title: GSM5473854: BMSC_ATACseq_3D_rep2; Mus musculus; ATAC-seq
library_construction_protocol: 5,000 freshly sorted mouse BMSCs (CD45-Ter119-Tie2-GFP+DsRed+) were derived from ScfGFP;Cxcl12DsRed mice bone marrow and lysed in Trizol. 5,000 2D-cultured BMSCs and 3D-cultured BMSCs were lysed in trizol. Total RNA was extracted, digested with DNase I and purified using RNAclean Kit. Mouse primary young HSCs were acquired directly from 8-12 weeks old mice and primary old HSCs were from 12-13 month old mice. Young and old 3D cultured HSCs were 3D-cultured from primary young and old HSCs. Total RNA was extracted following the manufacturer's instruction and purified by micro RNA purification kit (Tiangen).For ATAC-seq, 20,000 freshly isolated, 2D-cultured and 3D-cultured BMSCs were derived from ScfGFP;Cxcl12DsRed mice. RNA-seq libraries were constructed through a modified Smartseq2 method, and sequenced on a HiSeq X Ten system (Illumina) or Novaseq 6000 (Illumina) as paired-end 150-bp reads. ATAC-seq libraries were prepared according to TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD502-01), and sequenced on a HiSeq X Ten system (Illumina) as paired-end 150-bp reads.