GARP Next-Generation Sequencing

The Genomic and RNA Profiling core offers various RNA-seq chemistries for many sample types.

Total RNA-seq: Capture of both coding and non-coding RNAs. Compatible with degraded RNA. Full-length transcripts are captured. Recommended read depth is around 50-100 million reads/sample although deeper sequencing may be required in some cases.

Low-Input Total RNA-seq: Capture of both coding and non-coding RNAs. Compatbile with inputs down to 250 pg of RNA. Recommended for RNA-seq of cfRNA, rare cell populations or FACS-sorted cells.

PolyA-RNA-seq: Capture of coding RNAs. Requires intact RNA. Full-length transcripts are captured. Recommended read depth is 15-30 million reads/sample although deeper sequencing may be required in some cases.

3’ RNA-seq: Capture of coding RNAs. cDNA is generated from 3’end of transcript. Compatible with degraded RNA. Recommended read depth is 10-20 million reads/sample.

Micro-RNA-seq: Enables miRNA profiling and discovery with cfRNA and cellular RNA samples. Required read depth is 5-20 million reads/sample.

The Genomic and RNA Profiling core in partnership with the Human Tissue Acquisition and Pathology Core offers the 10X Genomics Visium technology for in situ spatial profiling of fresh-frozen and FFPE tissue samples. For more information, please visit the 10X website.

Chromatin immunoprecipitation sequencing allows for genome-wide profiling of protein-DNA interactions and of histone PTMs. GARP offers ChIP-seq library construction starting with ChIP and Input DNA.

Whole-Genome Bisulfite Sequencing (WGBS) allows for genome-wide DNA methylation (5-mC) profiling. The Genomic and RNA Profiling core offers a one-stop WGBS workflow starting with DNA fragmentation, bisulfite conversion, library preparation and ending with sequencing.

Nanpore sequencing is a third-generation sequencing technology that generates long reads. Our Oxford Nanopore PromethION sequencer can sequence up to 24 flow cells simultaneously, each flow cell generating around 100Gbs of data. Because Nanopore sequencing and basecalling rely on measuring electric current, sequence as well as base modifications can be detected.