NextSeq 500 sequencing; ChIP-seq in the cell line NALM-6 for RUNX1 and ETV6-RUNX1 to assess competition between the two proteins for DNA binding
ChIP-seq in the cell line NALM-6 for RUNX1 and ETV6-RUNX1 to assess competition between the two proteins for DNA binding
Cells were sorted to high purity for RUNX1b/Vector (Cherry) and ETV6-RUNX1/ETV6-RUNX1-R139G (GFP) co-expression, expanded in vitro, and approximately 10^8 cells harvested for subsequent ChIP experiments.  Cells were crosslinked with 1% formaldehyde and sonicated to yield chromatin of 100â€“500 bp. ChIP was performed by as previously described (May et al., 2013) using antibodies: RUNX1 (Abcam, ab23980), V5 (Abcam, ab9116). Libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645)