Transcriptome profiling of the mouse suprachiasmatic nucleus at single cell resolution

Circadian rhythms are governed by the hypothalamic suprachiasmatic nucleus (SCN) which consists of ca. 20,000 cellular oscillators bound together in a powerful time-keeping network. The goal of this study was to characterise its component cells and network structure by conducting single-cell sequencing of SCN organotypic slices. scRNASeq libraries were prepared using 10x Genomics Chromium Single Cell 3’ Library and Gel Bead v2 kit. SCN cells, diluted in 0.04% BSA-nuclease-free water, reverse transcription master mix and partitioning oil, were loaded on a ChromiumTM Single Cell A Chip and run on the Chromium Controller to obtain at target cell recovery rate of 8,000 cells. Final libraries were sequenced on one flow cell of an Illumina HiSeq 4000 with a read length of 26bp for read 1 (cell barcode and unique molecule identifier and sample barcode) and 98bp for read 2 (RNA read) to yield approximately 340 million reads per sample. We sequenced 13,324 cells from 52 SCN slices at circadian time 7.5 (mid-day) over three independent sequencing runs, and 16,996 cells from 36 SCN slices at circadian time 15.5 (mid-night) over two independent sequencing runs. 10X Genomics Single Cell Transcriptome Sequencing of the mouse SCN