SRX7191292 9804 Donor Microglia SRP230774 bp0 To detect microglia, cells were stained with antibodies against CD45.1 (A20, BioLegend), CD45.2 (104) (Thermo Fisher), and CD11b (M1/70) (BD Biosciences). Donor microglia, host microglia, and donor circulating monocytes were sorted separately. RNA-seq was performed by first isolating mRNA using DynaBead mRNA DIRECT kit (Thermo Fisher), followed by cDNA preparation using SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio), library preparation using NexteraXT DNA Library Preparation kit (illumina), and sequencing using HiSeq 4000 (illumina). STAR (70) (version 2.5.2b) was used to align reads to the mouse genome, version GRCm38.78. SRS5697308 9804_Donor_Microglia_S2_R1_001.fastq 9804 Donor Microglia RNA-Seq TRANSCRIPTOMIC Oligo-dT Illumina HiSeq 4000 SRX7191293 9982 Donor Microglia SRP230774 bp0 To detect microglia, cells were stained with antibodies against CD45.1 (A20, BioLegend), CD45.2 (104) (Thermo Fisher), and CD11b (M1/70) (BD Biosciences). Donor microglia, host microglia, and donor circulating monocytes were sorted separately. RNA-seq was performed by first isolating mRNA using DynaBead mRNA DIRECT kit (Thermo Fisher), followed by cDNA preparation using SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio), library preparation using NexteraXT DNA Library Preparation kit (illumina), and sequencing using HiSeq 4000 (illumina). STAR (70) (version 2.5.2b) was used to align reads to the mouse genome, version GRCm38.78. SRS5697309 9982_Donor_Microglia_S1_R1_001.fastq 9982 Donor Microglia RNA-Seq TRANSCRIPTOMIC Oligo-dT Illumina HiSeq 4000 SRX7191294 10045 Host Microglia SRP230774 bp0 To detect microglia, cells were stained with antibodies against CD45.1 (A20, BioLegend), CD45.2 (104) (Thermo Fisher), and CD11b (M1/70) (BD Biosciences). Donor microglia, host microglia, and donor circulating monocytes were sorted separately. RNA-seq was performed by first isolating mRNA using DynaBead mRNA DIRECT kit (Thermo Fisher), followed by cDNA preparation using SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio), library preparation using NexteraXT DNA Library Preparation kit (illumina), and sequencing using HiSeq 4000 (illumina). STAR (70) (version 2.5.2b) was used to align reads to the mouse genome, version GRCm38.78. SRS5697310 10045_Host_Microglia_S18_R1_001.fastq 10045 Host Microglia RNA-Seq TRANSCRIPTOMIC Oligo-dT Illumina HiSeq 4000 SRX7191295 10047 Host Microglia SRP230774 bp0 To detect microglia, cells were stained with antibodies against CD45.1 (A20, BioLegend), CD45.2 (104) (Thermo Fisher), and CD11b (M1/70) (BD Biosciences). Donor microglia, host microglia, and donor circulating monocytes were sorted separately. RNA-seq was performed by first isolating mRNA using DynaBead mRNA DIRECT kit (Thermo Fisher), followed by cDNA preparation using SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio), library preparation using NexteraXT DNA Library Preparation kit (illumina), and sequencing using HiSeq 4000 (illumina). STAR (70) (version 2.5.2b) was used to align reads to the mouse genome, version GRCm38.78. SRS5697311 10047_Host_Microglia_S20_R1_001.fastq 10047 Host Microglia RNA-Seq TRANSCRIPTOMIC Oligo-dT Illumina HiSeq 4000 SRX7191296 10041 Host Microglia SRP230774 bp0 To detect microglia, cells were stained with antibodies against CD45.1 (A20, BioLegend), CD45.2 (104) (Thermo Fisher), and CD11b (M1/70) (BD Biosciences). Donor microglia, host microglia, and donor circulating monocytes were sorted separately. RNA-seq was performed by first isolating mRNA using DynaBead mRNA DIRECT kit (Thermo Fisher), followed by cDNA preparation using SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio), library preparation using NexteraXT DNA Library Preparation kit (illumina), and sequencing using HiSeq 4000 (illumina). STAR (70) (version 2.5.2b) was used to align reads to the mouse genome, version GRCm38.78. SRS5697312 10041_Host_Microglia_S15_R1_001.fastq 10041 Host Microglia RNA-Seq TRANSCRIPTOMIC Oligo-dT Illumina HiSeq 4000 SRX7191297 10113 Host Microglia SRP230774 bp0 To detect microglia, cells were stained with antibodies against CD45.1 (A20, BioLegend), CD45.2 (104) (Thermo Fisher), and CD11b (M1/70) (BD Biosciences). Donor microglia, host microglia, and donor circulating monocytes were sorted separately. RNA-seq was performed by first isolating mRNA using DynaBead mRNA DIRECT kit (Thermo Fisher), followed by cDNA preparation using SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio), library preparation using NexteraXT DNA Library Preparation kit (illumina), and sequencing using HiSeq 4000 (illumina). STAR (70) (version 2.5.2b) was used to align reads to the mouse genome, version GRCm38.78. SRS5697313 10113_Host_Microglia_S9_R1_001.fastq 10113 Host Microglia RNA-Seq TRANSCRIPTOMIC Oligo-dT Illumina HiSeq 4000 SRX7191298 10117 Host Microglia SRP230774 bp0 To detect microglia, cells were stained with antibodies against CD45.1 (A20, BioLegend), CD45.2 (104) (Thermo Fisher), and CD11b (M1/70) (BD Biosciences). Donor microglia, host microglia, and donor circulating monocytes were sorted separately. RNA-seq was performed by first isolating mRNA using DynaBead mRNA DIRECT kit (Thermo Fisher), followed by cDNA preparation using SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio), library preparation using NexteraXT DNA Library Preparation kit (illumina), and sequencing using HiSeq 4000 (illumina). STAR (70) (version 2.5.2b) was used to align reads to the mouse genome, version GRCm38.78. SRS5697314 10117_Host_Microglia_S3_R1_001.fastq 10117 Host Microglia RNA-Seq TRANSCRIPTOMIC Oligo-dT Illumina HiSeq 4000 SRX7191299 9804 Donor Monocytes SRP230774 bp0 To detect microglia, cells were stained with antibodies against CD45.1 (A20, BioLegend), CD45.2 (104) (Thermo Fisher), and CD11b (M1/70) (BD Biosciences). Donor microglia, host microglia, and donor circulating monocytes were sorted separately. RNA-seq was performed by first isolating mRNA using DynaBead mRNA DIRECT kit (Thermo Fisher), followed by cDNA preparation using SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio), library preparation using NexteraXT DNA Library Preparation kit (illumina), and sequencing using HiSeq 4000 (illumina). STAR (70) (version 2.5.2b) was used to align reads to the mouse genome, version GRCm38.78. SRS5697315 9804_Donor_Monocytes_S11_R1_001.fastq 9804 Donor Monocytes RNA-Seq TRANSCRIPTOMIC Oligo-dT Illumina HiSeq 4000 SRX7191300 10035 Donor Monocytes SRP230774 bp0 To detect microglia, cells were stained with antibodies against CD45.1 (A20, BioLegend), CD45.2 (104) (Thermo Fisher), and CD11b (M1/70) (BD Biosciences). Donor microglia, host microglia, and donor circulating monocytes were sorted separately. RNA-seq was performed by first isolating mRNA using DynaBead mRNA DIRECT kit (Thermo Fisher), followed by cDNA preparation using SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio), library preparation using NexteraXT DNA Library Preparation kit (illumina), and sequencing using HiSeq 4000 (illumina). STAR (70) (version 2.5.2b) was used to align reads to the mouse genome, version GRCm38.78. SRS5697316 10035_Donor_Monocytes_S21_R1_001.fastq 10035 Donor Monocytes RNA-Seq TRANSCRIPTOMIC Oligo-dT Illumina HiSeq 4000 SRX7191301 10045 Donor Monocytes SRP230774 bp0 To detect microglia, cells were stained with antibodies against CD45.1 (A20, BioLegend), CD45.2 (104) (Thermo Fisher), and CD11b (M1/70) (BD Biosciences). Donor microglia, host microglia, and donor circulating monocytes were sorted separately. RNA-seq was performed by first isolating mRNA using DynaBead mRNA DIRECT kit (Thermo Fisher), followed by cDNA preparation using SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio), library preparation using NexteraXT DNA Library Preparation kit (illumina), and sequencing using HiSeq 4000 (illumina). STAR (70) (version 2.5.2b) was used to align reads to the mouse genome, version GRCm38.78. SRS5697317 10045_Donor_Monocytes_S16_R1_001.fastq 10045 Donor Monocytes RNA-Seq TRANSCRIPTOMIC Oligo-dT Illumina HiSeq 4000 SRX7191302 10047 Donor Monocytes SRP230774 bp0 To detect microglia, cells were stained with antibodies against CD45.1 (A20, BioLegend), CD45.2 (104) (Thermo Fisher), and CD11b (M1/70) (BD Biosciences). Donor microglia, host microglia, and donor circulating monocytes were sorted separately. RNA-seq was performed by first isolating mRNA using DynaBead mRNA DIRECT kit (Thermo Fisher), followed by cDNA preparation using SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio), library preparation using NexteraXT DNA Library Preparation kit (illumina), and sequencing using HiSeq 4000 (illumina). STAR (70) (version 2.5.2b) was used to align reads to the mouse genome, version GRCm38.78. SRS5697318 10047_Donor_Monocytes_S12_R1_001.fastq 10047 Donor Monocytes RNA-Seq TRANSCRIPTOMIC Oligo-dT Illumina HiSeq 4000 SRX7191303 10041 Donor Monocytes SRP230774 bp0 To detect microglia, cells were stained with antibodies against CD45.1 (A20, BioLegend), CD45.2 (104) (Thermo Fisher), and CD11b (M1/70) (BD Biosciences). Donor microglia, host microglia, and donor circulating monocytes were sorted separately. RNA-seq was performed by first isolating mRNA using DynaBead mRNA DIRECT kit (Thermo Fisher), followed by cDNA preparation using SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio), library preparation using NexteraXT DNA Library Preparation kit (illumina), and sequencing using HiSeq 4000 (illumina). STAR (70) (version 2.5.2b) was used to align reads to the mouse genome, version GRCm38.78. SRS5697319 10041_Donor_Monocytes_S23_R1_001.fastq 10041 Donor Monocytes RNA-Seq TRANSCRIPTOMIC Oligo-dT Illumina HiSeq 4000 SRX7191304 10035 Donor Microglia SRP230774 bp0 To detect microglia, cells were stained with antibodies against CD45.1 (A20, BioLegend), CD45.2 (104) (Thermo Fisher), and CD11b (M1/70) (BD Biosciences). Donor microglia, host microglia, and donor circulating monocytes were sorted separately. RNA-seq was performed by first isolating mRNA using DynaBead mRNA DIRECT kit (Thermo Fisher), followed by cDNA preparation using SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio), library preparation using NexteraXT DNA Library Preparation kit (illumina), and sequencing using HiSeq 4000 (illumina). STAR (70) (version 2.5.2b) was used to align reads to the mouse genome, version GRCm38.78. SRS5697320 10035_Donor_Microglia_S4_R1_001.fastq 10035 Donor Microglia RNA-Seq TRANSCRIPTOMIC Oligo-dT Illumina HiSeq 4000 SRX7191305 10113 Donor Monocytes SRP230774 bp0 To detect microglia, cells were stained with antibodies against CD45.1 (A20, BioLegend), CD45.2 (104) (Thermo Fisher), and CD11b (M1/70) (BD Biosciences). Donor microglia, host microglia, and donor circulating monocytes were sorted separately. RNA-seq was performed by first isolating mRNA using DynaBead mRNA DIRECT kit (Thermo Fisher), followed by cDNA preparation using SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio), library preparation using NexteraXT DNA Library Preparation kit (illumina), and sequencing using HiSeq 4000 (illumina). STAR (70) (version 2.5.2b) was used to align reads to the mouse genome, version GRCm38.78. SRS5697321 10113_Donor_Monocytes_S10_R1_001.fastq 10113 Donor Monocytes RNA-Seq TRANSCRIPTOMIC Oligo-dT Illumina HiSeq 4000 SRX7191306 10117 Donor Monocytes SRP230774 bp0 To detect microglia, cells were stained with antibodies against CD45.1 (A20, BioLegend), CD45.2 (104) (Thermo Fisher), and CD11b (M1/70) (BD Biosciences). Donor microglia, host microglia, and donor circulating monocytes were sorted separately. RNA-seq was performed by first isolating mRNA using DynaBead mRNA DIRECT kit (Thermo Fisher), followed by cDNA preparation using SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio), library preparation using NexteraXT DNA Library Preparation kit (illumina), and sequencing using HiSeq 4000 (illumina). STAR (70) (version 2.5.2b) was used to align reads to the mouse genome, version GRCm38.78. SRS5697322 10117_Donor_Monocytes_S14_R1_001.fastq 10117 Donor Monocytes RNA-Seq TRANSCRIPTOMIC Oligo-dT Illumina HiSeq 4000 SRX7191307 10045 Donor Microglia SRP230774 bp0 To detect microglia, cells were stained with antibodies against CD45.1 (A20, BioLegend), CD45.2 (104) (Thermo Fisher), and CD11b (M1/70) (BD Biosciences). Donor microglia, host microglia, and donor circulating monocytes were sorted separately. RNA-seq was performed by first isolating mRNA using DynaBead mRNA DIRECT kit (Thermo Fisher), followed by cDNA preparation using SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio), library preparation using NexteraXT DNA Library Preparation kit (illumina), and sequencing using HiSeq 4000 (illumina). STAR (70) (version 2.5.2b) was used to align reads to the mouse genome, version GRCm38.78. SRS5697323 10045_Donor_Microglia_S7_R1_001.fastq 10045 Donor Microglia RNA-Seq TRANSCRIPTOMIC Oligo-dT Illumina HiSeq 4000 SRX7191308 10047 Donor Microglia SRP230774 bp0 To detect microglia, cells were stained with antibodies against CD45.1 (A20, BioLegend), CD45.2 (104) (Thermo Fisher), and CD11b (M1/70) (BD Biosciences). Donor microglia, host microglia, and donor circulating monocytes were sorted separately. RNA-seq was performed by first isolating mRNA using DynaBead mRNA DIRECT kit (Thermo Fisher), followed by cDNA preparation using SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio), library preparation using NexteraXT DNA Library Preparation kit (illumina), and sequencing using HiSeq 4000 (illumina). STAR (70) (version 2.5.2b) was used to align reads to the mouse genome, version GRCm38.78. SRS5697324 10047_Donor_Microglia_S19_R1_001.fastq 10047 Donor Microglia RNA-Seq TRANSCRIPTOMIC Oligo-dT Illumina HiSeq 4000 SRX7191309 10041 Donor Microglia SRP230774 bp0 To detect microglia, cells were stained with antibodies against CD45.1 (A20, BioLegend), CD45.2 (104) (Thermo Fisher), and CD11b (M1/70) (BD Biosciences). Donor microglia, host microglia, and donor circulating monocytes were sorted separately. RNA-seq was performed by first isolating mRNA using DynaBead mRNA DIRECT kit (Thermo Fisher), followed by cDNA preparation using SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio), library preparation using NexteraXT DNA Library Preparation kit (illumina), and sequencing using HiSeq 4000 (illumina). STAR (70) (version 2.5.2b) was used to align reads to the mouse genome, version GRCm38.78. SRS5697325 10041_Donor_Microglia_S13_R1_001.fastq 10041 Donor Microglia RNA-Seq TRANSCRIPTOMIC Oligo-dT Illumina HiSeq 4000 SRX7191310 10117 Donor Microglia SRP230774 bp0 To detect microglia, cells were stained with antibodies against CD45.1 (A20, BioLegend), CD45.2 (104) (Thermo Fisher), and CD11b (M1/70) (BD Biosciences). Donor microglia, host microglia, and donor circulating monocytes were sorted separately. RNA-seq was performed by first isolating mRNA using DynaBead mRNA DIRECT kit (Thermo Fisher), followed by cDNA preparation using SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio), library preparation using NexteraXT DNA Library Preparation kit (illumina), and sequencing using HiSeq 4000 (illumina). STAR (70) (version 2.5.2b) was used to align reads to the mouse genome, version GRCm38.78. SRS5697326 10117_Donor_Microglia_S6_R1_001.fastq 10117 Donor Microglia RNA-Seq TRANSCRIPTOMIC Oligo-dT Illumina HiSeq 4000 SRX7191311 9804 Host Microglia SRP230774 bp0 To detect microglia, cells were stained with antibodies against CD45.1 (A20, BioLegend), CD45.2 (104) (Thermo Fisher), and CD11b (M1/70) (BD Biosciences). Donor microglia, host microglia, and donor circulating monocytes were sorted separately. RNA-seq was performed by first isolating mRNA using DynaBead mRNA DIRECT kit (Thermo Fisher), followed by cDNA preparation using SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio), library preparation using NexteraXT DNA Library Preparation kit (illumina), and sequencing using HiSeq 4000 (illumina). STAR (70) (version 2.5.2b) was used to align reads to the mouse genome, version GRCm38.78. SRS5697327 9804_Host_Microglia_S5_R1_001.fastq 9804 Host Microglia RNA-Seq TRANSCRIPTOMIC Oligo-dT Illumina HiSeq 4000 SRX7191312 9982 Host Microglia SRP230774 bp0 To detect microglia, cells were stained with antibodies against CD45.1 (A20, BioLegend), CD45.2 (104) (Thermo Fisher), and CD11b (M1/70) (BD Biosciences). Donor microglia, host microglia, and donor circulating monocytes were sorted separately. RNA-seq was performed by first isolating mRNA using DynaBead mRNA DIRECT kit (Thermo Fisher), followed by cDNA preparation using SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio), library preparation using NexteraXT DNA Library Preparation kit (illumina), and sequencing using HiSeq 4000 (illumina). STAR (70) (version 2.5.2b) was used to align reads to the mouse genome, version GRCm38.78. SRS5697328 9982_Host_Microglia_S8_R1_001.fastq 9982 Host Microglia RNA-Seq TRANSCRIPTOMIC Oligo-dT Illumina HiSeq 4000 SRX7191313 10035 Host Microglia SRP230774 bp0 To detect microglia, cells were stained with antibodies against CD45.1 (A20, BioLegend), CD45.2 (104) (Thermo Fisher), and CD11b (M1/70) (BD Biosciences). Donor microglia, host microglia, and donor circulating monocytes were sorted separately. RNA-seq was performed by first isolating mRNA using DynaBead mRNA DIRECT kit (Thermo Fisher), followed by cDNA preparation using SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio), library preparation using NexteraXT DNA Library Preparation kit (illumina), and sequencing using HiSeq 4000 (illumina). STAR (70) (version 2.5.2b) was used to align reads to the mouse genome, version GRCm38.78. SRS5697329 10035_Host_Microglia_S17_R1_001.fastq 10035 Host Microglia RNA-Seq TRANSCRIPTOMIC Oligo-dT Illumina HiSeq 4000