GSM9312304: HSC_bulk_Old_9; Mus musculus; RNA-Seq
For bulk RNAseq, ribosomal RNA-depleted RNA-seq libraries were generated using QIAseq® FastSelect −rRNA HMR (QIAGEN) with the KAPA® RNA HyperPrep Kit (Roche Sequencing). For scRNA, single cells suspended in PBS with 0.04% BSA were loaded, 10K cells per lane, on a Chromium Controller (10X Genomics). For bulk RNAseq, starting material was 100 ng of RNA dependent on availability per tissue type. RNA fragmentation was done at 85°C for 6 minutes. cDNA was ligated with 1.5 µM or 300 nM xGen Dual Index UMI Adapters (Integrated DNA Technologies) respective to RNA input. Ligated cDNA libraries were amplified using 14 PCR cycles, also respective to RNA input. Sequencing of the resulting libraries was done on NovaSeq 6000 (Illumina) using a 2x76, paired-end sequencing recipe. For scRNA, libraries were prepared using Chromium Next GEM Single Cell 3' Kit, v3.1 (10X Genomics) with single-index barcoding, according to the manufacturer's guidelines.