README.md

Data analysis for Helmsauer, Valieva, Ali et al. Enhancer hijacking determines extrachromosomal MYCN amplicon architecture in neuroblastoma (bioRxiv)

• IdentifyCandidateEnhancers.R integrates RNA-seq and ChIP-seq to identify MYCN-driving enhancers in neuroblastoma
• DepuydtDataMYCNAmplicon.R generates aggregate copy number profiles around MYCN
• AmpliconEnhancerCharacterization.R plots epigenetic data on MYCN amplicon.
• ChIPSeqTracksOverviewFigures.R plots H3K27ac ChIP-seq data around MYCN for different neuroblastoma cell lines
• RadaIglesias.R plots H3K27ac ChIP-seq around MYCN for developmental cell types
• MotifScanning.R scans enhancers for transcription factor binding motifs
• ReconstructAmplicon_{CHP212,IMR575}.R reconstructs the MYCN amplicon from structural rearrangement calls for neuroblastoma cell lines and plots the reconstruction together with epigenomic data
• FragileSites.R overlaps aggregate copy number profiles and common fragile sites
• ClassIIWGSRearrangementPlotting.R plots rearrangement data for three patients that lack the e4 enhancer
• EnhancerVsCRCChIPseq.R describes overlap between core regulatory circuit factor ChIP-seq and MYCN-driving enhancers
• prepareRNAseq.R parses and normalizes RNA-seq data
• PlotAssemblyMapping.R plots mapping of de novo assembled contigs to hg19
• virtual4C.R creates virtual 4C tracks

Please do not hesitate to contact us at henssenlab@gmail.com.