Changes in CD34 and Erythroid Progenitor Transcriptome After RUNX3 Kock-down

The associated publication describes a RUNX3-dependent defect in primary human CD34+ HSPC differentiation into the erythroid lineage. This study was designed to determine which genes are potential targets of RUNX3, and could contribute to regulation of erythropoiesis. Undifferentiated human CD34+ HSPCs were subjected to lentiviral knock-down of RUNX3. After selection, cells were either harvested as undifferentiated CD34+ cells, or grown for 24 hours in erythroid medium and then harvested. Samples underwent processing using the Qiagen RNeasy kit, and RNA was quantified using a Thermo Fisher Scientific Nanodrop One spectrophotometer. Sequencing was performed by Hudson Alpha Genomic Services Laboratory (ribosomal reduction, 100bp, paired-end, 50M reads, strand-specific) and data processing was performed using Galaxy Suite tools. Analysis across the three biological replicates included comparisons between erythroid and undifferentiated cells, as well as empty vector compared to RUNX3 knock-down in both erythroid and undifferentiated cells.