GSM8765382: sgGFP_T2(4w)_ATO_Thy_GEX_R2; Mus musculus; RNA-Seq
To generate scRNAseq profiles of week 2 thymocytes either CD45+ Live+ Lin- CD4- CD8- CD44hi/loCD25hi/lo was used respectively. To generate scRNAseq profiles of week 4 thymocytes (Figure 7)  CD45+ Live+ Lin- CD3+TCRb+ CD4+/CD8+ population was used. Single cell suspensions were run on a Chromium X instrument and libraries prepared following the Chromium Next GEM Single Cell 3' RNA-Seq Assay v3.1 Dual Index with Feature Barcode technology for CRISPR Screening user guide (10x Genomics, CG000316, RevD)128. We targeted 6,000 cells and used 12 cycles of cDNA amplification. Sample quality was confirmed using a Qubit (RNA HS kit; Thermo Fisher) to determine concentration and a Fragment Analyzer (Agilent) to determine RNA integrity. Every sample had an associated feature barcode except the control libraries.