Single Cell Genomics

Single cell genomics experiments are complex and require tight coordination between the researcher and our core. Consultation with core staff is required before projects are accepted and is provided free-of-charge. Services listed include the cost of sample QC using an automated fluorescent cell counter (Nexcellom K2) as well as all downstream library preparation and QC steps.

For all 10x genomics workflows, a "sample" is equivalent to one lane on the 10x instrument. Each lane can capture between 100-10,000 cells, depending on the concentration loaded onto the instrument.

A cost calculator is provided HERE to help budget for single cell experiments.

Sample Fixation for 10x Genomics Flex: $122/sample

  • Samples are provided as cell suspensions or tissues for fixation following the 10x Genomics Flex protocol.
  • Cells are stored at -80C in the GMBSR until ready for processing (within 1 year).

Tissue Processing for 10x Genomics: $222/sample

  • Nuclei isolation from fresh/frozen tissue
  • Tissue dissociation into single cell suspension (Off the shelf protocols available for some tissues. Those requiring optimization may incur additional charges.)

10x 3'/5' RNA-seq: $2,216/sample

  • Uses the 10x Genomics workflows for 3' and 5'-End RNA-seq. For standard gene expression measurements, 3' RNA-seq is the standard in the field. 5' RNA-seq is required where TCR and/or BCR (i.e. V(D)J) sequencing is performed.
  • Up to 96 unique barcodes are available for pooled sequencing.
  • Recommended sequencing depth is 30,000 reads per cell, but will vary depending on the RNA content of the cell type(s) to be analyzed.

10x Library Add-On: $348/library

  • Additional modalities can be applied to 10x RNA-seq samples to generate multi-omics datasets at single cell resolution. These include TCR/BCR sequencing, proteomic analyses (i.e. CITE-seq), sample multiplexing (via MULTI-seq or Total-seq) and other custom assays.
  • For each additional modality, a Library Add-On is required per sample.
  • Additional sequencing is also required, typically 5,000 reads per cell per library type.

10x Gene Expression Flex (A.K.A. Fixed RNA Profiling): Variable (See below)

  • The Flex assay enables single cell RNA-seq analysis of Human or Mouse cells or tissues that have been fixed following one of the 10x Demonstrated Protocols. Samples can be stored at -80C for up to 6 months. If samples are prepared in the GMBSR, -80C storage costs are included.
  • Once collected, samples can be thawed, uniquely barcoded and combined together onto a single 10x lane for processing. Pooling configurations and pricing are as follows:
    • 1 Barcode: $2,960/lane
    • 4 Barcodes: $4,885/lane
    • 16 Barcodes: $10,035/lane
  • Recommended sequencing depth is 20,000 reads/cell.

10x ATAC-seq: $2,369/sample

  • The 10x ATAC-seq workflow interrogates regions of open chromatin at single cell resolution.
  • As for all single cell experiments, users provide a viable single cell suspension and the core performs all downstream processing steps. For ATAC-seq, this includes sample QC, nuclei isolation/permeabilization, DNA transposition, cell capture and library preparation.
  • Up to 96 unique barcodes are available for pooled sequencing.
  • Recommended sequencing depth is 25,000 reads per cell.

10x Multiome (RNA+ATAC): $3,807/sample

  • The Multiome workflow generates paired RNA-seq and ATAC-seq data from the same nuclei in a given sample.
  • Specific requirements exist for preparing nuclei suspensions for this assay; this is included in the cost of the service. Users interested in providing their own nuclei suspensions should consult the GMBSR and 10x Genomics website for appropriate procedures.
  • Sequencing requirements are 25,000 reads per cell each for RNA and ATAC datasets (50,000 reads/cell total).

10x Instrument Training: FREE

  • The genomics core staff are available between 8am and 5pm, Monday-Friday to perform 10x experiments. Should users need access to the instrument outside these hours, they can be trained to operate the instrument independently.
  • Training takes ~2 hours and includes a discussion of the principles of the 10x workflow as well as hands on time with the instrument using "dummy" reagents.
  • Trained users will be provided access to the lab as well as the instrument reservation calendar via RaDar.

Prices shown reflect internal Dartmouth rates for FY2024. 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