MAML3 overexpression in neuroendocrine cell lines

The goal of this study was to determine differentially regulated pathways in neuroendocrine cells (SK-N-SH, BON-1, QGP-1) that over-expressed full length or exon 1 deleted MAML3 compared with vector control. Overall design: SK-N-SH, BON-1 and QGP-1 cells were transfected with vector control, FL MAML3 or dEx1 MAML3. Three biological replicates were plated in triplicate. On day three post transfection, RNA was harvested using Trizol (Invitrogen) and 1mcg total RNA was submitted to the Genomics and Microarray Core at the University of Colorado for library prep using an Illumina TruSeq mRNA library kit (Illumina, San Diego, CA, USA). Sequencing was performed on a NanoSeq 6000 (Illumina). During analysis, adapter sequences were removed with the help of Trimmomatic trimmer, and the “Tuxedo” pipeline was used for transcript expression analysis, as previously described. RNAseq reads were aligned to the hg19 reference genome with HISAT2; stringtie was used for transcriptome assembly and transcript abundance estimation.