Transcriptomics

Transcriptomics is the study of all RNA transcripts and their regulatory mechanism present in a cell or tissue. RNA transcripts consist of mRNA and non-coding RNA. We offer transcriptome sequencing including customized bioinformatic analysis service.

  • RNA quality check on bioanalyzer
  • Library prep of RNA
    Information of all transcript, mRNA and non-coding RNA
  • Library quality check on bioanalyzer
  • RNA sequencing
    NGS services (library generation, (multiplex) library sequencing) are offered using an Illumina instruments (HiSeq2000, Nextseq500)
  • Data processing
    Alignment performed on own high performance computing cluster, using your reference genome of interest
  • Data analysis
    Expression profiles of all transcripts, mRNA and non-coding RNA, as well as seperate profiles of splicing of mRNA transcripts, identifying isoforms abundance
    Expression profiles of small RNA, i.e. microRNA
  • Quality checks
    Our workflow includes several quality checks, such as starting RNA, library, sequencing depth and alignment percentage.

Workflow

Our workflow for RNA sequencing starts with the customer supplying total RNA, the amount depending on protocol. In our workflow we have several quality checks. The total RNA is being checked with a bioanalyzer chip. When the samples pass the quality criteria, library preperation is performed. Subsequently, the quality of the library is again checked using the bioanalyzer. The passed samples are being sequenced on a Illumina sequencer (HiSeq or NextSeq). Further quality checks are performed on the raw data from the sequencer, i.e. sufficient depth, and alignment performance, i.e. percentage of reads aligning to the reference genome. After all quality checks passed, the samples are used in the analysis, i.e. expression or isoform profiling and network analysis.

Contact

When planning an experiment involving transcriptomics, feel free to contact Kasper Derks for an initial consult.
E: gsm@mumc.nl