GSM9023314: C3HeB/FeJ_multiplex; Mus musculus; RNA-Seq
Cells were thawed and hybridised for 22 hours to probes from the Mouse 16-Plex Fixed Cell Profiler kit (10X Genomics), as per manufacturer's instructions. All samples were split in two and hybridised to two different barcoded probes to increase cell recovery, except for two out of three uninfected control samples from each mouse strain. Cells from C57BL/6 and C3HeB/FeJ mice were combined in equal numbers per barcode into individual pools, which were washed, concentrated and loaded on 10x chip Q where the fixed and probe-hybridized single cell suspensions were partitioned into nanolitre-scale Gel Beads-in-emulsion (GEMs). A pool of ~737,000 10x GEM Barcodes was sampled separately to index the contents of each partition. Inside the GEMs, probes were ligated and the 10x GEM Barcode was added, and all ligated probes within a GEM share a common 10x GEM Barcode. Barcoded and ligated probes were then pre-amplified in bulk, after which gene expression libraries were generated.