Software:Article Title: Type-I-interferon-responsive microglia shape cortical development and behavior.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Syn1:mIfnb1:NLS-EGFP This paper N/A Software and algorithms FIJI Open source https://imagej.net/software/fiji/ Imaris v9 Oxford Instruments https://imaris.oxinst.com/ GraphPad Prism 9.3.1 GraphPad https://www.graphpad.com/ Zeiss Zen 2.6 software Zeiss N/A Cell Ranger 2.1 10X Genomics https://www.10xgenomics.com/support/ software/cell-ranger/latest Seurat 3.1.4 Satija Lab https://satijalab.org/seurat Velocyto 0.17 La Manno et al.116 https://velocyto.org/ ScVelo 0.2.0 Bergen et al.55 https://scvelo.readthedocs.io/en/stable/ Code This paper https://github.com/lcdorman/ IFNresponseCode Other MACS beads (LS columns) Miltenyi Biotec Cat#130-042-401 MERSCOPE slides Vizgen PN#20400001 MERSCOPE Sample Prep Wash Buffer Vizgen PN#20300001 MERSCOPE Formamide Wash Buffer Vizgen PN#20300002 MERSCOPE PolyT Staining Reagent Vizgen PN#20300021 ll OPEN ACCESS Article .. REAGENT or RESOURCE SOURCE IDENTIFIER APC rat anti-CD11b 1:170 BioLegend Cat#101212; RRID:AB_312795 PE-Cy7 rat anti-CD11b 1:170 eBioscience Cat#25-0112-81; RRID:AB_469587 APC rat anti-P2RY12 1:200 Biolegend Cat#848005; RRID:AB_2721469 Goat anti-rabbit AF647 1:500 Thermo Fisher Cat#A-21244; RRID:AB_2535812 PE mouse anti-IFNAR1 1:150 Biolegend Cat#127311; RRID:AB_2248800 APC mouse anti-IFNAR1 1:150 Biolegend Cat#127313; RRID:AB_2122746 Chemicals, peptides, and recombinant proteins Recombinant IFN-b R&D Systems Cat#8234-MB-010/CF Poly(I:C) HMW Invivogen Cat#tlrl-pic Bafilomycin A1 Tocris Cat#1334 Tamoxifen, >99% Sigma-Aldrich Cat#T5648 ABT-263 (Navitoclax) MedChemExpress Cat#HY-10087 Lysotracker Red Thermo Fisher Cat#L7528 Critical commercial assays DeadEnd Fluorometric TUNEL system Promega Cat#G3250 RNAscope Fluorescent Multiplex Detection Reagents Advanced Cell Diagnostics Cat#320851 RNAscope Multiplex Fluorescent Reagent Kit v2 Advanced Cell Diagnostics Cat#323100 TSA Plus Cyanine 3 detection kit Akoya Biosciences Cat#NEL744001KT TSA Plus Cyanine 5 detection kit Akoya Biosciences Cat#NEL745001KT TSA Plus Fluorescein detection kit Akoya Biosciences Cat#NEL701A001KT Chromium single cell gene expression platform, version 3 (Microglial RNA-seq) 10x Genomics Library and gel bead kit – V3, 1000075: Chip B kit: 1000074 MERSCOPE Cell Boundary Staining Kit Vizgen PN#10400118 Rneasy Plus Mini Kit Qiagen Cat#74134 High Capacity cDNA Reverse Transcription kit Life Technologies Cat#4374966 Deposited data Single cell RNA-sequencing of microglia from postnatal day 5 and 7 barrel cortex after partial whisker follicle cauterization at postnatal day 2 This paper GeneExpression Omnibus (GEO) GEO: GSE173173 scRNA-seq: PS2APP;TauP301L with and without Trem2-/- Lee et al.37 GEO: GSE153895 scRNA-seq: 5xFAD Masuda et al.100 GEO: GSE148405 scRNA-seq: APP-PS1 with and without Apoe-/- Sala Frigerio et al.32 GEO: GSE127884 scRNA-seq: GBM model in mouse Ochocka et al.34 GEO: GSE136001 scRNA-seq: Coronavirus infection (3 days, 7 days post infection) Syage et al.38 Received from author scRNA-seq: Young (P4-P5), aging (P100, P540), LPC injection Hammond et al.28 GEO: GSE121654 scRNA-seq: PLX5622 recovery Zhan et al.33 GEO: GSE150169 scRNA-seq: tMCAO (5 days and 14 days post occlusion) Shi et al.36 GEO: GSE171169 Bulk seq: PS2APP Friedman et al.31 GEO: GSE89482 Bulk seq: 5XFAD Wang et al.101 GEO: GSE65067 Bulk seq: WT, APPswe/PS1dE9 Orre et al.102 GEO: GSE74615 Bulk seq: Thy1::hMAPT-P301L Friedman et al.31 GEO: GSE93179 (Continued on next page) ll OPEN ACCESS e2 Cell 187, 1936–1954.e1–e11, April 11, 2024 Article
Magnetic Cell Separation:Article Title: Type-I-interferon-responsive microglia shape cortical development and behavior.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Syn1:mIfnb1:NLS-EGFP This paper N/A Software and algorithms FIJI Open source https://imagej.net/software/fiji/ Imaris v9 Oxford Instruments https://imaris.oxinst.com/ GraphPad Prism 9.3.1 GraphPad https://www.graphpad.com/ Zeiss Zen 2.6 software Zeiss N/A Cell Ranger 2.1 10X Genomics https://www.10xgenomics.com/support/ software/cell-ranger/latest Seurat 3.1.4 Satija Lab https://satijalab.org/seurat Velocyto 0.17 La Manno et al.116 https://velocyto.org/ ScVelo 0.2.0 Bergen et al.55 https://scvelo.readthedocs.io/en/stable/ Code This paper https://github.com/lcdorman/ IFNresponseCode Other MACS beads (LS columns) Miltenyi Biotec Cat#130-042-401 MERSCOPE slides Vizgen PN#20400001 MERSCOPE Sample Prep Wash Buffer Vizgen PN#20300001 MERSCOPE Formamide Wash Buffer Vizgen PN#20300002 MERSCOPE PolyT Staining Reagent Vizgen PN#20300021 ll OPEN ACCESS Article .. REAGENT or RESOURCE SOURCE IDENTIFIER APC rat anti-CD11b 1:170 BioLegend Cat#101212; RRID:AB_312795 PE-Cy7 rat anti-CD11b 1:170 eBioscience Cat#25-0112-81; RRID:AB_469587 APC rat anti-P2RY12 1:200 Biolegend Cat#848005; RRID:AB_2721469 Goat anti-rabbit AF647 1:500 Thermo Fisher Cat#A-21244; RRID:AB_2535812 PE mouse anti-IFNAR1 1:150 Biolegend Cat#127311; RRID:AB_2248800 APC mouse anti-IFNAR1 1:150 Biolegend Cat#127313; RRID:AB_2122746 Chemicals, peptides, and recombinant proteins Recombinant IFN-b R&D Systems Cat#8234-MB-010/CF Poly(I:C) HMW Invivogen Cat#tlrl-pic Bafilomycin A1 Tocris Cat#1334 Tamoxifen, >99% Sigma-Aldrich Cat#T5648 ABT-263 (Navitoclax) MedChemExpress Cat#HY-10087 Lysotracker Red Thermo Fisher Cat#L7528 Critical commercial assays DeadEnd Fluorometric TUNEL system Promega Cat#G3250 RNAscope Fluorescent Multiplex Detection Reagents Advanced Cell Diagnostics Cat#320851 RNAscope Multiplex Fluorescent Reagent Kit v2 Advanced Cell Diagnostics Cat#323100 TSA Plus Cyanine 3 detection kit Akoya Biosciences Cat#NEL744001KT TSA Plus Cyanine 5 detection kit Akoya Biosciences Cat#NEL745001KT TSA Plus Fluorescein detection kit Akoya Biosciences Cat#NEL701A001KT Chromium single cell gene expression platform, version 3 (Microglial RNA-seq) 10x Genomics Library and gel bead kit – V3, 1000075: Chip B kit: 1000074 MERSCOPE Cell Boundary Staining Kit Vizgen PN#10400118 Rneasy Plus Mini Kit Qiagen Cat#74134 High Capacity cDNA Reverse Transcription kit Life Technologies Cat#4374966 Deposited data Single cell RNA-sequencing of microglia from postnatal day 5 and 7 barrel cortex after partial whisker follicle cauterization at postnatal day 2 This paper GeneExpression Omnibus (GEO) GEO: GSE173173 scRNA-seq: PS2APP;TauP301L with and without Trem2-/- Lee et al.37 GEO: GSE153895 scRNA-seq: 5xFAD Masuda et al.100 GEO: GSE148405 scRNA-seq: APP-PS1 with and without Apoe-/- Sala Frigerio et al.32 GEO: GSE127884 scRNA-seq: GBM model in mouse Ochocka et al.34 GEO: GSE136001 scRNA-seq: Coronavirus infection (3 days, 7 days post infection) Syage et al.38 Received from author scRNA-seq: Young (P4-P5), aging (P100, P540), LPC injection Hammond et al.28 GEO: GSE121654 scRNA-seq: PLX5622 recovery Zhan et al.33 GEO: GSE150169 scRNA-seq: tMCAO (5 days and 14 days post occlusion) Shi et al.36 GEO: GSE171169 Bulk seq: PS2APP Friedman et al.31 GEO: GSE89482 Bulk seq: 5XFAD Wang et al.101 GEO: GSE65067 Bulk seq: WT, APPswe/PS1dE9 Orre et al.102 GEO: GSE74615 Bulk seq: Thy1::hMAPT-P301L Friedman et al.31 GEO: GSE93179 (Continued on next page) ll OPEN ACCESS e2 Cell 187, 1936–1954.e1–e11, April 11, 2024 Article
Sample Prep:Article Title: Type-I-interferon-responsive microglia shape cortical development and behavior.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Syn1:mIfnb1:NLS-EGFP This paper N/A Software and algorithms FIJI Open source https://imagej.net/software/fiji/ Imaris v9 Oxford Instruments https://imaris.oxinst.com/ GraphPad Prism 9.3.1 GraphPad https://www.graphpad.com/ Zeiss Zen 2.6 software Zeiss N/A Cell Ranger 2.1 10X Genomics https://www.10xgenomics.com/support/ software/cell-ranger/latest Seurat 3.1.4 Satija Lab https://satijalab.org/seurat Velocyto 0.17 La Manno et al.116 https://velocyto.org/ ScVelo 0.2.0 Bergen et al.55 https://scvelo.readthedocs.io/en/stable/ Code This paper https://github.com/lcdorman/ IFNresponseCode Other MACS beads (LS columns) Miltenyi Biotec Cat#130-042-401 MERSCOPE slides Vizgen PN#20400001 MERSCOPE Sample Prep Wash Buffer Vizgen PN#20300001 MERSCOPE Formamide Wash Buffer Vizgen PN#20300002 MERSCOPE PolyT Staining Reagent Vizgen PN#20300021 ll OPEN ACCESS Article .. REAGENT or RESOURCE SOURCE IDENTIFIER APC rat anti-CD11b 1:170 BioLegend Cat#101212; RRID:AB_312795 PE-Cy7 rat anti-CD11b 1:170 eBioscience Cat#25-0112-81; RRID:AB_469587 APC rat anti-P2RY12 1:200 Biolegend Cat#848005; RRID:AB_2721469 Goat anti-rabbit AF647 1:500 Thermo Fisher Cat#A-21244; RRID:AB_2535812 PE mouse anti-IFNAR1 1:150 Biolegend Cat#127311; RRID:AB_2248800 APC mouse anti-IFNAR1 1:150 Biolegend Cat#127313; RRID:AB_2122746 Chemicals, peptides, and recombinant proteins Recombinant IFN-b R&D Systems Cat#8234-MB-010/CF Poly(I:C) HMW Invivogen Cat#tlrl-pic Bafilomycin A1 Tocris Cat#1334 Tamoxifen, >99% Sigma-Aldrich Cat#T5648 ABT-263 (Navitoclax) MedChemExpress Cat#HY-10087 Lysotracker Red Thermo Fisher Cat#L7528 Critical commercial assays DeadEnd Fluorometric TUNEL system Promega Cat#G3250 RNAscope Fluorescent Multiplex Detection Reagents Advanced Cell Diagnostics Cat#320851 RNAscope Multiplex Fluorescent Reagent Kit v2 Advanced Cell Diagnostics Cat#323100 TSA Plus Cyanine 3 detection kit Akoya Biosciences Cat#NEL744001KT TSA Plus Cyanine 5 detection kit Akoya Biosciences Cat#NEL745001KT TSA Plus Fluorescein detection kit Akoya Biosciences Cat#NEL701A001KT Chromium single cell gene expression platform, version 3 (Microglial RNA-seq) 10x Genomics Library and gel bead kit – V3, 1000075: Chip B kit: 1000074 MERSCOPE Cell Boundary Staining Kit Vizgen PN#10400118 Rneasy Plus Mini Kit Qiagen Cat#74134 High Capacity cDNA Reverse Transcription kit Life Technologies Cat#4374966 Deposited data Single cell RNA-sequencing of microglia from postnatal day 5 and 7 barrel cortex after partial whisker follicle cauterization at postnatal day 2 This paper GeneExpression Omnibus (GEO) GEO: GSE173173 scRNA-seq: PS2APP;TauP301L with and without Trem2-/- Lee et al.37 GEO: GSE153895 scRNA-seq: 5xFAD Masuda et al.100 GEO: GSE148405 scRNA-seq: APP-PS1 with and without Apoe-/- Sala Frigerio et al.32 GEO: GSE127884 scRNA-seq: GBM model in mouse Ochocka et al.34 GEO: GSE136001 scRNA-seq: Coronavirus infection (3 days, 7 days post infection) Syage et al.38 Received from author scRNA-seq: Young (P4-P5), aging (P100, P540), LPC injection Hammond et al.28 GEO: GSE121654 scRNA-seq: PLX5622 recovery Zhan et al.33 GEO: GSE150169 scRNA-seq: tMCAO (5 days and 14 days post occlusion) Shi et al.36 GEO: GSE171169 Bulk seq: PS2APP Friedman et al.31 GEO: GSE89482 Bulk seq: 5XFAD Wang et al.101 GEO: GSE65067 Bulk seq: WT, APPswe/PS1dE9 Orre et al.102 GEO: GSE74615 Bulk seq: Thy1::hMAPT-P301L Friedman et al.31 GEO: GSE93179 (Continued on next page) ll OPEN ACCESS e2 Cell 187, 1936–1954.e1–e11, April 11, 2024 Article
Staining:Article Title: Type-I-interferon-responsive microglia shape cortical development and behavior.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Syn1:mIfnb1:NLS-EGFP This paper N/A Software and algorithms FIJI Open source https://imagej.net/software/fiji/ Imaris v9 Oxford Instruments https://imaris.oxinst.com/ GraphPad Prism 9.3.1 GraphPad https://www.graphpad.com/ Zeiss Zen 2.6 software Zeiss N/A Cell Ranger 2.1 10X Genomics https://www.10xgenomics.com/support/ software/cell-ranger/latest Seurat 3.1.4 Satija Lab https://satijalab.org/seurat Velocyto 0.17 La Manno et al.116 https://velocyto.org/ ScVelo 0.2.0 Bergen et al.55 https://scvelo.readthedocs.io/en/stable/ Code This paper https://github.com/lcdorman/ IFNresponseCode Other MACS beads (LS columns) Miltenyi Biotec Cat#130-042-401 MERSCOPE slides Vizgen PN#20400001 MERSCOPE Sample Prep Wash Buffer Vizgen PN#20300001 MERSCOPE Formamide Wash Buffer Vizgen PN#20300002 MERSCOPE PolyT Staining Reagent Vizgen PN#20300021 ll OPEN ACCESS Article .. REAGENT or RESOURCE SOURCE IDENTIFIER APC rat anti-CD11b 1:170 BioLegend Cat#101212; RRID:AB_312795 PE-Cy7 rat anti-CD11b 1:170 eBioscience Cat#25-0112-81; RRID:AB_469587 APC rat anti-P2RY12 1:200 Biolegend Cat#848005; RRID:AB_2721469 Goat anti-rabbit AF647 1:500 Thermo Fisher Cat#A-21244; RRID:AB_2535812 PE mouse anti-IFNAR1 1:150 Biolegend Cat#127311; RRID:AB_2248800 APC mouse anti-IFNAR1 1:150 Biolegend Cat#127313; RRID:AB_2122746 Chemicals, peptides, and recombinant proteins Recombinant IFN-b R&D Systems Cat#8234-MB-010/CF Poly(I:C) HMW Invivogen Cat#tlrl-pic Bafilomycin A1 Tocris Cat#1334 Tamoxifen, >99% Sigma-Aldrich Cat#T5648 ABT-263 (Navitoclax) MedChemExpress Cat#HY-10087 Lysotracker Red Thermo Fisher Cat#L7528 Critical commercial assays DeadEnd Fluorometric TUNEL system Promega Cat#G3250 RNAscope Fluorescent Multiplex Detection Reagents Advanced Cell Diagnostics Cat#320851 RNAscope Multiplex Fluorescent Reagent Kit v2 Advanced Cell Diagnostics Cat#323100 TSA Plus Cyanine 3 detection kit Akoya Biosciences Cat#NEL744001KT TSA Plus Cyanine 5 detection kit Akoya Biosciences Cat#NEL745001KT TSA Plus Fluorescein detection kit Akoya Biosciences Cat#NEL701A001KT Chromium single cell gene expression platform, version 3 (Microglial RNA-seq) 10x Genomics Library and gel bead kit – V3, 1000075: Chip B kit: 1000074 MERSCOPE Cell Boundary Staining Kit Vizgen PN#10400118 Rneasy Plus Mini Kit Qiagen Cat#74134 High Capacity cDNA Reverse Transcription kit Life Technologies Cat#4374966 Deposited data Single cell RNA-sequencing of microglia from postnatal day 5 and 7 barrel cortex after partial whisker follicle cauterization at postnatal day 2 This paper GeneExpression Omnibus (GEO) GEO: GSE173173 scRNA-seq: PS2APP;TauP301L with and without Trem2-/- Lee et al.37 GEO: GSE153895 scRNA-seq: 5xFAD Masuda et al.100 GEO: GSE148405 scRNA-seq: APP-PS1 with and without Apoe-/- Sala Frigerio et al.32 GEO: GSE127884 scRNA-seq: GBM model in mouse Ochocka et al.34 GEO: GSE136001 scRNA-seq: Coronavirus infection (3 days, 7 days post infection) Syage et al.38 Received from author scRNA-seq: Young (P4-P5), aging (P100, P540), LPC injection Hammond et al.28 GEO: GSE121654 scRNA-seq: PLX5622 recovery Zhan et al.33 GEO: GSE150169 scRNA-seq: tMCAO (5 days and 14 days post occlusion) Shi et al.36 GEO: GSE171169 Bulk seq: PS2APP Friedman et al.31 GEO: GSE89482 Bulk seq: 5XFAD Wang et al.101 GEO: GSE65067 Bulk seq: WT, APPswe/PS1dE9 Orre et al.102 GEO: GSE74615 Bulk seq: Thy1::hMAPT-P301L Friedman et al.31 GEO: GSE93179 (Continued on next page) ll OPEN ACCESS e2 Cell 187, 1936–1954.e1–e11, April 11, 2024 Article
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