title: GSM8655947: NM50_tertiary_21_WGS; Mus musculus; OTHER
library_construction_protocol: DNA for WGS was isolated using the Qiagen AllPrep kit.  For ATAC-seq, 50,000 human leukemic cells were isolated from the spleens of PDX-bearing mice treated for 5 days and washed once in cold PBS before proceeding with cell lysis, nuclei extraction, tagmentation and library preparation as described in PMID 24097267.  Lysis and transposition were adjusted according to the Omni-ATAC protocol (PMID 28846090).  For scRNAseq, leukemic cells were human leukemic cells were isolated from the spleens of PDX-bearing mice treated for 4 weeks, washed three times in PBS + 0.04% BSA, and counted.  The volume of cells to load to have a desired recovery target of 8,000-10,000 cells was calculated and cells were loaded on Chromium Next GEM Chip K (10X Genomics).  Samples were processed using the 10X Genomics 5' kit (v2). Mouse genomic libraries were generated using the SureSelectXT kit specific for the Illumina HiSeq instrument (G9611B, Agilent Technologies).  ATAC-seq libraries were prepared as described in PMID 24097267 with double-sided bead purification.  Single cell RNA-seq libraries were prepared using Chromium Next GEM Single Cell 5' Reagent Kits v2 (10X Genomics) according to manufacturer's protocols.