8 Microglial subpopulations
Identification of Microglial Subpopulations after subsetting: recluster and reintegration
8.1 Subseting microglia from the complete dataset
The integrated scRNAseq dataset of all brain cell populations was subsetted to retain only cells annotated as microglia by the “expert committee”.
8.2 Reintegration microglia
The subseted Seurat object was split, SCTransformed, and reintegrated.
Dimensionality reduction was performed by principal component analysis (PCA) on the set of variable features. An elbow plot was generated to identify the inflection point, and the first 10 principal components were selected for neighborhood graph construction.
Elbowplot & cluster stability
Nearest neighbors in the reduced space were computed and an unsupervised clustering across a range of resolutions (0.1 to 1.0, step 0.2) was performed. Cluster stability across resolutions was evaluated with the clustree package, and a resolution of 0.3 was selected as a balance between capturing subpopulation diversity and avoiding overfragmentation.
The final clusters were visualized using UMAP.
8.3 RESOLUTION = 0.3
The reclustering with resolution = 0.3 identified 10 transcriptionally distinct microglial subpopulations, compared with the initial single microglia cluster in the whole-brain dataset. These clusters exhibited clear separation in UMAP space, indicating distinct transcriptional programs.
| 0 | 1 | 12 | 13 | 14 | 2 | 28 | 3 | 5 | 8 | |
|---|---|---|---|---|---|---|---|---|---|---|
| 0 | 5701 | 123 | 342 | 0 | 25 | 255 | 0 | 175 | 1 | 465 |
| 1 | 185 | 77 | 2 | 3 | 81 | 4333 | 0 | 8 | 274 | 52 |
| 2 | 152 | 3947 | 179 | 81 | 12 | 8 | 0 | 396 | 46 | 68 |
| 3 | 159 | 539 | 104 | 760 | 19 | 152 | 0 | 40 | 5 | 1832 |
| 4 | 2 | 142 | 23 | 153 | 18 | 77 | 0 | 8 | 3010 | 3 |
| 5 | 419 | 138 | 650 | 1 | 16 | 3 | 0 | 2106 | 0 | 28 |
| 6 | 121 | 63 | 17 | 3 | 12 | 32 | 0 | 978 | 97 | 10 |
| 7 | 15 | 119 | 6 | 1 | 780 | 3 | 0 | 10 | 12 | 0 |
| 8 | 132 | 91 | 12 | 10 | 7 | 46 | 0 | 11 | 100 | 20 |
| 9 | 6 | 2 | 4 | 5 | 6 | 2 | 141 | 5 | 3 | 3 |
8.4 Cluster markers
Cluster-specific marker genes were determined using a Wilcoxon rank-sum test, restricted to genes expressed in at least 30% of cells within a cluster.
The table represents the top 20 markers (according to the adjusted p-value) for each cluster:
8.5 Cluster interpretation (chatGPT 5)
8.5.1 Cluster 0
| Gene | Cell | Subtype | Regulation | Notes |
|---|---|---|---|---|
| Nfkbia | microglia | NF-κB/TNF-activated (IEG) | Up | NF-κB inhibitor; acute inflammatory response. |
| Il1b | microglia | NF-κB/TNF-activated (IEG) | Up | Pro-inflammatory cytokine; LPS/TLR hallmark. |
| Nfkbiz | microglia | NF-κB/TNF-activated (IEG) | Up | NF-κB co-regulator induced by TNF/IL-1. |
| Bcl2a1d | microglia | NF-κB/TNF-activated (IEG) | Up | NF-κB-induced survival/apoptosis modulator. |
| Bcl2a1b | microglia | NF-κB/TNF-activated (IEG) | Up | Similar to Bcl2a1d; activation/survival cue. |
| Ccl4 | microglia | NF-κB/TNF-activated (IEG) | Up | Chemokine from activated microglia. |
| Clic4 | microglia | NF-κB/TNF-activated (IEG) | Up | Stress/activation-linked ion channel. |
| Cd83 | microglia | NF-κB/TNF-activated (IEG) | Up | Activation marker; antigen-presenting bias. |
| Zfp36 | microglia | NF-κB/TNF-activated (IEG) | Down | ARE-mRNA decay; often induced with IEGs. |
| Junb | microglia | IEG/AP-1-activated | Down | AP-1 component; immediate-early program. |
| Cd14 | microglia | NF-κB/TNF-activated (IEG) | Up | LPS co-receptor; primed TLR signaling. |
| Pde4b | microglia | NF-κB/TNF-activated (IEG) | Up | cAMP regulator; inflammation coupling. |
| Ier2 | microglia | IEG/AP-1-activated | Up | Immediate-early transcriptional response. |
| Egr1 | microglia | IEG/AP-1-activated | Up | Activity-dependent IEG; rapid activation. |
| Tnf | microglia | NF-κB/TNF-activated (IEG) | Up | Canonical inflammatory cytokine. |
| Gadd45b | microglia | IEG/AP-1-activated | Up | Stress/IEG; activity-dependent chromatin. |
| Ppp1r15a | microglia | IEG/AP-1-activated | Up | Integrated stress response (GADD34). |
| Btg2 | microglia | IEG/AP-1-activated | Down | IEG; cell-cycle brake in activation. |
| Ier3 | microglia | IEG/AP-1-activated | Up | Immediate-early; NF-κB/AP-1 target. |
| Tnfaip3 | microglia | NF-κB/TNF-activated (IEG) | Down | A20; negative feedback to NF-κB. |
Brief Summary: Enriched NF-κB/IEG program (Il1b, Tnf, Nfkbia) indicates acutely activated microglia with chemokine output (Ccl4) and stress-response genes. Overall profile fits TNF/LPS-like activation.
8.5.2 Cluster 1
| Gene | Cell | Subtype | Regulation | Notes |
|---|---|---|---|---|
| Lpcat2 | microglia | Chemokine/activation-competent homeostatic | Up | LPS-responsive lipid remodeling enzyme. |
| Ccr5 | microglia | Chemokine/activation-competent homeostatic | Up | Chemokine receptor; migratory/immune tone. |
| Camk2n1 | neuron | Non-microglial signal | Up | Neuronal inhibitor peptide; likely cargo/doublet. |
| Zfhx3 | neuron | Non-microglial signal | Up | Neuronal TF; likely ambient RNA. |
| Marcks | microglia | Homeostatic (P2ry12/Tmem119-like) | Up | Cytoskeletal; ramified surveillant state. |
| Ecscr | endothelial | Non-microglial signal | Up | Endothelial marker; contamination/doublet. |
| Srgap2 | microglia | Homeostatic (P2ry12/Tmem119-like) | Up | Process dynamics; surveillant morphology. |
| Tsc22d3 | microglia | Homeostatic (anti-inflammatory bias) | Up | Glucocorticoid-induced anti-inflammatory. |
| Elmo1 | microglia | Homeostatic (phagocytic-competent) | Up | Engulfment adaptor; basal phagocytosis. |
| Herpud1 | microglia | Homeostatic (stress-buffered) | Up | ER stress response; adaptive homeostasis. |
| Glul | microglia | Homeostatic (metabolic) | Up | Glutamine synthetase; housekeeping. |
| Rhob | microglia | Homeostatic | Down | Rho GTPase; motility tone. |
| Tmem119 | microglia | Homeostatic (P2ry12/Tmem119-like) | Up | Core homeostatic microglia marker. |
| Otulinl | microglia | Homeostatic | Up | NF-κB pathway regulator; tonic restraint. |
| Txnip | microglia | Homeostatic/stress-responsive | Up | Redox sensor; mild stress priming. |
| Crybb1 | microglia | Homeostatic/stress-responsive | Up | Stress-inducible crystallin in myeloid cells. |
| Jun | microglia | IEG-tinge within homeostasis | Up | AP-1 component; mild activation tone. |
| Il1a | microglia | Chemokine/activation-competent homeostatic | Up | Early activation cytokine; low-grade alert. |
| Nr4a1 | microglia | IEG-tinge within homeostasis | Up | Tolerance/IEG; limits excessive activation. |
| Tgm2 | microglia | Homeostatic (phagocytic-competent) | Up | Efferocytosis/ECM interaction. |
Brief Summary: Predominantly homeostatic microglia (Tmem119, Marcks) with chemokine/activation competence (Ccr5, Il1a) and stress-buffering genes. Neuron/endothelial signals suggest minor doublets.
8.5.3 Cluster 2
| Gene | Cell | Subtype | Regulation | Notes |
|---|---|---|---|---|
| Trem2 | microglia | DAM—early/intermediate (phagolysosomal) | Up | Core DAM receptor; phagocytic switch. |
| Serpine2 | microglia | DAM—early/intermediate | Up | ECM/protease balance during remodeling. |
| Ctsd | microglia | DAM—early/intermediate | Up | Lysosomal protease; debris clearance. |
| Lyz2 | microglia | DAM—early/intermediate | Down | Myeloid enzyme; variable in early DAM. |
| Cst7 | microglia | DAM—early/intermediate | Down | DAM marker; lower suggests pre-late DAM. |
| Syngr1 | neuron | Non-microglial signal | Up | Synaptic gene; likely cargo/doublet. |
| B2m | microglia | DAM—early/intermediate | Up | MHC-I component; activation context. |
| Ctsz | microglia | DAM—early/intermediate | Up | Lysosomal cathepsin; phagocytosis. |
| Rpl23 | microglia | DAM—early/intermediate | Up | Translation ramping during activation. |
| Cst3 | microglia | DAM—early/intermediate | Up | Cystatin C; injury/DAM contexts. |
| Rpl21 | microglia | DAM—early/intermediate | Up | Ribosomal; biosynthetic increase. |
| Cd63 | microglia | DAM—early/intermediate | Down | Exosome/lysosome tetraspanin; stage-specific. |
| Rps4x | microglia | DAM—early/intermediate | Up | Ribosomal; activation support. |
| Rps24 | microglia | DAM—early/intermediate | Up | Ribosomal; activation support. |
| Rpl13 | microglia | DAM—early/intermediate | Up | Ribosomal; activation support. |
| Eef1a1 | microglia | DAM—early/intermediate | Up | Translation elongation; biosynthesis. |
| Cacna1a | neuron | Non-microglial signal | Down | Neuronal channel; phagocytic cargo. |
| Baiap2l2 | microglia | DAM—early/intermediate | Up | Actin/ruffles; phagocytic morphology. |
| Fau | microglia | DAM—early/intermediate | Up | Translation component; activation. |
| Rps14 | microglia | DAM—early/intermediate | Up | Ribosomal; activation support. |
Brief Summary: Early/intermediate DAM signature driven by Trem2 with lysosomal and translational upregulation. Some neuronal RNA suggests engulfment/doublets.
8.5.4 Cluster 3
| Gene | Cell | Subtype | Regulation | Notes |
|---|---|---|---|---|
| Plxdc2 | microglia | Injury-response/remodeling | Up | Angiogenic/axon cues; remodeling microglia. |
| Ptchd1 | neuron | Non-microglial signal | Up | Neuronal gene; ambient RNA. |
| Klf6 | microglia | Injury-response/remodeling | Up | Injury TF; motility/axon-associated cues. |
| Cacna1a | neuron | Non-microglial signal | Up | Neuronal channel; cargo/doublet. |
| Gm37168 | microglia | Injury-response/remodeling | Up | Predicted; co-varies with activation. |
| Malat1 | microglia | Injury-response/remodeling | Up | Stress/activation lncRNA. |
| Apbb2 | microglia | Injury-response/remodeling | Up | APP adaptor; neurodegeneration context. |
| Myo1f | microglia | Injury-response/remodeling | Down | Motility myosin; state-specific shift. |
| Il6st | microglia | Injury-response/remodeling | Up | gp130; cytokine responsiveness. |
| Kcnj2 | neuron | Non-microglial signal | Up | Neuronal/astro channel; contamination. |
| Abcd2 | microglia | Injury-response/remodeling | Down | Peroxisomal lipid flux shift. |
| Fgf13 | neuron | Non-microglial signal | Up | Neuronal MAP; ambient RNA. |
| Jmjd1c | microglia | Injury-response/remodeling | Up | Epigenetic regulator in activation. |
| St6gal1 | microglia | Injury-response/remodeling | Up | Glycosylation changes in activation. |
| Myo1e | microglia | Injury-response/remodeling | Up | Actin/adhesion; process dynamics. |
| Vps13c | microglia | Injury-response/remodeling | Up | Mitochondria/lysosome contact; stress. |
| Cdk19 | microglia | Injury-response/remodeling | Up | Transcriptional modulation in activation. |
| Tmcc3 | microglia | Injury-response/remodeling | Up | ER/trafficking; remodeling. |
| Fnip2 | microglia | Injury-response/remodeling | Up | AMPK partner; metabolic reprogramming. |
| Myo5a | microglia | Injury-response/remodeling | Up | Vesicle transport in activation. |
Brief Summary: Remodeling/axon-interaction program with cytokine sensitivity (Il6st) and metabolic/vesicular rewiring. Several neuronal RNAs suggest cargo or doublets.
8.5.5 Cluster 4
| Gene | Cell | Subtype | Regulation | Notes |
|---|---|---|---|---|
| Zfhx3 | neuron | Non-microglial signal | Up | Neuronal TF; ambient RNA. |
| Gm10790 | microglia | Homeostatic (P2ry12/Tmem119-like) | Up | Predicted gene co-expressed with homeostasis. |
| Dock4 | microglia | Homeostatic (P2ry12/Tmem119-like) | Up | Rac GEF; ramified process control. |
| Chd9 | microglia | Homeostatic | Up | Chromatin regulator; basal state. |
| Otulinl | microglia | Homeostatic | Up | NF-κB restraint; tonic control. |
| Elmo1 | microglia | Homeostatic (phagocytic-competent) | Up | Engulfment adaptor at baseline. |
| Frmd4a | microglia | Homeostatic | Up | Polarity/adhesion in surveillant cells. |
| P2ry12 | microglia | Homeostatic (P2ry12/Tmem119-like) | Up | Gold-standard homeostatic marker. |
| Srgap2 | microglia | Homeostatic | Up | Process dynamics in surveillant microglia. |
| Lpcat2 | microglia | Homeostatic/primed | Up | LPS-responsive enzyme at low tone. |
| Dock10 | microglia | Homeostatic | Up | Rho GTPase GEF; branching morphology. |
| 8030442B05Rik | microglia | Homeostatic | Up | Predicted; co-expressed with signatures. |
| Gm2629 | microglia | Homeostatic | Up | Predicted; homeostatic module. |
| Ophn1 | microglia | Homeostatic | Up | RhoGAP; process stability. |
| Tanc2 | microglia | Homeostatic | Up | Scaffold; baseline signaling. |
| Rapgef5 | microglia | Homeostatic | Up | cAMP/Rap; process motility. |
| Ssh2 | microglia | Homeostatic | Down | Actin regulator; morphology tuning. |
| A830008E24Rik | microglia | Homeostatic | Up | Predicted; homeostatic co-expression. |
| Tmem119 | microglia | Homeostatic (P2ry12/Tmem119-like) | Up | Core homeostatic microglia marker. |
| Ivns1abp | microglia | Homeostatic | Up | Actin/stress chaperone; baseline. |
Brief Summary: Canonical homeostatic microglia (P2ry12, Tmem119) with cytoskeletal/GEF modules that support ramified surveillance. Minor neuronal RNA present.
8.5.6 Cluster 5
| Gene | Cell | Subtype | Regulation | Notes |
|---|---|---|---|---|
| Spp1 | microglia | DAM—late (Spp1+/Gpnmb+/Itgax+) | Up | Osteopontin; hallmark late DAM. |
| Fabp5 | microglia | DAM—late | Up | Lipid handling in DAM/LAM states. |
| Gpnmb | microglia | DAM—late | Up | DAM marker; reparative/phagocytic. |
| Myof | microglia | DAM—late | Up | Membrane repair; phagocytosis. |
| Igf1 | microglia | DAM—late | Up | Trophic factor; plaque-proximal microglia. |
| Atp6v0d2 | microglia | DAM—late | Up | V-ATPase; acidified lysosomes. |
| Fam20c | microglia | DAM—late | Up | Secretory kinase; matrix remodeling. |
| Itgax | microglia | DAM—late | Up | CD11c; classical late DAM. |
| Pianp | neuron | Non-microglial signal | Up | Neuronal adhesion; cargo/doublet. |
| Dkk2 | microglia | DAM—late | Up | WNT modulator in DAM/LAM. |
| Cd63 | microglia | DAM—late | Up | Exosome/lysosome tetraspanin. |
| Aplp2 | microglia | DAM—late | Up | APP family; amyloid milieu. |
| Lgals3 | microglia | DAM—late | Up | Galectin-3; phagocytosis/inflammation. |
| Pld3 | microglia | DAM—late | Up | Endolysosomal nuclease; DAM enriched. |
| Mamdc2 | microglia | DAM—late | Up | Adhesion/ECM; lesion-associated. |
| Hectd2os | microglia | DAM—late | Up | Non-coding; co-expressed with DAM. |
| Anxa5 | microglia | DAM—late | Up | Annexin; apoptotic corpse handling. |
| Ctsb | microglia | DAM—late | Up | Lysosomal protease; debris clearance. |
| Ctsd | microglia | DAM—late | Up | Lysosomal protease; debris clearance. |
| Trpc4 | microglia | DAM—late | Up | Ca²⁺ channel; activation signaling. |
Brief Summary: Classic late-stage DAM/LAM profile centered on Spp1/Gpnmb/Itgax with robust lysosomal and lipid programs. Neuronal RNA minimal.
8.5.7 Cluster 6
| Gene | Cell | Subtype | Regulation | Notes |
|---|---|---|---|---|
| H2-Aa | microglia | Antigen-presenting (MHC-II+) | Up | MHC-II α chain; APC state. |
| H2-Eb1 | microglia | Antigen-presenting (MHC-II+) | Up | MHC-II β chain; APC state. |
| Cp | microglia | Antigen-presenting (MHC-II+) | Up | Ceruloplasmin; inflammatory context. |
| Cd74 | microglia | Antigen-presenting (MHC-II+) | Up | Invariant chain; MHC-II trafficking. |
| H2-Ab1 | microglia | Antigen-presenting (MHC-II+) | Up | MHC-II; definitive APC signature. |
| Ly6e | microglia | Antigen-presenting (MHC-II+) | Up | IFN/activation-linked GPI protein. |
| Cox6a2 | neuron | Non-microglial signal | Up | Neuronal oxidative subunit; contamination. |
| Rad51b | microglia | Antigen-presenting (MHC-II+) | Up | DNA repair; proliferative/activated bias. |
| Hpse | microglia | Antigen-presenting (MHC-II+) | Up | Heparanase; matrix/antigen processing. |
| C1qa | microglia | Antigen-presenting (MHC-II+) | Up | Complement; immune activation. |
| Siglech | microglia | Antigen-presenting (MHC-II+) | Up | Microglia marker; here in APC context. |
| Ccl6 | microglia | Antigen-presenting (MHC-II+) | Up | Chemokine; activated APC microglia. |
| Lsp1 | microglia | Antigen-presenting (MHC-II+) | Up | Leukocyte cytoskeleton; activation. |
| H2-D1 | microglia | Antigen-presenting (MHC-II+) | Up | MHC-I; antigen display tone. |
| Ly6a | microglia | Antigen-presenting (MHC-II+) | Up | Sca-1; activation marker. |
| Cd52 | microglia | Antigen-presenting (MHC-II+) | Up | Lymphoid-like marker; immune tone. |
| AW112010 | microglia | Antigen-presenting (MHC-II+) | Up | Non-coding; activation co-expression. |
| Cxcl13 | microglia | Antigen-presenting (MHC-II+) | Up | B-cell chemokine; APC microglia feature. |
| Fgl2 | microglia | Antigen-presenting (MHC-II+) | Up | Pro-coagulant/immune regulator. |
| Rgs16 | microglia | Antigen-presenting (MHC-II+) | Up | GPCR modulator; activated state. |
Brief Summary: Strong MHC-II antigen-presenting microglia with chemokine output (Cxcl13) and complement. One neuronal oxidative subunit suggests minor contamination.
8.5.8 Cluster 7
| Gene | Cell | Subtype | Regulation | Notes |
|---|---|---|---|---|
| Ifit3 | microglia | Interferon-responsive (IFN-I) | Up | ISG; antiviral response. |
| Ifit3b | microglia | Interferon-responsive (IFN-I) | Up | ISG; IFN-I hallmark. |
| Ifit2 | microglia | Interferon-responsive (IFN-I) | Up | ISG; translational control. |
| Oasl1 | microglia | Interferon-responsive (IFN-I) | Up | ISG; RNA sensing. |
| Ifi211 | microglia | Interferon-responsive (IFN-I) | Up | ISG; murine IFI family. |
| Isg15 | microglia | Interferon-responsive (IFN-I) | Up | Ubiquitin-like; antiviral effector. |
| Irf7 | microglia | Interferon-responsive (IFN-I) | Up | Master TF for IFN-I amplification. |
| Ifi213 | microglia | Interferon-responsive (IFN-I) | Up | ISG; antiviral program. |
| Ifi206 | microglia | Interferon-responsive (IFN-I) | Up | ISG; dsDNA sensing. |
| Iigp1 | microglia | Interferon-responsive (IFN-I) | Up | Immunity-related GTPase; IFN-induced. |
| Mx1 | microglia | Interferon-responsive (IFN-I) | Up | GTPase; antiviral hallmark. |
| Ifi209 | microglia | Interferon-responsive (IFN-I) | Up | ISG; murine IFI family. |
| Oasl2 | microglia | Interferon-responsive (IFN-I) | Up | ISG; viral RNA recognition. |
| Zbp1 | microglia | Interferon-responsive (IFN-I) | Up | Z-DNA/RNA sensor; necroptosis linkage. |
| Ifi204 | microglia | Interferon-responsive (IFN-I) | Up | ISG; cytosolic DNA sensing. |
| Slfn5 | microglia | Interferon-responsive (IFN-I) | Up | SLFN family ISG. |
| Rtp4 | microglia | Interferon-responsive (IFN-I) | Up | ISG; GPCR trafficking in IFN context. |
| Gm4951 | microglia | Interferon-responsive (IFN-I) | Up | ISG-linked predicted gene. |
| Rnf213 | microglia | Interferon-responsive (IFN-I) | Up | ISG; innate immunity. |
| Phf11d | microglia | Interferon-responsive (IFN-I) | Up | ISG-associated chromatin factor. |
Brief Summary: Canonical type-I interferon microglia with broad ISG induction and antiviral machinery.
8.5.9 Cluster 8
| Gene | Cell | Subtype | Regulation | Notes |
|---|---|---|---|---|
| Slc1a2 | astrocyte | Non-microglial (astrocyte) | Up | EAAT2; definitive astrocyte marker. |
| Sparcl1 | astrocyte | Non-microglial (astrocyte) | Up | Astroependymal/ECM glycoprotein. |
| Cpe | neuron | Non-microglial (neuronal) | Up | Peptidyl-processing; neuronal. |
| Ndrg2 | astrocyte | Non-microglial (astrocyte) | Up | High in protoplasmic astrocytes. |
| Gpm6b | neuron | Non-microglial (neuronal) | Up | Neuronal membrane glycoprotein. |
| Atp1a2 | astrocyte | Non-microglial (astrocyte) | Up | Astrocytic Na⁺/K⁺ ATPase α2. |
| Gfap | astrocyte | Non-microglial (astrocyte) | Up | Canonical astrocyte filament. |
| Aldoc | astrocyte | Non-microglial (astrocyte) | Up | Astrocyte metabolic enzyme. |
| Igfbp5 | astrocyte | Non-microglial (astrocyte) | Up | Astro-secreted factor. |
| S100b | astrocyte | Non-microglial (astrocyte) | Up | Calcium-binding astrocyte protein. |
| Slc4a4 | astrocyte | Non-microglial (astrocyte) | Up | Astro bicarbonate transporter. |
| Kif5a | neuron | Non-microglial (neuronal) | Up | Neuronal kinesin heavy chain. |
| Camk2n1 | neuron | Non-microglial (neuronal) | Up | Neuronal inhibitor peptide. |
| mt-Nd4 | microglia | Mitochondrial signal | Up | Mitochondrial transcript; metabolic tone. |
| Acsl3 | astrocyte | Non-microglial (astrocyte) | Up | Lipid enzyme enriched in astrocytes. |
| Scd2 | astrocyte | Non-microglial (astrocyte) | Up | Lipogenesis enzyme; astrocyte-high. |
| Mt2 | microglia | Stress/metal handling | Down | Metallothionein; glial stress module. |
| mt-Atp6 | microglia | Mitochondrial signal | Up | Mitochondrial transcript; metabolic tone. |
| mt-Cytb | microglia | Mitochondrial signal | Up | Mitochondrial transcript; metabolic tone. |
| Pla2g7 | microglia | Myeloid/activation-competent | Up | Platelet-activating factor acetylhydrolase. |
Brief Summary: Strong astrocyte and neuronal signatures indicate doublets or engulfed RNA. Microglial mitochondrial reads present but non-dominant.
8.5.10 Cluster 9
| Gene | Cell | Subtype | Regulation | Notes |
|---|---|---|---|---|
| Mki67 | microglia | Proliferating (cycling) | Up | Cell-cycle marker; division. |
| Birc5 | microglia | Proliferating (cycling) | Up | Survivin; G2/M. |
| Stmn1 | microglia | Proliferating (cycling) | Up | Microtubule dynamics; cycling. |
| H2az1 | microglia | Proliferating (cycling) | Up | Histone variant; S-phase. |
| Hmgb2 | microglia | Proliferating (cycling) | Up | Chromatin protein; cycling bias. |
| Smc2 | microglia | Proliferating (cycling) | Up | Condensin; mitosis. |
| Cdca8 | microglia | Proliferating (cycling) | Up | Borealin; mitotic chromosomal passenger. |
| Tpx2 | microglia | Proliferating (cycling) | Up | Spindle assembly; G2/M. |
| Cks1b | microglia | Proliferating (cycling) | Up | Cell-cycle kinase subunit. |
| Smc4 | microglia | Proliferating (cycling) | Up | Condensin; mitosis. |
| Diaph3 | microglia | Proliferating (cycling) | Up | Cytokinesis actin regulator. |
| Tubb5 | microglia | Proliferating (cycling) | Up | β-tubulin; division cytoskeleton. |
| Top2a | microglia | Proliferating (cycling) | Up | DNA topoisomerase; S/G2. |
| Racgap1 | microglia | Proliferating (cycling) | Up | Cytokinesis GAP; G2/M. |
| Tuba1b | microglia | Proliferating (cycling) | Up | α-tubulin; mitotic spindle. |
| Cdca3 | microglia | Proliferating (cycling) | Up | Cell-cycle E3 ligase adaptor. |
| Cks2 | microglia | Proliferating (cycling) | Up | Cell-cycle kinase subunit. |
| Cenpe | microglia | Proliferating (cycling) | Up | Kinetochore motor; mitosis. |
| Kif20b | microglia | Proliferating (cycling) | Up | Mitotic kinesin; cytokinesis. |
| Kif23 | microglia | Proliferating (cycling) | Up | Mitotic kinesin; midbody formation. |
Brief Summary: Clear cycling microglia with strong G2/M and spindle assembly module; classic proliferative state.
Global Note: Gene lists per cluster come from the user-provided markers file.
8.6 Heatmap & hierarchical cluster
8.7 Correlation between clusters
8.8 Trajectory analysis
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