A single-cell genomic strategy for alternative TSSs identification [scTSS-seq]

Alternative transcription start sites (TSSs) usage plays a critical role in gene transcription regulation in mammals. However, precisely identifying alternative TSSs remains challenging at the genome-wide level. Here, we report a single-cell genomic technology for alternative TSSs annotation and cell heterogeneity detection. Here, we utilize Fluidigm C1 system to capture individual cells of interest, SMARTer cDNA synthesis kit to recover full-length cDNA, then dual priming oligonucleotide system to specifically enrich 5’-end tags for genomic analysis. Apply single-cell TSS-seq in a genome-wide study of alternative TSSs identification in IFN-β stimulated mouse fibroblast cells (MEFs).