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Fig. 1 | Breast Cancer Research

Fig. 1

From: Decoding breast cancer tissue–stroma interactions using species-specific sequencing

Fig. 1

Species-specific sequencing—separation of mouse and human transcriptomes in silico. a Schematic flowchart of the principle steps in the S3 technology. A specimen of mixed human and mouse cells (for example, from a tumor–stroma xenograft experiment) is subjected to RNA-seq. The mixed transcriptome is bioinformatically separated into human and mouse transcriptomes, discarding transcripts with a defined maximum number of mismatches. b Fraction of reads that are species-ambiguous; i.e., cannot be assigned only to one species and therefore discarded. c Fraction of misassigned reads; i.e., species-specific reads that align to mouse genes for human samples or to human genes for mouse samples. Data in b and c are from three human (79 bp reads, in blue) and three mouse (51 bp reads, in pink) samples. d Percentage of expressed genes with full (orange) or partial (purple) loss of reads after S3 in the three human (H1–3) and mouse (M1–3) samples. e Scatterplot and Spearman correlation between a mouse sample (M1) and mouse expression values from S3 applied to a mix of human (H1) and mouse (M1) samples. f Spearman correlations for the human (blue) and mouse (pink) S3 components of in silico mixes of H1 + M1, H2 + M2 and H3 + M3. g The number of reads assigned by S3 as human, mouse or rat for three rat samples, normalized by the number of rat reads

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