Differentiation arrest is a hallmark of acute lymphoblastic leukemia (ALL). Among a variety of structural and chromosomal alterations, mutations in genes encoding for regulators of B cell differentiation are especially common. The objective of this study was a comprehensive assessment of transcriptional dysregulation and high-resolution genomic profiling of B cell differentiation factors. Here we provide extended materials and methods regarding transcriptome and genome-wide copy number variation analyses published by Harder et al. [1]. Our data provide a resource for the identification of yet undefined factors that play a putative functional role in leukemogenesis such as ZNF423, whose aberrant expression interferes with B-cell differentiation.