Additional file 1: of Blood handling and leukocyte isolation methods impact the global transcriptome of immune cells

Supplemental Material contains the following data: Figure S1. Sorting strategy used to profile peripheral blood mononuclear cells (PBMCs) from blood of healthy donors across all conditions tested. Antibodies are listed in Table 1. Figure S2. Exon/intergenic ratios are plotted for each indicated condition for (A) monocytes, (B) T cells and (C) for filtration as compared to ficoll. Statistically significant comparisons are indicated and were calculated by one-way ANOVA with Tukey’s multiple comparisons test. Figure S3. Pairwise scatter plots of coding transcriptomes generated from monocytes for each indicated comparison. Regression lines and R2 values are shown on each plot for (A) ficoll, percoll and lysis processing conditions, and (B) ficoll, 4 °C for 1 day or 20 °C for 1 day conditions. Figure S4. Pairwise scatter plots of coding transcriptomes generated from CD8+ T cells for each indicated comparison. Regression lines and R2 values are shown on each plot for (A) ficoll, percoll and lysis processing conditions, and (B) ficoll, 4 °C for 1 day or 20 °C for 1 day conditions. Figure S5. ssGSEA results for ficoll and filter methods for isolation of PBMCs. Forest plots of top 15 significantly altered gene sets when PBMCs are isolated using filters for monocytes (A) and CD8+ T cells (B). Figure S6. Flow cytometry isolation scheme for sequencing data generated from cells isolated from intracerebral hemorrhage (ICH) and matched healthy donors (HD). Figure S7. Quality control metrics for sequencing data generated from cells isolated from intracerebral hemorrhage (ICH) and matched healthy donors (HD). (A) Exon/intergenic ratio for each indicated condition. No statistically significant differences were found when comparing healthy to ICH within each cell type by students t test. (B) Percent mapped reads for each indicated condition. No statistically significant differences were found when comparing healthy to ICH within each cell type by students t test for each percent metric plotted. Table S1. Antibodies used for cell sorting in this study. Table S2. Summary statistics performed by one-way ANOVA with Tukey’s multiple comparisons test for data shown in Fig. 2. (DOCX 3717 kb)