Journal: bioRxiv
Article Title: Expanding single-cell toolbox with a cost-effective full-length total RNA droplet-based sequencing technology
doi: 10.1101/2025.02.23.639726
Figure Lengend Snippet: a) Single cell and barcode beads are co-encapsulated by microfluidics platform. The primers on the barcode beads are equipped with handles for library preparation and single cell barcode and ended with rDS (red) or polyT5C8N (blue), which target both polyA+ and polyA-RNA transcripts. b) Gene-body coverage across all genes based on merged single cells data showing strong 3’ bias for inDrops and mostly uniform with a small 3’ bias for sc-rDSeq. Each gene is divided into 40 segments and counts failing into each segment are calculated for coverage. Ribbon area shows the SEM around mean. c) The boxplot displays nUMI/cell for sc-rDSeq and inDrops. On average, sc-rDSeq captures 90k nUMI/cell, inDrops captures 7.4k nUMI/cell. d) Distribution of uniquely mapped reads in each type of genomic locations with merged single cells data. e) Percentage of genes detected by sc-rDSeq compared to inDrops. f) Histogram showing normalized distribution of the fraction of transcripts per biotype expressed in single cells, comparing sc-rDSeq to inDrops. g) Cost comparison of sc-rDSeq and other single RNA-seq technologies. Top bars (red) for instrument cost, and bottom bars (blue) for library and sequencing cost per cell. h) UMAP of PC9 cells (n = 680) based on total transcriptome, revealing four clusters of populations. i) Differentially expressed genes were identified using KNN unsupervised clustering of total transcriptome expression. The average expression of selected marker genes for each cluster are presented in dot plot. j) Top five GO terms enriched in each cluster, ranked by fold enrichment. k) The average expression of polyA-RNAs showed heterogeneity, including histone RNAs, lncRNAs, sncRNAs, and microRNAs.
Article Snippet: The single cell isolation is based on Fluidigm C1 microfluidics chips, which has limited throughput, and the method does not incorporate UMIs for PCR deduplication.
Techniques: Comparison, RNA Sequencing, Sequencing, Expressing, Marker
