GSE191028
ZNF384 fusion oncoproteins drive lineage aberrancy in acute leukemia [RNA-seq 2]
To investigate usage of exon 8 in ZNF384 in different myeloid/lymphoid populations from MPAL/BALL PDX and cell lines Overall design: PDX cells from SJBALL004031_X18-4052 (primary engrafted NSG-SGM3 PDX) and SJMPAL046472_X2-PAVRCX-063S5-1411 (secondary engrafted NSG-SGM3 PDX) and JIH-5 cells  were thawed and stained with the following human specific antibodies (all from BD Biosciences, catalogue number in parentheses): anti-CD45-FITC (345808), anti-CD19-BV605 (562653) and anti-CD33 PE-Cy7 (333946). Cells were then sorted in 2 or more of the following CD45+ tumor populations (PT): PT1: CD33+CD19+; PT2: CD33-CD19-; PT3: CD33-CD19+; PT4: CD33-CD19-. Sorted cells were collected, resuspended in RLT buffer (Qiagen, Cat. No. 79216) and processed for DNA and RNA extraction by the AllPrep DNA/RNA Mini Kit (Qiagen, Cat. No. 80204). RNA samples were sequenced by total stranded RNA-seq (SJMPAL046472_X2-PAVRCX-063S5-1411_PT1 and SJMPAL047180_C2-JIH5_PT1) or low input RNA-seq (SJBALL004031_X16-4052: PT1, PT2, PT3 and PT4; SJMPAL046472_X3-PAVRCX-063S5-1411_PT2 and SJMPAL047180_C4-JIH5_PT3).