Supplementary Materials

An environment-dependent transcriptional network specifies human microglia identity

David Gosselin, Dylan Skola, Nicole G. Coufal, Inge R. Holtman, Johannes C. M. Schlachetzki, Eniko Sajti, Baptiste N. Jaeger, Carolyn O'Connor, Conor Fitzpatrick, Martina P. Pasillas, Monique Pena, Amy Adair, David G. Gonda, Michael L. Levy, Richard M. Ransohoff, Fred H. Gage, Christopher K. Glass

Materials/Methods, Supplementary Text, Tables, Figures, and/or References

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  • Materials and Methods
  • Figs. S1 to S17
  • Captions for tables S1 to S6
  • References
Table S1
Patient Information and Assays
Table summarizing patient information, including primary diagnosis, age, sex, ethnicity, localization of the brain tissue resected, medication administered, and assays performed with the microglia isolated.
Table S2
Human RNA-seq data
Table providing RNA-seq data for all human samples analyzed, including ex vivo microglia, microglia culture time course, and intact brain cortical region. Data is provided in the form of raw counts and TPM normalization (see tabs).
Table S3
Microglia genes vs Brain disease gene sets - overlap
Table summarizing overlap for the genes expressed in ex vivo human microglia that are also modulated in brain disorders. Information provided includes statistical summary, listing of the overlapping genes, and the references of the brain disorder studies used for this analysis.
Table S4
Mouse RNA-seq data
Table providing RNA-seq data for all mouse samples analyzed, including ex vivo microglia, microglia culture time course, and intact brain cortical region. Data is provided in the form of raw counts and TPM normalization (see tabs).
Table S5
Microglia gene expression - Human vs Mouse ortholog comparisons
Table summarizing comparison of human - mouse orthologous gene expression in microglia. Information provided also includes species-bias genes (i.e. expression 10-fold higher in one species over the other, FDR 0.05), Metascape functional enrichment analysis for species-bias genes, and overlap of orthologous genes with microglia signature genes as defined in mice by higher expression in microglia compared to other tissue-resident macrophage subsets (see main text).
Table S6
Human microglia super-enhancers - Ex vivo - In vitro
Table providing fold change difference in expression value of genes associated with super-enhancers, comparing ex vivo microglia to microglia maintained for 7 days in tissue culture environment. Table also includes Metascape functional enrichment analysis for genes belonging to each "environment vs change"� category (e.g. ex vivo–higher).