Comprehensive single cell transcriptional profiling of a multicellular organism by combinatorial indexing

We developed a combinatorial indexing strategy to profile the transcriptomes of large numbers of single cells or nuclei (Single cell Combinatorial Indexing RNA-seq or sci-RNA-seq). We applied sci-RNA-seq to profile nearly 50,000 cells from C. elegans at the L2 stage, effectively ~56-fold “shotgun cellular coverage” of its somatic cell composition.