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 Walter Eckalbar.  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 Core’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 Core 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.

RNA quality control

Core users prepare RNA samples and submit these to the Core. When sufficient RNA is available for analysis (≥ 10ng), samples should be analyzed by spectrophotometry (Nanodrop) and by electrophoresis (Agilent Bioanalyzer) prior to preparing sequencing libraries. Agilent Fragment Analyzer analysis is offered as a service to users at a cost of $11.27 per sample.

RNA-seq library preparation

The Core 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 projects with fewer than 4, or more than 48, samples, please contact us to discuss pricing.

Library type Method Cost per sample
PolyA RNA Universal Plus mRNA (>10ng total RNA) [Tecan] $260
Total RNA (ribo and/or globin RNA depletion) Universal Plus + FastSelect (>50ng total RNA) [Tecan] [QIAgen] $406
Low input total RNA

SMART-Seq v4 + Nextera Flex (>10pg total RNA or 1-1000 cells) [Takara Bio] [illumina]


Small RNA (including miRNA) TruSeq small RNA (>10ng total RNA) [illumina] $329
ChIP-Seq library prep NexteraXT (>1ng DNA) [illumina] $198


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 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 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.