Bulk Cell Genomic Assays

Library preparation

The Genomics CoLab prepares libraries that are suitable for sequencing on Illumina sequencers. Library preparation includes quality control, normalization, pooling, and sample submission to UCSF sequencing cores. 

Bulk Sequencing

We submit libraries prepared in our core to the UCSF Center for Advanced Technology and the UCSF Institute for Human Genetics Genomics Core. Both Cores have Illumina HiSeq and NovaSeq instruments that can run in high output and rapid run modes. Prices are determined by these cores and change periodically to reflect changes in reagent and other costs. We typically aim for 30-50 million reads per sample for standard RNA-Seq projects. Sequencing costs are approximately $30-50/sample for paired-end 50bp sequencing and $75/sample for paired-end 150bp sequencing.

Analysis Costs

Analysis pricing is charged on a per project basis and is determined by the complexity of the experimental design. Typical costs for a bulk RNA-seq experiment range from $1000-$2500.  Additional analysis or stand alone bioinformatic service costs vary by project complexity and are based on $89/hour rate. For stand alone bioinformatic analysis, please contact  Walter Eckalbar.

Single Cell Genomics Assays

Library preparation

The Genomics CoLab carries out all standard 10x Genomics workflows for single cell RNA-seq, ATAC-seq or Multiome (scRNA+scATAC-seq) assays. First sample costs reflect fixed cost for up to 8 samples at a time. In certain situations, first sample costs can be shared across projects or increased to cover more than 8 samples. Please contact us for more details.

NEW POLICY FOR 2025: We are charging for 10x Reagents as pass through costs. This will more easily allow for clients/collaborators to provide reagents to us. Below is price both with and without reagents provided by the Genomics CoLab.

Single Cell Sequencing

As with bulk cell sequencing project, we submit libraries prepared in our core to the UCSF Center for Advanced Technology and the UCSF Institute for Human Genetics Genomics Core. We typically aim for ~450 million reads per 10x genomics well for standard single cell RNA-Seq projects. Based on this sequencing costs typically average $400-600/sample based on project goals.

Analysis Costs

The Genomics CoLab supports standard alignment and gene counts table generation for single cell RNA-seq/ATAC-seq projects following the 10x Genomics cellranger work flows.  Cost for this basic processing is $500 for up to 8 samples. Additional analysis or stand alone bioinformatic services may be possible, however for single cell RNA-seq/ATAC-seq project we typically recommend more collaborative models, rather than fee-for-service. For more information, please contact  Walter Eckalbar.

Spatial Transcriptomics

The Genomics CoLab supports multiple spatial transcriptomics platforms. This includes the 10x Genomics CytAssist enabled Visium, and will soon be expanded to 10x Genomics Xenium and Nanostring CosMX platforms. 

Whole transcriptome assays: The Genomics CoLab now supports the CytAssist enabled Visium platform and can accept pre-sectioned and imaged slides for processing of this spatial transcriptomic method.

Subcellular resolution, gene-panel assays: The Genomics CoLab now supports the 10x Genomics Xenium platform. We can process slides after sectioning for both standard and custom pannel designs. For custom pannels, we suggest purchasing directly through 10x Genomics and either carrying out the hybridizaiton in your own lab or providing the probes to us, where we will carry out the hybridization step. If carrying out your hybridization and wishing to run slides on the Xenium, please coordinate with the Genomics CoLab before carrying out the hyb. The post-hyb slides have a limited shelf life and we need to schedule a run with you. If carrying out the hyb on your own, you will only need to pay for the Imaging run cost below. 

Pricing note: All 'with reagent' pricing below does not include the probe set. These costs are highly variable depending on standard panel, with or with out custom add ons, or full-custom panel designs or how many genes are included in the custom designs. Full pricing will require a consultation and quote from 10x Genomics.

Sectioning support: The CoLabs may be able to help with your sectioning needs. Please reach out to Walter Eckalbar.

Note * : Due to 10x Genomics bundling of reagents all reagents for the 5K Pannel are billed with the imaging run, but also include reagents for the hybridization.