Experiment Types

  • Whole genome sequencing (WGS)
  • Whole exome sequencing (WES)
  • Target sequencing (TS)
  • Whole transcriptome sequencing (RNA)
  • ChIP-seq for transcription factors (TF-ChIP)
  • ChIP-seq for histone marks (HM-ChIP)
  • Formaldehyde-assisted isolation of regulatory elements (FAIRE)
  • DNase I hypersensitive site sequencing (Dnase)
  • Nucleosome positioning sequencing (Mnase)
  • Whole genome bisulfite sequencing (WGBS)
  • Reduced representation bisulfite sequencing (RRBS)
  • Oxidative bisulfite sequencing (oxBS)
  • TET-assisted bisulfite sequencing (TAB)
  • Nucleosome occupancy and methylome sequencing (NOMe)
  • Infinium 45K (Infinium)

Analyses

  • Functional annotation (GO, PPI, Pathyway) - ALL
  • NCBI deposit - ALL
  • Quality assessment - ALL
  • Read mapping - ALL
  • Alternative splicing - RNA
  • Differential expression - RNA
  • Expression profile - RNA
  • Gene fusion - RNA
  • Gene set enrichment analysis - RNA
  • Sequence variants - WGS, WES, TS
  • Structure variants - WGS
  • De novo genome assembly - WGS, RNA
  • De novo transcriptome assembly - RNA
  • Methylation profile - WGBS, RRBS, oxBS, TAB, NOMe, Infinium
  • Differential methylation - WGBS, RRBS, oxBS, TAB, NOMe, Infinium
  • Enrichment identification - TF-ChIP, HM-ChIP, FAIRE, Dnase, Mnase
  • Differential enrichment - TF-ChIP, HM-ChIP, FAIRE, Dnase, Mnase
  • Sequence motif - TF-ChIP