NextSeq 500 sequencing; Identification of MEIS2 binding sites through ChIP-seq in the neuroblastoma Kelly and BE(2)-C cell lines.
Identification of MEIS2 binding sites through ChIP-seq in the neuroblastoma Kelly and BE(2)-C cell lines.
In total, 100x106 SK-N-BE(2)-C and Kelly neuroblastoma cells were processed for ChIP-sequencing. Kelly and BE2C neuroblastoma cell lines were obtained from the American Type Culture Collection (BE2C) and DSMZ (Kelly). All cell lines used for the genome-scale CRISPR–Cas9 screen have been previously described7. All cell lines were short tandem repeat (STR) tested for identity. Neuroblastoma cell lines were cultured in RPMI media containing 10% fetal bovine serum and 1% penicillin-streptomycin and validated to be free of Mycoplasma species. The pellets from the samples were prepared by fixing cells in 1% formaldehyde for 15 minutes, and quenching in 1M Tris pH 7.5. Nuclei were prepared using the Sigma Nuclei Isolation Kit (#NUC-101), and sonicated using a Branson Digital Sonifier. ChIP-seq libraries were prepared using the KAPA HyperPrep ChIP library kit following the manufacturer's settings.