SRX5210334 GSM3543741 SRP176108 SRS4214649 GSM3543741 RNA-Seq TRANSCRIPTOMIC cDNA Cortical microglia were isolated from four independent ∼12-week-old two- color animals (Cx3Cr1GFP/+; Hoxb8IRES-Cre/+; ROSA26CAG-LSL-tdTomato/+). Animals were humanely euthanized by isoflurane, cortical tissue dissected and meninges removed, minced and trypsin digested (1% trypsin, 37°C, 30min in HBSS). Cortical single-cell suspensions were generated by mechanical trituration and successive filtration (70 and 30 μm mesh) and glia enriched via capture with anti-Cd11b (Itgam) magnetic beads (Miltenyi Biotec). Bead-associated cortical microglia were then sorted on a BD FACSAriaII gating on tdTomato and GFP with collection into RNAlater solution, flash frozen and stored at −80°C Total RNA was isolated and cloned by the University of Utah High-throughput Genomics Core using a Clontech UltraLow RNA isolation kit, and barcoded libraries sequenced on an Illumina HiSeq platform (50 bp nonstranded single-end reads), resulting in ∼25-30 million sequences per biological replicate. Sequence quality was confirmed by FastQC. Raw fastq reads were mapped using STAR (2.4.1c) (Dobin et al., 2013). Indices for STAR were built based upon the Gencode GRCm38v3 release M5 of the mouse genome. The index for STAR was constructed based upon the primary assembly and included splice junction information from the GTF file. Illumina HiSeq 2500 gds 303543741 GSM3543741 GEO Accession GSM3543741 SRX5210335 GSM3543742 SRP176108 SRS4214650 GSM3543742 RNA-Seq TRANSCRIPTOMIC cDNA Cortical microglia were isolated from four independent ∼12-week-old two- color animals (Cx3Cr1GFP/+; Hoxb8IRES-Cre/+; ROSA26CAG-LSL-tdTomato/+). Animals were humanely euthanized by isoflurane, cortical tissue dissected and meninges removed, minced and trypsin digested (1% trypsin, 37°C, 30min in HBSS). Cortical single-cell suspensions were generated by mechanical trituration and successive filtration (70 and 30 μm mesh) and glia enriched via capture with anti-Cd11b (Itgam) magnetic beads (Miltenyi Biotec). Bead-associated cortical microglia were then sorted on a BD FACSAriaII gating on tdTomato and GFP with collection into RNAlater solution, flash frozen and stored at −80°C Total RNA was isolated and cloned by the University of Utah High-throughput Genomics Core using a Clontech UltraLow RNA isolation kit, and barcoded libraries sequenced on an Illumina HiSeq platform (50 bp nonstranded single-end reads), resulting in ∼25-30 million sequences per biological replicate. Sequence quality was confirmed by FastQC. Raw fastq reads were mapped using STAR (2.4.1c) (Dobin et al., 2013). Indices for STAR were built based upon the Gencode GRCm38v3 release M5 of the mouse genome. The index for STAR was constructed based upon the primary assembly and included splice junction information from the GTF file. Illumina HiSeq 2500 gds 303543742 GSM3543742 GEO Accession GSM3543742 SRX5210336 GSM3543743 SRP176108 SRS4214651 GSM3543743 RNA-Seq TRANSCRIPTOMIC cDNA Cortical microglia were isolated from four independent ∼12-week-old two- color animals (Cx3Cr1GFP/+; Hoxb8IRES-Cre/+; ROSA26CAG-LSL-tdTomato/+). Animals were humanely euthanized by isoflurane, cortical tissue dissected and meninges removed, minced and trypsin digested (1% trypsin, 37°C, 30min in HBSS). Cortical single-cell suspensions were generated by mechanical trituration and successive filtration (70 and 30 μm mesh) and glia enriched via capture with anti-Cd11b (Itgam) magnetic beads (Miltenyi Biotec). Bead-associated cortical microglia were then sorted on a BD FACSAriaII gating on tdTomato and GFP with collection into RNAlater solution, flash frozen and stored at −80°C Total RNA was isolated and cloned by the University of Utah High-throughput Genomics Core using a Clontech UltraLow RNA isolation kit, and barcoded libraries sequenced on an Illumina HiSeq platform (50 bp nonstranded single-end reads), resulting in ∼25-30 million sequences per biological replicate. Sequence quality was confirmed by FastQC. Raw fastq reads were mapped using STAR (2.4.1c) (Dobin et al., 2013). Indices for STAR were built based upon the Gencode GRCm38v3 release M5 of the mouse genome. The index for STAR was constructed based upon the primary assembly and included splice junction information from the GTF file. Illumina HiSeq 2500 gds 303543743 GSM3543743 GEO Accession GSM3543743 SRX5210337 GSM3543744 SRP176108 SRS4214652 GSM3543744 RNA-Seq TRANSCRIPTOMIC cDNA Cortical microglia were isolated from four independent ∼12-week-old two- color animals (Cx3Cr1GFP/+; Hoxb8IRES-Cre/+; ROSA26CAG-LSL-tdTomato/+). Animals were humanely euthanized by isoflurane, cortical tissue dissected and meninges removed, minced and trypsin digested (1% trypsin, 37°C, 30min in HBSS). Cortical single-cell suspensions were generated by mechanical trituration and successive filtration (70 and 30 μm mesh) and glia enriched via capture with anti-Cd11b (Itgam) magnetic beads (Miltenyi Biotec). Bead-associated cortical microglia were then sorted on a BD FACSAriaII gating on tdTomato and GFP with collection into RNAlater solution, flash frozen and stored at −80°C Total RNA was isolated and cloned by the University of Utah High-throughput Genomics Core using a Clontech UltraLow RNA isolation kit, and barcoded libraries sequenced on an Illumina HiSeq platform (50 bp nonstranded single-end reads), resulting in ∼25-30 million sequences per biological replicate. Sequence quality was confirmed by FastQC. Raw fastq reads were mapped using STAR (2.4.1c) (Dobin et al., 2013). Indices for STAR were built based upon the Gencode GRCm38v3 release M5 of the mouse genome. The index for STAR was constructed based upon the primary assembly and included splice junction information from the GTF file. Illumina HiSeq 2500 gds 303543744 GSM3543744 GEO Accession GSM3543744 SRX5210338 GSM3543745 SRP176108 SRS4214653 GSM3543745 RNA-Seq TRANSCRIPTOMIC cDNA Cortical microglia were isolated from four independent ∼12-week-old two- color animals (Cx3Cr1GFP/+; Hoxb8IRES-Cre/+; ROSA26CAG-LSL-tdTomato/+). Animals were humanely euthanized by isoflurane, cortical tissue dissected and meninges removed, minced and trypsin digested (1% trypsin, 37°C, 30min in HBSS). Cortical single-cell suspensions were generated by mechanical trituration and successive filtration (70 and 30 μm mesh) and glia enriched via capture with anti-Cd11b (Itgam) magnetic beads (Miltenyi Biotec). Bead-associated cortical microglia were then sorted on a BD FACSAriaII gating on tdTomato and GFP with collection into RNAlater solution, flash frozen and stored at −80°C Total RNA was isolated and cloned by the University of Utah High-throughput Genomics Core using a Clontech UltraLow RNA isolation kit, and barcoded libraries sequenced on an Illumina HiSeq platform (50 bp nonstranded single-end reads), resulting in ∼25-30 million sequences per biological replicate. Sequence quality was confirmed by FastQC. Raw fastq reads were mapped using STAR (2.4.1c) (Dobin et al., 2013). Indices for STAR were built based upon the Gencode GRCm38v3 release M5 of the mouse genome. The index for STAR was constructed based upon the primary assembly and included splice junction information from the GTF file. Illumina HiSeq 2500 gds 303543745 GSM3543745 GEO Accession GSM3543745 SRX5210339 GSM3543746 SRP176108 SRS4214654 GSM3543746 RNA-Seq TRANSCRIPTOMIC cDNA Cortical microglia were isolated from four independent ∼12-week-old two- color animals (Cx3Cr1GFP/+; Hoxb8IRES-Cre/+; ROSA26CAG-LSL-tdTomato/+). Animals were humanely euthanized by isoflurane, cortical tissue dissected and meninges removed, minced and trypsin digested (1% trypsin, 37°C, 30min in HBSS). Cortical single-cell suspensions were generated by mechanical trituration and successive filtration (70 and 30 μm mesh) and glia enriched via capture with anti-Cd11b (Itgam) magnetic beads (Miltenyi Biotec). Bead-associated cortical microglia were then sorted on a BD FACSAriaII gating on tdTomato and GFP with collection into RNAlater solution, flash frozen and stored at −80°C Total RNA was isolated and cloned by the University of Utah High-throughput Genomics Core using a Clontech UltraLow RNA isolation kit, and barcoded libraries sequenced on an Illumina HiSeq platform (50 bp nonstranded single-end reads), resulting in ∼25-30 million sequences per biological replicate. Sequence quality was confirmed by FastQC. Raw fastq reads were mapped using STAR (2.4.1c) (Dobin et al., 2013). Indices for STAR were built based upon the Gencode GRCm38v3 release M5 of the mouse genome. The index for STAR was constructed based upon the primary assembly and included splice junction information from the GTF file. Illumina HiSeq 2500 gds 303543746 GSM3543746 GEO Accession GSM3543746 SRX5210340 GSM3543747 SRP176108 SRS4214655 GSM3543747 RNA-Seq TRANSCRIPTOMIC cDNA Cortical microglia were isolated from four independent ∼12-week-old two- color animals (Cx3Cr1GFP/+; Hoxb8IRES-Cre/+; ROSA26CAG-LSL-tdTomato/+). Animals were humanely euthanized by isoflurane, cortical tissue dissected and meninges removed, minced and trypsin digested (1% trypsin, 37°C, 30min in HBSS). Cortical single-cell suspensions were generated by mechanical trituration and successive filtration (70 and 30 μm mesh) and glia enriched via capture with anti-Cd11b (Itgam) magnetic beads (Miltenyi Biotec). Bead-associated cortical microglia were then sorted on a BD FACSAriaII gating on tdTomato and GFP with collection into RNAlater solution, flash frozen and stored at −80°C Total RNA was isolated and cloned by the University of Utah High-throughput Genomics Core using a Clontech UltraLow RNA isolation kit, and barcoded libraries sequenced on an Illumina HiSeq platform (50 bp nonstranded single-end reads), resulting in ∼25-30 million sequences per biological replicate. Sequence quality was confirmed by FastQC. Raw fastq reads were mapped using STAR (2.4.1c) (Dobin et al., 2013). Indices for STAR were built based upon the Gencode GRCm38v3 release M5 of the mouse genome. The index for STAR was constructed based upon the primary assembly and included splice junction information from the GTF file. Illumina HiSeq 2500 gds 303543747 GSM3543747 GEO Accession GSM3543747