library_construction_protocol: HSCs were sorted using an Influx instrument (BD Biosciences, San Jose, CA, USA), and lysed with Tri Reagent RT (Molecular Research Center, Cincinnati, OH, USA. Mice were sacrificed by cervical dislocation, femurs and tibias were isolated, and crunched using pestle and mortar. After obtaining single-cell suspensions, red blood cells were lysed. WT HSCs were exposed in vivo to WT or CMO BM niche. RNA was isolated using RNEasy MinElute Cleanup Kit (Qiagen, Venlo, Netherlands). Libraries (300 pg per sample) were prepared with SMARTer® Stranded Total RNA-Seq – Pico Input Mammalian library preparation kit v2 (Takara).