Figure 2. Cortical region-specific and neuroinflammation time-specific transcriptional alterations in astrocytes.

(A–C) Principal component analysis (top 1,000 most variable genes) of NIM and control astrocyte RNA, from PFC and VCX, 1 (A), 2 (B) and 14 days (C) after LPS or PBS injection.

(D) Number of astrocyte DEGs between 1-day control PFC and VCX (FDR < 0.05, FPKM > 1).

(E) Number of astrocyte DEGs between 1-day NIM PFC and VCX (FDR < 0.05, FPKM > 1).

(F) Overlap of PFC-enriched genes (compared to VCX) between 1-day control and NIM conditions.

(G) Overlap of VCX-enriched genes (compared to PFC) between 1-day control and NIM conditions.

(H) Top 20 PFC-enriched genes when compared to VCX in both 1-day control and NIM conditions (see F).

(I) Top 20 VCX-enriched genes when compared to PFC in both 1-day control and NIM conditions (see G).

(J and K) Number of PFC (J) or VCX (K) NIM versus control DEGs (FDR < 0.05, FPKM > 1) in astrocytes at 1, 2, and 14 days.

(L) Overlap of 1-day NIM versus control DEGs between PFC and VCX (FDR < 0.05, FPKM > 1).

(M) Overlap of NIM versus control astrocyte DEGs (FDR < 0.05, FPKM > 1) between PFC and VCX at 1 and 2 days.

(N) Top 20 NIM versus control upregulated (top) and downregulated (bottom) genes that are common across 1-day PFC, 1-day VCX, 2-day PFC, and 2-day VCX astrocytes.

(O) Top 20 NIM versus control upregulated (top) and downregulated (bottom) genes that are uniquely altered (FDR < 0.05, FPKM > 1) in 1-day PFC astrocytes.

For the whole figure, n = 3–4 biological samples per group; each biological sample was generated from the tissue of two mice.