-HMGB1 (Lys29) Thermo Fisher Scientific Cat#: PA5-120416 RRID: AB_2913988 Rabbit anti-Iba1 Wako Cat#: 019-19741; RRID: AB_839504 Rabbit anti-MBP Abcam Cat#: ab40390 RRID: AB_1141521 Goat anti-Iba1 Abcam Cat#: ab5076 RRID: AB_2224402 Guinea Pig anti-NeuN Millipore Cat#: ABN90; RRID: AB_11205592 Mouse anti-SIRT1 Abcam Cat#: ab110304 RRID: AB_10864359 Rabbit anti-S100b Abcam Cat#: ab52642; RRID: AB_882426 Rabbit anti-TUJ1 Biolegend Cat#: 802001; RRID: AB_2564645 Donkey anti-mouse Biotin-SP Jackson Immuno Research Labs Cat#: 715-065-150; RRID: AB_2307438 Donkey anti-mouse Alexa Fluor 488 Abcam Cat#: ab150105; RRID: AB_2732856 Donkey anti-rabbit Alexa Fluor 488 Abcam Cat#: ab150073; RRID: AB_2636877 Donkey anti-rat Alexa Fluor 488 Abcam Cat#: ab150153; RRID: AB_2737355 Donkey anti-mouse Alexa Fluor 594 Abcam Cat#: ab150108 RRID: AB_2732073 Donkey anti-rabbit Alexa Fluor 594 Abcam Cat#: ab150076 RRID: AB_2782993 Donkey anti-guinea pig 594 Jackson Immuno Research Labs Cat#: 706-585-148; RRID: AB_2340474 Donkey anti-mouse 647 Abcam Cat#: ab150107; RRID: AB_2890037 Donkey anti-rabbit 647 Abcam Cat#ab150075; RRID: AB_2752244 Donkey anti-guinea pig 647 Jackson Immuno Research Labs Cat#: 706-605-148; RRID: AB_2340476 Donkey anti-mouse IRDye 800CW LI-COR Cat#: 926-32212; RRID: AB_621847 Donkey anti-rabbit IRDye 680RD LI-COR Cat#: 926-68073; RRID: AB_10954442 Chemicals, peptides, and recombinant proteins Artificial CSF Harvard Apparatus Cat#: 59-7316 Biotinylated donkey anti-mouse Jackson Immuno Research Labs Cat#: 715-065-150 Benzonase Nuclease Sigma-Aldrich Cat#: E1014 (Continued on next page) 22 Cell Reports 42, 113252, October 31, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER cOmplete Protease Inhibitor Cocktail Roche Cat#: 11836145001 DAPI Thermofischer Cat#: 62248 DPX mounting medium Sigma-Aldrich Cat#: 6522 Ethyl Pyruvate Sigma-Aldrich Cat#: 8066170500 Glycyrrhizic Acid Sigma-Aldrich Cat#: 50531-50G Intercept Blocking Buffer (PBS) LI-COR Cat#: 927-70001 M.O.M. blocking buffer Vector Labs Cat#: MKB-2213-1 NewBlot IR Stripping Buffer LICOR Cat#: 928-40028 Normal Donkey Serum Jackson Immuno Research Labs Cat#: 17000121 NuPage 12% Bis-Tris gel Invitrogen Cat#: NP0343 NuPage MOPS SDS Running Buffer Novex Cat#: NP0001 Paraformaldehyde Electron Microscopy Sciences Cat#: 15710-S ProLong Gold mounting medium Vector Labs Cat#: P36930 PhosSTOP phosphatase inhibitor Roche Cat#: 04-906-845-001 RAB buffer G Biosciences Cat#: 786-91 Recombinant Human HMGB1 protein R&D Systems Cat#: 1690-HMB-050 RIPA buffer Thermo Fisher Scientific Cat#: 89900 Saline (0.9%) Fisher Scientific Cat#: Z1376 Sudan Black B Sigma-Aldrich Cat#: 199664 Critical commercial assays Avidin/Biotin blocking kit Vector Labs Cat#: SP-2001 ABC-HRP Kit, Peroxidase Vector Labs Cat#: PK-6100 DAB Substrate Kit Vector Labs Cat#: SK-4100 Chromium Next GEM Single Cell 3ʹ Library and Gel Bead kit v3.1 10x Genomics Cat#: 1000128 Mouse HMGB1 ELISA kit Novus Biologicals Cat#: NBP2-62767 V-PLEX Plus Mouse Cytokine 19-Plex kit Meso Scal Diagnostics Cat#: K15255G NE-PER nuclear and cytoplasmic extraction reagents Thermo Fisher Scientific Cat#: 78835 Deposited data Raw snRNA-seq data This paper GEO accession number: GSE242153 Processed snRNA-seq data This paper Tables S1, S2, S3, S4, S5, S6 Experimental models: Organisms/strains Mouse: APOE3-KI: Apoetm2(APOE_i3)Yhg Yadong Huang Bien-Ly et. al.49, 2012 Mouse: APOE4-KI: Apoetm3(APOE_i4)Yhg Yadong Huang Bien-Ly et. al.49, 2012 Mouse; PS19-E4 APOE4-KI crossbred to Tau-P301S (PS19 line) (Jax #008169) This paper N/A Mouse: PS19-E3 APOE3-KI crossbred to Tau-P301S (PS19 line) (Jax #008169) This paper N/A Mouse: PS19-E4/Syn1-Cre APOE4-KI crossbred to Tau P301S (PS19 line; Jax #008169) crossbred to Syn1-Cre (Jax 003966) This paper N/A Mouse: Wildtype The Jackson Laboratory Cat#: 000664 Human: Brain tissue from ROSMAP cohort Bennett et al932018 radc.rush.edu (Continued on next page) Cell Reports 42, 113252, October 31, 2023 23 OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides Software and algorithms GraphPad Prism 9 for Mac GraphPad Software https://www.graphpad.com/ scientific-software/prism/ Fiji v2.3 Schindelin et al, 2012 https://imagej.net/software/fiji/downloads Image Studio Lite v.5.2.5 LI-COR https://www.licor.com/bio/ image-studio-lite/resources Seurat v4.0.5 Hao et al94, 2021 https://satijalab.org/seurat/articles/install. html Cellranger v6.1.1 10x Genomics https://support.10xgenomics.com/ single-cell-gene-expression/software/ downloads/6.1/ glmGamPoi v1.6.0 Ahlmann-Eltze et al95, 2021 https://bioconductor.org/packages/ release/bioc/html/glmGamPoi.html lme4 v.1.1-27.1 Bates et al96, 2015 https://cran.r-project.org/web/packages/ lme4/index.html lme4 v.1.1-30 Bates et al96, 2015 https://cran.r-project.org/web/packages/ lme4/index.html R v4.1.2 R Core Team https://www.R-project.org Codes generated in this study This paper https://github.com/ADNetworksPPG/ YH_NK01_APOE4_HMGB1_paper/ Codes generated in this study This paper https://doi.org/10.5281/zenodo.8309839.
Saline:Article Title: APOE4-promoted gliosis and degeneration in tauopathy are ameliorated by pharmacological inhibition of HMGB1 release.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse anti-AT8 Thermo Fisher Scientific Cat#: MN1020; RRID: AB_223647 Rat anti-CD68 Bio-Rad Cat#: MCA1957; RRID: AB_322219 Mouse anti-GAPDH Cell Signaling Cat#: 97166; RRID: AB_2756824 Mouse anti-GFAP Millipore Cat#: MAB3402; RRID: AB_94844 Rabbit anti-HMGB1 Abcam Cat#: ab18256; RRID: AB_444360 Rabbit anti-Acetyl-HMGB1 (Lys29) Thermo Fisher Scientific Cat#: PA5-120416 RRID: AB_2913988 Rabbit anti-Iba1 Wako Cat#: 019-19741; RRID: AB_839504 Rabbit anti-MBP Abcam Cat#: ab40390 RRID: AB_1141521 Goat anti-Iba1 Abcam Cat#: ab5076 RRID: AB_2224402 Guinea Pig anti-NeuN Millipore Cat#: ABN90; RRID: AB_11205592 Mouse anti-SIRT1 Abcam Cat#: ab110304 RRID: AB_10864359 Rabbit anti-S100b Abcam Cat#: ab52642; RRID: AB_882426 Rabbit anti-TUJ1 Biolegend Cat#: 802001; RRID: AB_2564645 Donkey anti-mouse Biotin-SP Jackson Immuno Research Labs Cat#: 715-065-150; RRID: AB_2307438 Donkey anti-mouse Alexa Fluor 488 Abcam Cat#: ab150105; RRID: AB_2732856 Donkey anti-rabbit Alexa Fluor 488 Abcam Cat#: ab150073; RRID: AB_2636877 Donkey anti-rat Alexa Fluor 488 Abcam Cat#: ab150153; RRID: AB_2737355 Donkey anti-mouse Alexa Fluor 594 Abcam Cat#: ab150108 RRID: AB_2732073 Donkey anti-rabbit Alexa Fluor 594 Abcam Cat#: ab150076 RRID: AB_2782993 Donkey anti-guinea pig 594 Jackson Immuno Research Labs Cat#: 706-585-148; RRID: AB_2340474 Donkey anti-mouse 647 Abcam Cat#: ab150107; RRID: AB_2890037 Donkey anti-rabbit 647 Abcam Cat#ab150075; RRID: AB_2752244 Donkey anti-guinea pig 647 Jackson Immuno Research Labs Cat#: 706-605-148; RRID: AB_2340476 Donkey anti-mouse IRDye 800CW LI-COR Cat#: 926-32212; RRID: AB_621847 Donkey anti-rabbit IRDye 680RD LI-COR Cat#: 926-68073; RRID: AB_10954442 Chemicals, peptides, and recombinant proteins Artificial CSF Harvard Apparatus Cat#: 59-7316 Biotinylated donkey anti-mouse Jackson Immuno Research Labs Cat#: 715-065-150 Benzonase Nuclease Sigma-Aldrich Cat#: E1014 (Continued on next page) 22 Cell Reports 42, 113252, October 31, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER cOmplete Protease Inhibitor Cocktail Roche Cat#: 11836145001 DAPI Thermofischer Cat#: 62248 DPX mounting medium Sigma-Aldrich Cat#: 6522 Ethyl Pyruvate Sigma-Aldrich Cat#: 8066170500 Glycyrrhizic Acid Sigma-Aldrich Cat#: 50531-50G Intercept Blocking Buffer (PBS) LI-COR Cat#: 927-70001 M.O.M. blocking buffer Vector Labs Cat#: MKB-2213-1 NewBlot IR Stripping Buffer LICOR Cat#: 928-40028 Normal Donkey Serum Jackson Immuno Research Labs Cat#: 17000121 NuPage 12% Bis-Tris gel Invitrogen Cat#: NP0343 NuPage MOPS SDS Running Buffer Novex Cat#: NP0001 Paraformaldehyde Electron Microscopy Sciences Cat#: 15710-S ProLong Gold mounting medium Vector Labs Cat#: P36930 PhosSTOP phosphatase inhibitor Roche Cat#: 04-906-845-001 RAB buffer G Biosciences Cat#: 786-91 Recombinant Human HMGB1 protein R&D Systems Cat#: 1690-HMB-050 RIPA buffer Thermo Fisher Scientific Cat#: 89900 Saline (0.9%) Fisher Scientific Cat#: Z1376 Sudan Black B Sigma-Aldrich Cat#: 199664 Critical commercial assays Avidin/Biotin blocking kit Vector Labs Cat#: SP-2001 ABC-HRP Kit, Peroxidase Vector Labs Cat#: PK-6100 DAB Substrate Kit Vector Labs Cat#: SK-4100 Chromium Next GEM Single Cell 3ʹ Library and Gel Bead kit v3.1 10x Genomics Cat#: 1000128 Mouse HMGB1 ELISA kit Novus Biologicals Cat#: NBP2-62767 V-PLEX Plus Mouse Cytokine 19-Plex kit Meso Scal Diagnostics Cat#: K15255G NE-PER nuclear and cytoplasmic extraction reagents Thermo Fisher Scientific Cat#: 78835 Deposited data Raw snRNA-seq data This paper GEO accession number: GSE242153 Processed snRNA-seq data This paper Tables S1, S2, S3, S4, S5, S6 Experimental models: Organisms/strains Mouse: APOE3-KI: Apoetm2(APOE_i3)Yhg Yadong Huang Bien-Ly et. al.49, 2012 Mouse: APOE4-KI: Apoetm3(APOE_i4)Yhg Yadong Huang Bien-Ly et. al.49, 2012 Mouse; PS19-E4 APOE4-KI crossbred to Tau-P301S (PS19 line) (Jax #008169) This paper N/A Mouse: PS19-E3 APOE3-KI crossbred to Tau-P301S (PS19 line) (Jax #008169) This paper N/A Mouse: PS19-E4/Syn1-Cre APOE4-KI crossbred to Tau P301S (PS19 line; Jax #008169) crossbred to Syn1-Cre (Jax 003966) This paper N/A Mouse: Wildtype The Jackson Laboratory Cat#: 000664 Human: Brain tissue from ROSMAP cohort Bennett et al932018 radc.rush.edu (Continued on next page) Cell Reports 42, 113252, October 31, 2023 23 OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides Software and algorithms GraphPad Prism 9 for Mac GraphPad Software https://www.graphpad.com/ scientific-software/prism/ Fiji v2.3 Schindelin et al, 2012 https://imagej.net/software/fiji/downloads Image Studio Lite v.5.2.5 LI-COR https://www.licor.com/bio/ image-studio-lite/resources Seurat v4.0.5 Hao et al94, 2021 https://satijalab.org/seurat/articles/install. html Cellranger v6.1.1 10x Genomics https://support.10xgenomics.com/ single-cell-gene-expression/software/ downloads/6.1/ glmGamPoi v1.6.0 Ahlmann-Eltze et al95, 2021 https://bioconductor.org/packages/ release/bioc/html/glmGamPoi.html lme4 v.1.1-27.1 Bates et al96, 2015 https://cran.r-project.org/web/packages/ lme4/index.html lme4 v.1.1-30 Bates et al96, 2015 https://cran.r-project.org/web/packages/ lme4/index.html R v4.1.2 R Core Team https://www.R-project.org Codes generated in this study This paper https://github.com/ADNetworksPPG/ YH_NK01_APOE4_HMGB1_paper/ Codes generated in this study This paper https://doi.org/10.5281/zenodo.8309839.
Avidin-Biotin Assay:Article Title: APOE4-promoted gliosis and degeneration in tauopathy are ameliorated by pharmacological inhibition of HMGB1 release.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse anti-AT8 Thermo Fisher Scientific Cat#: MN1020; RRID: AB_223647 Rat anti-CD68 Bio-Rad Cat#: MCA1957; RRID: AB_322219 Mouse anti-GAPDH Cell Signaling Cat#: 97166; RRID: AB_2756824 Mouse anti-GFAP Millipore Cat#: MAB3402; RRID: AB_94844 Rabbit anti-HMGB1 Abcam Cat#: ab18256; RRID: AB_444360 Rabbit anti-Acetyl-HMGB1 (Lys29) Thermo Fisher Scientific Cat#: PA5-120416 RRID: AB_2913988 Rabbit anti-Iba1 Wako Cat#: 019-19741; RRID: AB_839504 Rabbit anti-MBP Abcam Cat#: ab40390 RRID: AB_1141521 Goat anti-Iba1 Abcam Cat#: ab5076 RRID: AB_2224402 Guinea Pig anti-NeuN Millipore Cat#: ABN90; RRID: AB_11205592 Mouse anti-SIRT1 Abcam Cat#: ab110304 RRID: AB_10864359 Rabbit anti-S100b Abcam Cat#: ab52642; RRID: AB_882426 Rabbit anti-TUJ1 Biolegend Cat#: 802001; RRID: AB_2564645 Donkey anti-mouse Biotin-SP Jackson Immuno Research Labs Cat#: 715-065-150; RRID: AB_2307438 Donkey anti-mouse Alexa Fluor 488 Abcam Cat#: ab150105; RRID: AB_2732856 Donkey anti-rabbit Alexa Fluor 488 Abcam Cat#: ab150073; RRID: AB_2636877 Donkey anti-rat Alexa Fluor 488 Abcam Cat#: ab150153; RRID: AB_2737355 Donkey anti-mouse Alexa Fluor 594 Abcam Cat#: ab150108 RRID: AB_2732073 Donkey anti-rabbit Alexa Fluor 594 Abcam Cat#: ab150076 RRID: AB_2782993 Donkey anti-guinea pig 594 Jackson Immuno Research Labs Cat#: 706-585-148; RRID: AB_2340474 Donkey anti-mouse 647 Abcam Cat#: ab150107; RRID: AB_2890037 Donkey anti-rabbit 647 Abcam Cat#ab150075; RRID: AB_2752244 Donkey anti-guinea pig 647 Jackson Immuno Research Labs Cat#: 706-605-148; RRID: AB_2340476 Donkey anti-mouse IRDye 800CW LI-COR Cat#: 926-32212; RRID: AB_621847 Donkey anti-rabbit IRDye 680RD LI-COR Cat#: 926-68073; RRID: AB_10954442 Chemicals, peptides, and recombinant proteins Artificial CSF Harvard Apparatus Cat#: 59-7316 Biotinylated donkey anti-mouse Jackson Immuno Research Labs Cat#: 715-065-150 Benzonase Nuclease Sigma-Aldrich Cat#: E1014 (Continued on next page) 22 Cell Reports 42, 113252, October 31, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER cOmplete Protease Inhibitor Cocktail Roche Cat#: 11836145001 DAPI Thermofischer Cat#: 62248 DPX mounting medium Sigma-Aldrich Cat#: 6522 Ethyl Pyruvate Sigma-Aldrich Cat#: 8066170500 Glycyrrhizic Acid Sigma-Aldrich Cat#: 50531-50G Intercept Blocking Buffer (PBS) LI-COR Cat#: 927-70001 M.O.M. blocking buffer Vector Labs Cat#: MKB-2213-1 NewBlot IR Stripping Buffer LICOR Cat#: 928-40028 Normal Donkey Serum Jackson Immuno Research Labs Cat#: 17000121 NuPage 12% Bis-Tris gel Invitrogen Cat#: NP0343 NuPage MOPS SDS Running Buffer Novex Cat#: NP0001 Paraformaldehyde Electron Microscopy Sciences Cat#: 15710-S ProLong Gold mounting medium Vector Labs Cat#: P36930 PhosSTOP phosphatase inhibitor Roche Cat#: 04-906-845-001 RAB buffer G Biosciences Cat#: 786-91 Recombinant Human HMGB1 protein R&D Systems Cat#: 1690-HMB-050 RIPA buffer Thermo Fisher Scientific Cat#: 89900 Saline (0.9%) Fisher Scientific Cat#: Z1376 Sudan Black B Sigma-Aldrich Cat#: 199664 Critical commercial assays Avidin/Biotin blocking kit Vector Labs Cat#: SP-2001 ABC-HRP Kit, Peroxidase Vector Labs Cat#: PK-6100 DAB Substrate Kit Vector Labs Cat#: SK-4100 Chromium Next GEM Single Cell 3ʹ Library and Gel Bead kit v3.1 10x Genomics Cat#: 1000128 Mouse HMGB1 ELISA kit Novus Biologicals Cat#: NBP2-62767 V-PLEX Plus Mouse Cytokine 19-Plex kit Meso Scal Diagnostics Cat#: K15255G NE-PER nuclear and cytoplasmic extraction reagents Thermo Fisher Scientific Cat#: 78835 Deposited data Raw snRNA-seq data This paper GEO accession number: GSE242153 Processed snRNA-seq data This paper Tables S1, S2, S3, S4, S5, S6 Experimental models: Organisms/strains Mouse: APOE3-KI: Apoetm2(APOE_i3)Yhg Yadong Huang Bien-Ly et. al.49, 2012 Mouse: APOE4-KI: Apoetm3(APOE_i4)Yhg Yadong Huang Bien-Ly et. al.49, 2012 Mouse; PS19-E4 APOE4-KI crossbred to Tau-P301S (PS19 line) (Jax #008169) This paper N/A Mouse: PS19-E3 APOE3-KI crossbred to Tau-P301S (PS19 line) (Jax #008169) This paper N/A Mouse: PS19-E4/Syn1-Cre APOE4-KI crossbred to Tau P301S (PS19 line; Jax #008169) crossbred to Syn1-Cre (Jax 003966) This paper N/A Mouse: Wildtype The Jackson Laboratory Cat#: 000664 Human: Brain tissue from ROSMAP cohort Bennett et al932018 radc.rush.edu (Continued on next page) Cell Reports 42, 113252, October 31, 2023 23 OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides Software and algorithms GraphPad Prism 9 for Mac GraphPad Software https://www.graphpad.com/ scientific-software/prism/ Fiji v2.3 Schindelin et al, 2012 https://imagej.net/software/fiji/downloads Image Studio Lite v.5.2.5 LI-COR https://www.licor.com/bio/ image-studio-lite/resources Seurat v4.0.5 Hao et al94, 2021 https://satijalab.org/seurat/articles/install. html Cellranger v6.1.1 10x Genomics https://support.10xgenomics.com/ single-cell-gene-expression/software/ downloads/6.1/ glmGamPoi v1.6.0 Ahlmann-Eltze et al95, 2021 https://bioconductor.org/packages/ release/bioc/html/glmGamPoi.html lme4 v.1.1-27.1 Bates et al96, 2015 https://cran.r-project.org/web/packages/ lme4/index.html lme4 v.1.1-30 Bates et al96, 2015 https://cran.r-project.org/web/packages/ lme4/index.html R v4.1.2 R Core Team https://www.R-project.org Codes generated in this study This paper https://github.com/ADNetworksPPG/ YH_NK01_APOE4_HMGB1_paper/ Codes generated in this study This paper https://doi.org/10.5281/zenodo.8309839.
Single Cell:Article Title: APOE4-promoted gliosis and degeneration in tauopathy are ameliorated by pharmacological inhibition of HMGB1 release.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse anti-AT8 Thermo Fisher Scientific Cat#: MN1020; RRID: AB_223647 Rat anti-CD68 Bio-Rad Cat#: MCA1957; RRID: AB_322219 Mouse anti-GAPDH Cell Signaling Cat#: 97166; RRID: AB_2756824 Mouse anti-GFAP Millipore Cat#: MAB3402; RRID: AB_94844 Rabbit anti-HMGB1 Abcam Cat#: ab18256; RRID: AB_444360 Rabbit anti-Acetyl-HMGB1 (Lys29) Thermo Fisher Scientific Cat#: PA5-120416 RRID: AB_2913988 Rabbit anti-Iba1 Wako Cat#: 019-19741; RRID: AB_839504 Rabbit anti-MBP Abcam Cat#: ab40390 RRID: AB_1141521 Goat anti-Iba1 Abcam Cat#: ab5076 RRID: AB_2224402 Guinea Pig anti-NeuN Millipore Cat#: ABN90; RRID: AB_11205592 Mouse anti-SIRT1 Abcam Cat#: ab110304 RRID: AB_10864359 Rabbit anti-S100b Abcam Cat#: ab52642; RRID: AB_882426 Rabbit anti-TUJ1 Biolegend Cat#: 802001; RRID: AB_2564645 Donkey anti-mouse Biotin-SP Jackson Immuno Research Labs Cat#: 715-065-150; RRID: AB_2307438 Donkey anti-mouse Alexa Fluor 488 Abcam Cat#: ab150105; RRID: AB_2732856 Donkey anti-rabbit Alexa Fluor 488 Abcam Cat#: ab150073; RRID: AB_2636877 Donkey anti-rat Alexa Fluor 488 Abcam Cat#: ab150153; RRID: AB_2737355 Donkey anti-mouse Alexa Fluor 594 Abcam Cat#: ab150108 RRID: AB_2732073 Donkey anti-rabbit Alexa Fluor 594 Abcam Cat#: ab150076 RRID: AB_2782993 Donkey anti-guinea pig 594 Jackson Immuno Research Labs Cat#: 706-585-148; RRID: AB_2340474 Donkey anti-mouse 647 Abcam Cat#: ab150107; RRID: AB_2890037 Donkey anti-rabbit 647 Abcam Cat#ab150075; RRID: AB_2752244 Donkey anti-guinea pig 647 Jackson Immuno Research Labs Cat#: 706-605-148; RRID: AB_2340476 Donkey anti-mouse IRDye 800CW LI-COR Cat#: 926-32212; RRID: AB_621847 Donkey anti-rabbit IRDye 680RD LI-COR Cat#: 926-68073; RRID: AB_10954442 Chemicals, peptides, and recombinant proteins Artificial CSF Harvard Apparatus Cat#: 59-7316 Biotinylated donkey anti-mouse Jackson Immuno Research Labs Cat#: 715-065-150 Benzonase Nuclease Sigma-Aldrich Cat#: E1014 (Continued on next page) 22 Cell Reports 42, 113252, October 31, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER cOmplete Protease Inhibitor Cocktail Roche Cat#: 11836145001 DAPI Thermofischer Cat#: 62248 DPX mounting medium Sigma-Aldrich Cat#: 6522 Ethyl Pyruvate Sigma-Aldrich Cat#: 8066170500 Glycyrrhizic Acid Sigma-Aldrich Cat#: 50531-50G Intercept Blocking Buffer (PBS) LI-COR Cat#: 927-70001 M.O.M. blocking buffer Vector Labs Cat#: MKB-2213-1 NewBlot IR Stripping Buffer LICOR Cat#: 928-40028 Normal Donkey Serum Jackson Immuno Research Labs Cat#: 17000121 NuPage 12% Bis-Tris gel Invitrogen Cat#: NP0343 NuPage MOPS SDS Running Buffer Novex Cat#: NP0001 Paraformaldehyde Electron Microscopy Sciences Cat#: 15710-S ProLong Gold mounting medium Vector Labs Cat#: P36930 PhosSTOP phosphatase inhibitor Roche Cat#: 04-906-845-001 RAB buffer G Biosciences Cat#: 786-91 Recombinant Human HMGB1 protein R&D Systems Cat#: 1690-HMB-050 RIPA buffer Thermo Fisher Scientific Cat#: 89900 Saline (0.9%) Fisher Scientific Cat#: Z1376 Sudan Black B Sigma-Aldrich Cat#: 199664 Critical commercial assays Avidin/Biotin blocking kit Vector Labs Cat#: SP-2001 ABC-HRP Kit, Peroxidase Vector Labs Cat#: PK-6100 DAB Substrate Kit Vector Labs Cat#: SK-4100 Chromium Next GEM Single Cell 3ʹ Library and Gel Bead kit v3.1 10x Genomics Cat#: 1000128 Mouse HMGB1 ELISA kit Novus Biologicals Cat#: NBP2-62767 V-PLEX Plus Mouse Cytokine 19-Plex kit Meso Scal Diagnostics Cat#: K15255G NE-PER nuclear and cytoplasmic extraction reagents Thermo Fisher Scientific Cat#: 78835 Deposited data Raw snRNA-seq data This paper GEO accession number: GSE242153 Processed snRNA-seq data This paper Tables S1, S2, S3, S4, S5, S6 Experimental models: Organisms/strains Mouse: APOE3-KI: Apoetm2(APOE_i3)Yhg Yadong Huang Bien-Ly et. al.49, 2012 Mouse: APOE4-KI: Apoetm3(APOE_i4)Yhg Yadong Huang Bien-Ly et. al.49, 2012 Mouse; PS19-E4 APOE4-KI crossbred to Tau-P301S (PS19 line) (Jax #008169) This paper N/A Mouse: PS19-E3 APOE3-KI crossbred to Tau-P301S (PS19 line) (Jax #008169) This paper N/A Mouse: PS19-E4/Syn1-Cre APOE4-KI crossbred to Tau P301S (PS19 line; Jax #008169) crossbred to Syn1-Cre (Jax 003966) This paper N/A Mouse: Wildtype The Jackson Laboratory Cat#: 000664 Human: Brain tissue from ROSMAP cohort Bennett et al932018 radc.rush.edu (Continued on next page) Cell Reports 42, 113252, October 31, 2023 23 OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides Software and algorithms GraphPad Prism 9 for Mac GraphPad Software https://www.graphpad.com/ scientific-software/prism/ Fiji v2.3 Schindelin et al, 2012 https://imagej.net/software/fiji/downloads Image Studio Lite v.5.2.5 LI-COR https://www.licor.com/bio/ image-studio-lite/resources Seurat v4.0.5 Hao et al94, 2021 https://satijalab.org/seurat/articles/install. html Cellranger v6.1.1 10x Genomics https://support.10xgenomics.com/ single-cell-gene-expression/software/ downloads/6.1/ glmGamPoi v1.6.0 Ahlmann-Eltze et al95, 2021 https://bioconductor.org/packages/ release/bioc/html/glmGamPoi.html lme4 v.1.1-27.1 Bates et al96, 2015 https://cran.r-project.org/web/packages/ lme4/index.html lme4 v.1.1-30 Bates et al96, 2015 https://cran.r-project.org/web/packages/ lme4/index.html R v4.1.2 R Core Team https://www.R-project.org Codes generated in this study This paper https://github.com/ADNetworksPPG/ YH_NK01_APOE4_HMGB1_paper/ Codes generated in this study This paper https://doi.org/10.5281/zenodo.8309839.
Enzyme-linked Immunosorbent Assay:Article Title: APOE4-promoted gliosis and degeneration in tauopathy are ameliorated by pharmacological inhibition of HMGB1 release.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse anti-AT8 Thermo Fisher Scientific Cat#: MN1020; RRID: AB_223647 Rat anti-CD68 Bio-Rad Cat#: MCA1957; RRID: AB_322219 Mouse anti-GAPDH Cell Signaling Cat#: 97166; RRID: AB_2756824 Mouse anti-GFAP Millipore Cat#: MAB3402; RRID: AB_94844 Rabbit anti-HMGB1 Abcam Cat#: ab18256; RRID: AB_444360 Rabbit anti-Acetyl-HMGB1 (Lys29) Thermo Fisher Scientific Cat#: PA5-120416 RRID: AB_2913988 Rabbit anti-Iba1 Wako Cat#: 019-19741; RRID: AB_839504 Rabbit anti-MBP Abcam Cat#: ab40390 RRID: AB_1141521 Goat anti-Iba1 Abcam Cat#: ab5076 RRID: AB_2224402 Guinea Pig anti-NeuN Millipore Cat#: ABN90; RRID: AB_11205592 Mouse anti-SIRT1 Abcam Cat#: ab110304 RRID: AB_10864359 Rabbit anti-S100b Abcam Cat#: ab52642; RRID: AB_882426 Rabbit anti-TUJ1 Biolegend Cat#: 802001; RRID: AB_2564645 Donkey anti-mouse Biotin-SP Jackson Immuno Research Labs Cat#: 715-065-150; RRID: AB_2307438 Donkey anti-mouse Alexa Fluor 488 Abcam Cat#: ab150105; RRID: AB_2732856 Donkey anti-rabbit Alexa Fluor 488 Abcam Cat#: ab150073; RRID: AB_2636877 Donkey anti-rat Alexa Fluor 488 Abcam Cat#: ab150153; RRID: AB_2737355 Donkey anti-mouse Alexa Fluor 594 Abcam Cat#: ab150108 RRID: AB_2732073 Donkey anti-rabbit Alexa Fluor 594 Abcam Cat#: ab150076 RRID: AB_2782993 Donkey anti-guinea pig 594 Jackson Immuno Research Labs Cat#: 706-585-148; RRID: AB_2340474 Donkey anti-mouse 647 Abcam Cat#: ab150107; RRID: AB_2890037 Donkey anti-rabbit 647 Abcam Cat#ab150075; RRID: AB_2752244 Donkey anti-guinea pig 647 Jackson Immuno Research Labs Cat#: 706-605-148; RRID: AB_2340476 Donkey anti-mouse IRDye 800CW LI-COR Cat#: 926-32212; RRID: AB_621847 Donkey anti-rabbit IRDye 680RD LI-COR Cat#: 926-68073; RRID: AB_10954442 Chemicals, peptides, and recombinant proteins Artificial CSF Harvard Apparatus Cat#: 59-7316 Biotinylated donkey anti-mouse Jackson Immuno Research Labs Cat#: 715-065-150 Benzonase Nuclease Sigma-Aldrich Cat#: E1014 (Continued on next page) 22 Cell Reports 42, 113252, October 31, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER cOmplete Protease Inhibitor Cocktail Roche Cat#: 11836145001 DAPI Thermofischer Cat#: 62248 DPX mounting medium Sigma-Aldrich Cat#: 6522 Ethyl Pyruvate Sigma-Aldrich Cat#: 8066170500 Glycyrrhizic Acid Sigma-Aldrich Cat#: 50531-50G Intercept Blocking Buffer (PBS) LI-COR Cat#: 927-70001 M.O.M. blocking buffer Vector Labs Cat#: MKB-2213-1 NewBlot IR Stripping Buffer LICOR Cat#: 928-40028 Normal Donkey Serum Jackson Immuno Research Labs Cat#: 17000121 NuPage 12% Bis-Tris gel Invitrogen Cat#: NP0343 NuPage MOPS SDS Running Buffer Novex Cat#: NP0001 Paraformaldehyde Electron Microscopy Sciences Cat#: 15710-S ProLong Gold mounting medium Vector Labs Cat#: P36930 PhosSTOP phosphatase inhibitor Roche Cat#: 04-906-845-001 RAB buffer G Biosciences Cat#: 786-91 Recombinant Human HMGB1 protein R&D Systems Cat#: 1690-HMB-050 RIPA buffer Thermo Fisher Scientific Cat#: 89900 Saline (0.9%) Fisher Scientific Cat#: Z1376 Sudan Black B Sigma-Aldrich Cat#: 199664 Critical commercial assays Avidin/Biotin blocking kit Vector Labs Cat#: SP-2001 ABC-HRP Kit, Peroxidase Vector Labs Cat#: PK-6100 DAB Substrate Kit Vector Labs Cat#: SK-4100 Chromium Next GEM Single Cell 3ʹ Library and Gel Bead kit v3.1 10x Genomics Cat#: 1000128 Mouse HMGB1 ELISA kit Novus Biologicals Cat#: NBP2-62767 V-PLEX Plus Mouse Cytokine 19-Plex kit Meso Scal Diagnostics Cat#: K15255G NE-PER nuclear and cytoplasmic extraction reagents Thermo Fisher Scientific Cat#: 78835 Deposited data Raw snRNA-seq data This paper GEO accession number: GSE242153 Processed snRNA-seq data This paper Tables S1, S2, S3, S4, S5, S6 Experimental models: Organisms/strains Mouse: APOE3-KI: Apoetm2(APOE_i3)Yhg Yadong Huang Bien-Ly et. al.49, 2012 Mouse: APOE4-KI: Apoetm3(APOE_i4)Yhg Yadong Huang Bien-Ly et. al.49, 2012 Mouse; PS19-E4 APOE4-KI crossbred to Tau-P301S (PS19 line) (Jax #008169) This paper N/A Mouse: PS19-E3 APOE3-KI crossbred to Tau-P301S (PS19 line) (Jax #008169) This paper N/A Mouse: PS19-E4/Syn1-Cre APOE4-KI crossbred to Tau P301S (PS19 line; Jax #008169) crossbred to Syn1-Cre (Jax 003966) This paper N/A Mouse: Wildtype The Jackson Laboratory Cat#: 000664 Human: Brain tissue from ROSMAP cohort Bennett et al932018 radc.rush.edu (Continued on next page) Cell Reports 42, 113252, October 31, 2023 23 OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides Software and algorithms GraphPad Prism 9 for Mac GraphPad Software https://www.graphpad.com/ scientific-software/prism/ Fiji v2.3 Schindelin et al, 2012 https://imagej.net/software/fiji/downloads Image Studio Lite v.5.2.5 LI-COR https://www.licor.com/bio/ image-studio-lite/resources Seurat v4.0.5 Hao et al94, 2021 https://satijalab.org/seurat/articles/install. html Cellranger v6.1.1 10x Genomics https://support.10xgenomics.com/ single-cell-gene-expression/software/ downloads/6.1/ glmGamPoi v1.6.0 Ahlmann-Eltze et al95, 2021 https://bioconductor.org/packages/ release/bioc/html/glmGamPoi.html lme4 v.1.1-27.1 Bates et al96, 2015 https://cran.r-project.org/web/packages/ lme4/index.html lme4 v.1.1-30 Bates et al96, 2015 https://cran.r-project.org/web/packages/ lme4/index.html R v4.1.2 R Core Team https://www.R-project.org Codes generated in this study This paper https://github.com/ADNetworksPPG/ YH_NK01_APOE4_HMGB1_paper/ Codes generated in this study This paper https://doi.org/10.5281/zenodo.8309839.
Extraction:Article Title: APOE4-promoted gliosis and degeneration in tauopathy are ameliorated by pharmacological inhibition of HMGB1 release.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse anti-AT8 Thermo Fisher Scientific Cat#: MN1020; RRID: AB_223647 Rat anti-CD68 Bio-Rad Cat#: MCA1957; RRID: AB_322219 Mouse anti-GAPDH Cell Signaling Cat#: 97166; RRID: AB_2756824 Mouse anti-GFAP Millipore Cat#: MAB3402; RRID: AB_94844 Rabbit anti-HMGB1 Abcam Cat#: ab18256; RRID: AB_444360 Rabbit anti-Acetyl-HMGB1 (Lys29) Thermo Fisher Scientific Cat#: PA5-120416 RRID: AB_2913988 Rabbit anti-Iba1 Wako Cat#: 019-19741; RRID: AB_839504 Rabbit anti-MBP Abcam Cat#: ab40390 RRID: AB_1141521 Goat anti-Iba1 Abcam Cat#: ab5076 RRID: AB_2224402 Guinea Pig anti-NeuN Millipore Cat#: ABN90; RRID: AB_11205592 Mouse anti-SIRT1 Abcam Cat#: ab110304 RRID: AB_10864359 Rabbit anti-S100b Abcam Cat#: ab52642; RRID: AB_882426 Rabbit anti-TUJ1 Biolegend Cat#: 802001; RRID: AB_2564645 Donkey anti-mouse Biotin-SP Jackson Immuno Research Labs Cat#: 715-065-150; RRID: AB_2307438 Donkey anti-mouse Alexa Fluor 488 Abcam Cat#: ab150105; RRID: AB_2732856 Donkey anti-rabbit Alexa Fluor 488 Abcam Cat#: ab150073; RRID: AB_2636877 Donkey anti-rat Alexa Fluor 488 Abcam Cat#: ab150153; RRID: AB_2737355 Donkey anti-mouse Alexa Fluor 594 Abcam Cat#: ab150108 RRID: AB_2732073 Donkey anti-rabbit Alexa Fluor 594 Abcam Cat#: ab150076 RRID: AB_2782993 Donkey anti-guinea pig 594 Jackson Immuno Research Labs Cat#: 706-585-148; RRID: AB_2340474 Donkey anti-mouse 647 Abcam Cat#: ab150107; RRID: AB_2890037 Donkey anti-rabbit 647 Abcam Cat#ab150075; RRID: AB_2752244 Donkey anti-guinea pig 647 Jackson Immuno Research Labs Cat#: 706-605-148; RRID: AB_2340476 Donkey anti-mouse IRDye 800CW LI-COR Cat#: 926-32212; RRID: AB_621847 Donkey anti-rabbit IRDye 680RD LI-COR Cat#: 926-68073; RRID: AB_10954442 Chemicals, peptides, and recombinant proteins Artificial CSF Harvard Apparatus Cat#: 59-7316 Biotinylated donkey anti-mouse Jackson Immuno Research Labs Cat#: 715-065-150 Benzonase Nuclease Sigma-Aldrich Cat#: E1014 (Continued on next page) 22 Cell Reports 42, 113252, October 31, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER cOmplete Protease Inhibitor Cocktail Roche Cat#: 11836145001 DAPI Thermofischer Cat#: 62248 DPX mounting medium Sigma-Aldrich Cat#: 6522 Ethyl Pyruvate Sigma-Aldrich Cat#: 8066170500 Glycyrrhizic Acid Sigma-Aldrich Cat#: 50531-50G Intercept Blocking Buffer (PBS) LI-COR Cat#: 927-70001 M.O.M. blocking buffer Vector Labs Cat#: MKB-2213-1 NewBlot IR Stripping Buffer LICOR Cat#: 928-40028 Normal Donkey Serum Jackson Immuno Research Labs Cat#: 17000121 NuPage 12% Bis-Tris gel Invitrogen Cat#: NP0343 NuPage MOPS SDS Running Buffer Novex Cat#: NP0001 Paraformaldehyde Electron Microscopy Sciences Cat#: 15710-S ProLong Gold mounting medium Vector Labs Cat#: P36930 PhosSTOP phosphatase inhibitor Roche Cat#: 04-906-845-001 RAB buffer G Biosciences Cat#: 786-91 Recombinant Human HMGB1 protein R&D Systems Cat#: 1690-HMB-050 RIPA buffer Thermo Fisher Scientific Cat#: 89900 Saline (0.9%) Fisher Scientific Cat#: Z1376 Sudan Black B Sigma-Aldrich Cat#: 199664 Critical commercial assays Avidin/Biotin blocking kit Vector Labs Cat#: SP-2001 ABC-HRP Kit, Peroxidase Vector Labs Cat#: PK-6100 DAB Substrate Kit Vector Labs Cat#: SK-4100 Chromium Next GEM Single Cell 3ʹ Library and Gel Bead kit v3.1 10x Genomics Cat#: 1000128 Mouse HMGB1 ELISA kit Novus Biologicals Cat#: NBP2-62767 V-PLEX Plus Mouse Cytokine 19-Plex kit Meso Scal Diagnostics Cat#: K15255G NE-PER nuclear and cytoplasmic extraction reagents Thermo Fisher Scientific Cat#: 78835 Deposited data Raw snRNA-seq data This paper GEO accession number: GSE242153 Processed snRNA-seq data This paper Tables S1, S2, S3, S4, S5, S6 Experimental models: Organisms/strains Mouse: APOE3-KI: Apoetm2(APOE_i3)Yhg Yadong Huang Bien-Ly et. al.49, 2012 Mouse: APOE4-KI: Apoetm3(APOE_i4)Yhg Yadong Huang Bien-Ly et. al.49, 2012 Mouse; PS19-E4 APOE4-KI crossbred to Tau-P301S (PS19 line) (Jax #008169) This paper N/A Mouse: PS19-E3 APOE3-KI crossbred to Tau-P301S (PS19 line) (Jax #008169) This paper N/A Mouse: PS19-E4/Syn1-Cre APOE4-KI crossbred to Tau P301S (PS19 line; Jax #008169) crossbred to Syn1-Cre (Jax 003966) This paper N/A Mouse: Wildtype The Jackson Laboratory Cat#: 000664 Human: Brain tissue from ROSMAP cohort Bennett et al932018 radc.rush.edu (Continued on next page) Cell Reports 42, 113252, October 31, 2023 23 OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides Software and algorithms GraphPad Prism 9 for Mac GraphPad Software https://www.graphpad.com/ scientific-software/prism/ Fiji v2.3 Schindelin et al, 2012 https://imagej.net/software/fiji/downloads Image Studio Lite v.5.2.5 LI-COR https://www.licor.com/bio/ image-studio-lite/resources Seurat v4.0.5 Hao et al94, 2021 https://satijalab.org/seurat/articles/install. html Cellranger v6.1.1 10x Genomics https://support.10xgenomics.com/ single-cell-gene-expression/software/ downloads/6.1/ glmGamPoi v1.6.0 Ahlmann-Eltze et al95, 2021 https://bioconductor.org/packages/ release/bioc/html/glmGamPoi.html lme4 v.1.1-27.1 Bates et al96, 2015 https://cran.r-project.org/web/packages/ lme4/index.html lme4 v.1.1-30 Bates et al96, 2015 https://cran.r-project.org/web/packages/ lme4/index.html R v4.1.2 R Core Team https://www.R-project.org Codes generated in this study This paper https://github.com/ADNetworksPPG/ YH_NK01_APOE4_HMGB1_paper/ Codes generated in this study This paper https://doi.org/10.5281/zenodo.8309839.
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