ATAC-seq of immunophenotypic LT-HSC and ST-HSC from umblical cord blood in cytokine-rich ex vivo culture conditions following sphingolipid modulation

To investigate how ex vivo culture affects chromatin accessibility in cultured HSC, we performed the Assay for Transposase Accessible Chromatin with high-throughput sequencing (ATAC-Seq) on cLT (CD34+CD90+CD45RA-) and cST populations purified from 8 day cultured lineage depleted cord blood (lin- CB) cells treated with 3-Factor (4HPR+UM171+SR1), U+S or 4HPR as well as untreated and vehicle-treated (DMSO) control populations. The subsequent ATAC-seq data was compared to chromatin accessibility signatures generated from uncultured hematopoietic stem and progenitor populations (Takayama, et al.). We found that ex vivo culture shifted cLT and cST cells isolated from control or untreated samples to a chromatin accessibility profiles not found in LT-HSC, suggesting some loss of a stem-cell associated chromatin state. By contrast, 4HPR-treated, to some extent, and 3-Factor-treated HSC maintained chromatin accessibility features of uncultured LT-HSC. ATAC-seq profiling of RNA from 4 pools of human cord blood enriched for stem and progenitor cells by lineage depletion (lin- CB) cultured with the indicated small molecules at the indicated times >>>Submitter states that raw data have been submitted to EGA due to patient privacy concerns<<<