Fig. 4: Analysis of RoCK and ROI target enrichment data and quantification of eGFP mRNAs. | Nature Communications

Fig. 4: Analysis of RoCK and ROI target enrichment data and quantification of eGFP mRNAs.

From: RoCK and ROI: single-cell transcriptomics with multiplexed enrichment of selected transcripts and region-specific sequencing

Fig. 4: Analysis of RoCK and ROI target enrichment data and quantification of eGFP mRNAs.The alternative text for this image may have been generated using AI.

a Barnyard plot colored by detection of eGFP and tdTomato CDS in WTA and TSO data. b Sequencing coverage and depth along eGFP in mouse cells for TSO (olive green) and WTA (off white). c Sequencing coverage and depth along tdTomato in human cells for TSO (red purple) and WTA (light mauve). Bars at the bottom of c and d indicate regions in the eGFP and tdTomato transcript and CDS, also used for counting. The CDS is indicated in green or magenta, respectively, while the UTRs are indicated in white. d Detection of eGFP and tdTomato in TSO vs. WTA data, per cell. Number of counts for ROIeGFP (e), sum of ROI 1 and 3 (f) and sum of ROI 2 and 4 (g). h Percent of cells with detectable eGFP CDS (mouse cells) or tdTomato CDS (human cells) in TSO plus WTA data, per condition. i Number of eGFP mRNAs in mouse cells detected by RNAscope. egfp1 and egfp2: biological replicates. Negative controls: L-cells expressing tdTomato and wt L-cells (untransduced). Number of analyzed cells: eGFP1 n = 294, egfp2 n = 242, tdTomato n = 292, wt n = 72. Boxplots show the median (center line), the first and third quartiles (bounds of the box; 25th and 75th percentiles), the lower and upper whiskers (1.5 × IQR from the box). Source data are provided as a Source Data file. j Number of counts from combining WTA and TSO data for the eGFP CDS and transcript (tx). Boxplots show the median (center line), the first and third quartiles (bounds of the box; 25th and 75th percentiles), the lower and upper whiskers (1.5 × IQR from the box).

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