Single cell profiling of mouse blood cells using CEL-seq2

Gene expression in mouse blood cells from sorted via FACS analysis into a 384-well plate were profiled using a modified CEL-seq2 protocol. B lymphocytes (B220+ FSC-Alow), erythroblasts (Ter119+ CD44+, FSC-Amid/high), granulocytes (Mac1+ Gr1+) and high-end progenitor/stem (Lin- Kit+ Sca1+) were sorted from the bone marrow of a C57BL/6 10-13 week old female. T cells (CD3+ FSC-Alow) were isolated from the thymus of the same mouse. Bone marrow and thymus were dissociated mechanically, washed and stained with antibodies for 1hr on ice. Single cells were deposited on a 384 well plate using an Aria cell sorter (Beckman). Index data was collected and an adapted CEL-seq2 protocol used to generate a library for sequencing. The reads were sequenced by Illumina Nextseq and preprocessed by the scPipe R/Bioconductor software.