GSM5115763: CT15.5 SCN cells run 1 (mmSCN5); Mus musculus; RNA-Seq
Brains were retrieved from mouse pups at p10-12 and cut into 300µm thick slices using a McIlwain Tissue Chopper. The slices were examined under a bright-light microscope to sort those containing optimal SCN preparations and trimmed accordingly. Single SCN cells were isolated by proteolytic enzymatic digestion using the Worthington Papain dissociation kit. To ensure the cells were properly dissociated the mixture was filtered through a 40µm mesh. scRNASeq libraries were prepared using the Chromium Single Cell Controller. Cells were treated following the manufacturer's protocols using 10x Genomics ChromiumTM Single Cell 3' Library and Gel Bead Kit v2 and ChromiumTM Single Cell A Chip Kit. Final libraries were sequenced on one flow cell of an Illumina HiSeq 4000 with a read length of 26 bp for read 1 and 98 bp for read 2 to yield approximately 340 million reads per sample.