Additional file 1 of Neuroinflammatory transcriptional programs induced in rhesus pre-frontal cortex white matter during acute SHIV infection

Abstract

Additional file 1: Fig. S1. Ranked genes by median normalized read counts in units of Log2 counts per million (Log2CPM) in the subcortical white matter of the pre-frontal cortex (PFCw), and gray matter of the superior temporal sulcus (STS), caudate nucleus (CN), and hippocampus (HP) of uninfected animals. Dotted lines indicate location of marker genes associated with neurons (MAP2), astrocytes (GFAP), microglia (P2RY12), and oligodendrocytes (MOG) within ranked distribution. Fig. S2. T-stochastic neighborhood embedding analysis (t-SNE) of gene expression profiles from the pre-frontal cortex white matter (black), superior temporal sulcus (blue), caudate nucleus (red), and hippocampus (green) of uninfected animals. Outlier sample [Animal 43661 pre-frontal cortex white matter] is included. Symbols represent individual animals. Circles indicate 95% confidence intervals. Fig. S3. Regional eigengene expression and corresponding top fifteen most significantly enriched (p < 0.01 by Fisher’s exact test) biological processes GO terms within region specific modules (PFCw-specific [MEmagenta, MEmidnightblue], STS-specific [MEtan], CN-specific [MEpurple, MEred], HP-specific [MEsalmon]) determined by weighted gene co-expression network analysis from uninfected animals. *p < 0.05 by linear mixed effects model (region effect). Boxplots represent quartiles. Fig. S4. Normalized read counts of genes encoding for chemokines in the STS (blue), PFCw (black), CN (red), and HP (green) of uninfected animals. Expression levels are displayed in normalized read counts in units of Log2 counts per million (Log2CPM). Brackets indicate structural chemokine classes. Fig. S5. Log2 Fold change of genes regulating inflammatory processes and synaptic functions between SHIV infected and uninfected animals in all brain regions (gray), STS (blue), and PFCw (red). Dotted line indicates a fold change of 1. Fig. S6. T-stochastic neighborhood embedding (t-SNE) analysis of gene expression profiles from SHIV infected and uninfected animals. (Left) t-SNE plot indicates clustering of gene expression profiles by region and SHIV infection status (SHIV infected [pink], uninfected [black]) with removal of outlier sample [Animal 43661 Pre-frontal cortex white matter]. (Right) t-SNE plot shows all samples including the outlier with data points indicating regions (pre-frontal cortex white matter (P), superior temporal sulcus [S], caudate nucleus [C], hippocampus [H]) and infection status (color) and individual animals (symbols). Circles indicate 95% confidence intervals. Fig. S7 Expression levels of genes (expressed as normalized read counts in units of Log2 Counts per million [CPM]) related to synaptic functions, endoplasmic reticulum stress, and ATP synthase subunits in the PFCw of SHIV infected (red) and uninfected (gray) animals. Violin plots indicate quartiles. P values determined by linear mixed effects model. Table S1 Animal/Sample Data. Animal information—Animal ID, Sex, Age, SHIV infection status, and medical cull rationale. Sample Information—Sample ID, Sample Code, Tissue identity, Tissue weight (mg), purified RNA absorbance ratios (A260/A280 and A260/A230), and sample RNA yield. Table S3. Reagents used for flow cytometric analysis