Fig. 1

A single-cell RNA-sequencing approach to studying host–pathogen interaction. a Heterogeneity of outcomes of intracellular infection is due to both Salmonella and macrophage states. scDual-Seq simultaneously produces the transcriptome of both the host and the pathogen and allows the identification of cellular subpopulations during infection. b Schematic of the scDual-Seq method. Reverse transcription is primed using random hexamers, followed by RNase treatment and 3’ polyA tailing. The second strand is synthesized using the CEL-Seq2 barcoded primers (see “Methods”). The samples are pooled together before the complementary DNA (cDNA) undergoes linear amplification by in vitro transcription. The amplified RNA is then reverse transcribed using a random primer with an overhang of the sequence complementary to the Illumina 3’ adaptor. cDNA with both Illumina adaptors are selected by polymerase chain reaction and the DNA library is sequenced using paired-end Illumina sequencing. c Mean number of unique transcripts identified across five technical replicates, for mouse (black) and Salmonella (red). Circles and error bars represent the mean and standard deviation. d Plot between the expression of the two technical replicates of 10 pg mouse RNA and 10 pg Salmonella RNA. e Boxplots indicating the correlation coefficients across replicates with the sum expression of all 20 samples for mouse and for five replicates in each dilution for Salmonella. Mouse indicated in black, Salmonella dilutions indicated in red