Getting Started

We strongly recommend that you schedule a project meeting with us before you start your experiment.

First Step

To initiate a project, please fill out the project description form and e-mail it to [email protected].  When we receive the completed form, we will contact you to schedule an initial project meeting. During the meeting we will discuss experimental design, protocols, analysis needs, timeline, and cost.



The Genomics CoLab's recharge system is used to cover labor and supply costs for most projects. Other arrangements, such as subcontracts, are available for larger or more complex projects.

Standard pricing is available for certain commonly used protocols. For other work, the Genomics CoLab can give you a price estimate prior to starting on your project. Pricing is adjusted periodically to reflect changes in our costs. Users outside of the University of California system will be assessed a 26% surcharge.

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. Sequencing costs are not included (see below). For small projects, first sample costs can be shared to drastically reduce costs. In most cases this will not impact turn around times.

Library Type Method Cost for First Sample Cost per Additional sample
PolyA RNA Universal Plus mRNA (>10ng total RNA) $2,737 $120
Total RNA (ribo and/or globin RNA depletion) Universal Plus + FastSelect (>50ng total RNA) $2,737 $120
Low input total RNA

SMART-Seq v4 + Nextera Flex

(>10pg total RNA or 1-1000 cells)



Small RNA (including miRNA) NEB small RNA (>10ng total RNA)  $3,057 $88
DNA-seq/ChIP-Seq library prep Nextera Flex (>1ng DNA)  $1,978 $106
Whole Exome Sequencing Nextera Flex With Exome Enrichment $3,036 $117
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 40-50 million reads per sample for standard RNA-Seq projects. Sequencing costs are approximately $125/sample for single-end 50bp sequencing and $250/sample for paired-end 100bp/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.

Assay Type Cost for first sample

Cost per Additional Sample

(up to 8 total)

3'/5' Gene Expression  $2,916 $1610
Additional TCR, BCR or Feature Barcode additions $242 $30
Single Cell ATAC-seq $2,916 $1610
Combined Single Cell RNA-seq and ATAC-seq $5,001 $2,676
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 $1500, but can vary 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 or STARsolo processing (only for 3' gene expression).  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.