RNA-seq

To assist user in determining the most appropriate RNA-seq workflow for their project we have created tool that can be accessed HERE. It is always recommended to consult with core staff (free-of-charge) before finalizing an RNA-seq experimental design.

Ribodepletion: $165.42/sample (based on 30 sample batch)

  • Provides full-length sequencing coverage for mRNAs as well as long non-coding (lnc) RNAs.
  • Ideal for full transcriptome characterization.
  • The only RNA-seq option available for prokaryotic samples.
  • Recommended sequencing depth ~30M reads per sample for typical mammalian genomes. Less coverage required for small prokaryotic genomes.
  • Up to 192 samples can be uniquely barcoded for pooled sequencing.

3' End-Counting: $89.78/sample (based on 30 sample batch)

  • Cost-effective option for differential expression analysis from eukaryotic samples.
  • Oligo dT probes are used to capture polyadenylated RNA. Captured RNA is fragmented and the 3' end is selectively amplified by PCR.
  • As most of the reads are associated with 3' UTR sequences, this approach is best suited for organisms with well-annotated genomes (Human, Mouse and Rat).
  • This method cannot be used to identify splice isoforms.
  • Recommended sequencing depth 10M reads per sample.
  • Up to 96 samples can be uniquely barcoded for pooled sequencing.

miRNA/smRNA: $188.83/sample (based on 30 sample batch)

  • miRNAs/smRNAs are too small to be captured by the Ribodepletion and 3' End-Counting workflows described above.
  • This method uses direct ligation of RNA adapters to attach universal sequences to the miRNA/smRNA molecules. These sequences serve as priming sites for PCR amplification and sample barcoding.
  • miRNA/smRNA libraries include Universal Molecular Identifiers (UMIs) to accurately count miRNA/smRNA molecules and minimize PCR bias.
  • Recommended sequencing depth is 1-10M reads per sample.
  • Up to 96 samples can be uniquely barcoded for pooled sequencing.

Low Input RNA-seq: $151.26/sample (based on 30 sample batch)

  • Designed for samples with lower input amounts (250 pg-10 ng)
  • rRNA is removed using a probe-based method, which is better for low input samples
  • Low input RNA-seq libraries include Universal Molecular Identifiers (UMIs) to accurately count RNA molecules and minimize PCR bias.
  • Recommended sequencing depth ~30M reads per sample for typical mammalian genomes

Prices shown reflect internal Dartmouth rates for FY2025. External users and those with large projects should contact the core directly for pricing information. Actual prices may vary based on batch size.

All services provided by the GMBSR are supported by an NCI Cancer Center Support Grant (5P30CA023108) which MUST be cited in any publications or other materials using data generated in the core.

Single cell sequencing services are provided through the Single Cell Genomics Core and are subsidized by a COBRE grant (P20GM130454). This grant MUST be cited in all publications and materials using single cell data generated in the core.

Genomics Services