RNA-seq of relapse ALL
Total RNA was extracted from bone marrow cells stored in PAXgene tubes, PBMCs from peripheral blood, and mononucleated cells from bone marrow according to the manufacturers instructions (Qiagen). Integrity was checked on the Agilent TapeStation (RIN), followed by preparation for sequencing using the TruSeq RNA v2 prep (Illumina). High-throughput sequencing was performed on an Illumina HiSeq 2500 platform to a target depth of 50 million paired-end reads per sample