title: GSM6131950: Sample II cko; Mus musculus; RNA-Seq
library_construction_protocol: Cells for single cell sequencing were obtained from two tamoxifen-treated littermates with the genotypes Jaridfl/fl; Rax-CreERT2 (cKO) and Jaridfl/fl (control). Two freshly dissected retinas from an individual animal were pooled for each sample and dissociated in PBS, 50 mM HEPES, 0.05 mg/ml DNase I (Sigma D4513) and 0.025 mg/ml Liberase (Sigma 5401119001) for 35 min with intermediate trituration. Cells were passed through a 70 mm nylon cell strainer, washed with washing buffer (1X PBS, 2 % BSA, 0.1% sodium azide, 0.05% EDTA), and red blood cells were lysed in RBC lysis buffer (eBioscience 00-4333-57). Cell counts were determined using a Countess (Invitrogen C10228). 1x 106 cells was resuspended in 1mL DPBS and provided to the High Throughput Genomics Core for library prep. This protocol was repeated on two different days to provide cells for batch I and batch II. Single cell libraries were generated with Single Cell 3' Gene Expression Library Prep v3 reagents for batch I and Next GEM Single Cell 3' Gene Expression Library prep v3.1 with UDI for batch II, according to manufacturer's protocol (10X Genomics PN-1000092 and PN-1000128). Sequencing libraries were applied to a NovaSeq flow cell using XP chemistry workflow v1 and v1.5 for batch I and batch II samples respectively (Illumina 20021664 and 20043131). A 150 x 150 cycle paired end sequence run was performed using an Illumina NovaSeq 6000 instrument and NovaSeq S2 reagent Kit for batch I or S4 reagent Kit v1.5 for batch II (Illumina 20012860 and 20028312). Batch I libraries were sequenced in two separate runs to a read depth of > 600 million reads per sample. Batch II libraries were sequenced to > 200 million reads per sample in a single run.