Recent technological innovations have enabled genomic analysis of single cells and identifying role of genes and mechanisms regulating their expression in various biological processes such as cell differentiation. Among the techniques, droplet based single cell RNA-Seq has advanced rapidly allowing parallel analysis of tens of thousands of cells from a population using short reads from 3’ or 5’ end of transcripts. This approach has been very useful for clustering cells into various types based on gene expression signatures. However, in humans, majority of genes are spliced or transcribed alternatively giving rise to isoforms with different and sometimes opposing biological roles. Consequently, current high throughput methods lack the potential to investigate biological role or preferential expression of isoforms in different cell types.
To unveil the diversity of transcripts isoforms and their role in cell differentiation and other biological processes it is essential to cost effectively and concurrently characterise full-length transcripts of single cells along with quantitative expression analysis. To achieve this we have developed a method that takes advantage of 10x Genomics Chromium single cell solution to package cells in droplets for barcoding transcripts. We use cell-specific barcoded cDNA resulting from reverse transcription of polyA RNA content of a single-cell for standard 10x analysis using Illumina short read sequencing, and examine full-length transcripts of the same cells with PacBio Sequel platform. In this work we report application of the method to human post-mortem retina cells and discuss library characteristic and analysis results.