title: GSM8113086: Crispr Mouse with ReDeeM, Batch2, RNA, sample 15; Mus musculus; RNA-Seq
library_construction_protocol: Mouse experiments were approved by the Massachusetts Institute of Technology Institutional Animal Care and Use Committee (IACUC) (institutional animal welfare assurance no. A-3125-01). A male mouse embryonic stem cell (mESC) line harbouring the conditional alleles KrasLSL-G12D/+ and Trp53fl/fl (KP) was engineered with the lineage tracer cassettes. The detailed engineering process, including vector information, tumour harvest and single-cell suspension were prepared as described in Yang et al.  Two independent mESC lines were used for batch-1 and batch-2 experiments. The single cells of batch-2 from multiple tumors were labelled with Cell Hash and were profiled using ReDeeM except the following modification. Additional Target Site libraries were needed. The amplified cDNA libraries were further amplified with Target Site-specific primers containing Illumina-compatible adapters and sample indices (oDYT023-oDYT038, forward:5′CAAGCAGAAGACGGCATACGAGATNNNNNNNNGTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGAATCCAGCTAGCTGTGCAGC; reverse:5′-AATGATACGGCGACCACCGAGATCTACACNNNNNNNNTCTTTCCCTACACGACGCTCTTCCGATCT; “N” denotes sample indices) using Kapa HiFi ReadyMix (Roche), as described. For sequencing scRNA, scATAC, mtDNA libraries, the same strategy as described for ReDeeM were used, except that four sets of mouse specific probes were designed to enrich mitochondrial fragments. For sequencing Target Site libraries, 15,000 total reads per cell were expected, and the following read lengths were used: Read1: 26 cycles, i7: 8 cycles, Read2: 290 cycles).