Fig. 2: The Spatially-Resolved Laser-Activated Cell Sorting (SLACS) device produces high-quality spatial-histopathological examination-linked epitranscriptomics converged with transcriptomics with sequencing (Select-seq) data from single cells and ten cells.

Source data are provided as a Source Data file. a Experimental design and an example of single-cell isolation. b Single-cell isolation of the SLACS device. Scale bar, 100 µm. c Fragments per kilobase of transcript per million mapped reads (FPKM) values for the paraformaldehyde (PFA)- and methanol (MeOH)-fixed cells (n = 60 biologically independent cells examined over 2 independent experiments). Interquartile range (IQR) of boxplot is between Q1 and Q3 and centre line indicates median value. Whiskers of boxplot is extended to the maxima and minima. Maxima is Q3 + 1.5*IQR and minima is Q1 − 1.5*IQR. d Correlation between the mRNA sequencing profiles from bulk mRNA-seq and Select-seq with ten types of PFA-fixed cells and Select-seq with ten types of MeOH-fixed cells. e Number of genes detected (FPKM) (left) and exon alignment percentage in three different cell lines fixed with PFA (right) (n = 92 biologically independent cells examined over 3 independent experiments). Interquartile range (IQR) of boxplot is between Q1 and Q3 and centre line indicates median value. Whiskers of boxplot is extended to the maxima and minima. Maxima is Q3 + 1.5*IQR and minima is Q1 − 1.5*IQR. f Representative 3’ end bias of the full-length transcriptomes. g Principal component analysis (PCA) and h unsupervised clustering heatmap of the cells analyzed with Select-seq. i Representative transcript isoform diversity from two samples. j B cell receptor (BCR) analysis of the IM-9 cell line.