Figure S1.

Cell-Type Markers for Seq-Well and CyTOF Clusters, Related to Figure 2

(A) Overview of study cohorts and blood draw timelines. Animals were grouped into cohorts with pre-scheduled necropsy times (at baseline, or day post infection [DPI] 3, 4, 5, 6 - n = 3 each), or allowed to progress until clinical score exceeded 10 (terminal), predetermined euthanasia criteria. Dots: scheduled blood draws for each cohort; red: intermediate (non-necropsy) draw; gray: draw that coincided with euthanasia and necropsy. Necropsy and baseline normal draws were used for Seq-Well and CyTOF, while intermediate post-infection draws were available only for CyTOF.

(B) Expression profiles of cell-type marker genes (columns) for cell-type clusters (rows) based on the in vivo Seq-Well data. Circle area represents the percentage of cells in each group in which the gene was detected, and color denotes the average expression level (log_e TP10K).

(C) Average expression (Z-normalized CyTOF intensity) profiles of cell-type marker genes (columns), for cell-type clusters (rows), based on the CyTOF data.

(D) Uniform Manifold Approximation and Projection (UMAP) embedding of post-integration Seq-Well data, colored by the sample source (NHP, DPI, and whether the sample was loaded for Seq-Well without any freezing [.fresh] or was frozen with cryoprotectant and thawed prior to Seq-Well [.FRZ]). A maximum of 500 cells per sample is plotted to increase representation across samples.

(E) UMAP embedding of Seq-Well data, colored by whether cells were processed fresh (orange) or after freeze/thaw (blue) prior to Seq-Well.

(F) UMAP embedding of Seq-Well data, colored by depletion of abundant sequences by hybridization (DASH) treatment. We developed a DASH-based method to remove a PCR adaptor artifact from some Seq-Well sequencing libraries (STAR Methods), and performed this 0 times (No DASH, blue), 1 time (DASH, orange), or 2 times sequentially (DASHx2, red). For a few samples, we sequenced ‘No DASH’ and ‘DASH’ libraries and merged the reads (mixed, green).

(G) UMAP embedding of batch-corrected CyTOF data, colored by the multiplex batch in which it was pooled and analyzed by CyTOF.

(H) Receiver operating characteristic curves for identifying EBOV-infected cells. Estimates of sensitivity to detect an infected cell at various false positive rate thresholds in vivo (left) and ex vivo (right). Curves are estimated separately for a hypothetical viral load of 0.1% (blue line) and 1% (orange line).