Extended Data Figure 4: Comparison of genomic data from astrocytes and non-astrocyte cells from WT and STAT3-CKO mice after SCI.

a, Heat maps depicting all significantly differentially expressed genes (DEG), as determined by RNA-seq, for wild-type (WT) and STAT3-CKO astrocytes and non-astrocytes from independent biological replicates two weeks after SCI relative to uninjured wild-type control. Red upregulated, green downregulated. b, Total numbers and Venn diagrams of significant DEGs in wild-type and STAT3-CKO astrocytes and non-astrocytes two weeks after SCI relative to uninjured control. Red and green numerical values indicate significantly upregulated and downregulated genes, respectively. c, Comparison of altered gene expression in our SCI-reactive astrocytes and previously reported forebrain stroke-reactive astrocytes²⁷. Of the 200 most highly elevated genes in forebrain astrocytes one week following stroke²⁷, 58.5% (red line) are also significantly elevated in astrocytes after SCI, relative to uninjured. d, Comparison of expression by wild-type SCI and STAT3-CKO SCI reactive astrocytes of a selected cross-section of genes that are highly regulated after SCI by wild-type reactive astrocytes. Many of the regulated genes exhibit changes that are expected and implicated in wild-type reactive astrogliosis mechanisms and roles, and some of the changes appear to be newly identified in this context. Note that many of the genes are not regulated or exhibit attenuated changes in STAT3-CKO SCI astrocytes. n = 4 mice each for uninjured and wild-type SCI; n = 3 mice for STAT3-CKO SCI (SCI-STAT3). FDR < 0.1 for differential expression and enrichment analysis.