GSM8396169: Pdgfbret/+, replicate 2, scRNAseq; Mus musculus; RNA-Seq
Whole tumors were minced into smaller slices with a scalpel and incubated for 30 min with the supplier's enzyme mixes, while being heated at 37°C and mechanically grinded in the gentle MACS Octo Dissociater with Heaters (Miltenyi). Samples were resuspended and applied to a 70 μm MACS SmartStrainer (Miltenyi), after which the single cell suspension underwent subsequent steps for debris removal and lysis of erythrocytes. For library preparation, 18,000 cells / 45 μl in 0.04% BSA. Singlecell 3´ RNA-seq libraries were prepared using 10x Chromium system (v3.1). Samples were run using Read 1 28 cycles, i7 index 5 cycles, i5 index 0 cycles, Read 2 91 cycles on the Illumina NovaSeq 6000 to a depth of 50,000 reads/cell. This was performed in two different batches (time points). The first batch (batch1) included 3 samples, while the second batch (batch2) included 8 samples.