FAQ
The UCSF Genomics CoLab supports investigators from experimental design and grant planning through sample processing, library preparation, sequencing coordination, bioinformatic analysis, and interpretation. The answers below provide general guidance. Final sample requirements, assay eligibility, pricing, and timelines are confirmed for each project before work begins.
Jump to topic:
Getting started
Experimental design
Samples and submission
Services, sequencing, and timelines
Pricing, billing, and project changes
Data and bioinformatic analysis
Facilities, collaboration and publications
Still have a question?
Getting started
What services does the Genomics CoLab provide?
We support bulk RNA sequencing, small RNA and microRNA sequencing, whole-genome and whole-exome sequencing, bulk ATAC-seq, CUT&RUN, CUT&Tag, single-cell and single-nucleus omics, spatial transcriptomics, and bioinformatic analysis. Depending on the project, our work may include experimental-design consultation, sample or nuclei preparation, assay execution, library preparation, quality control, sequencing coordination, data processing, and biological interpretation.
Who can work with the Genomics CoLab?
Our services are available to UCSF investigators. We also work with investigators from other University of California campuses, external nonprofit institutions, and commercial organizations, subject to project fit, capacity, and the applicable rate.
How do I start a project?
Begin by sending us a project description that includes the biological question, assay or data type under consideration, sample type, organism, number of biological samples, experimental groups, available material, and desired data or analysis. Projects involving new investigators, valuable samples, complex designs, or nonstandard workflows generally begin with a consultation.
Do I need to know which assay I want before contacting you?
No. It is helpful to describe the biological question, available samples, required resolution, number of biological replicates, and desired output. We can then discuss which of our supported approaches is technically and financially appropriate.
Can the CoLab help with experimental design?
Yes. We can help plan biological replication, controls, batch balance, sample collection, assay configuration, sequencing requirements, and analysis. We strongly recommend contacting us before collecting, fixing, freezing, sectioning, or shipping valuable samples when the workflow has assay-specific requirements.
Can the CoLab help with a grant proposal?
Yes. We can provide project-specific technical guidance, preliminary estimates, letters of support, and descriptions of relevant facilities and equipment. Please contact us early enough to review the proposed assay, sample numbers, sequencing, analysis, timeline, and budget before the submission deadline.
Download the 2026 facilities and equipment description
Experimental design
How many biological replicates should I include?
The appropriate number depends on biological variability, effect size, study design, and analysis plan. For many straightforward comparisons, three to four biological replicates per group may provide a starting point, but more may be needed for heterogeneous samples, small expected effects, complex models, or cell-composition comparisons. Technical replicates are usually less valuable than additional independent biological replicates. We recommend discussing replication before sample collection.
What is the difference between a biological and technical replicate?
A biological replicate is an independently derived biological sample, such as a different animal, donor, culture, or experimental unit. A technical replicate repeats measurement of the same biological material. Technical replicates can help evaluate technical variability, but they do not replace independent biological replication.
How should I handle samples collected in multiple batches?
Avoid making processing batch identical to biological condition. When all samples cannot be collected or processed together, distribute the major biological groups across collection, extraction, assay, and sequencing batches whenever possible. Keep detailed metadata describing collection time, operator, processing batch, storage, and other variables that may influence the data.
What controls should I include?
Controls are assay- and question-specific. They may include untreated or reference samples, matched normal samples, isotype or negative antibodies, positive-control targets, input controls, or reference materials. Appropriate controls should be included as part of the experimental sample count and budget rather than added after the experiment is complete.
When should I begin with a pilot experiment?
We recommend a pilot for new assay types, unfamiliar or challenging sample types, new antibodies, unusual preservation conditions, limited material, or workflows with substantial technical uncertainty. A pilot of approximately four to eight samples is often more informative than testing one or two isolated samples, particularly when it represents the major sample conditions. Pilot success criteria, stopping points, and the decision to proceed should be defined before work begins.
Can the CoLab perform a new or customized assay?
Potentially. New assays require review of the biological need, protocol maturity, sample and control availability, equipment, staff effort, validation plan, and funding. We may recommend a staged pilot or collaborative project rather than a standard fee-for-service workflow.
Samples and submission
What sample types do you accept?
Accepted material depends on the assay and may include purified RNA or DNA, cultured or sorted cells, fresh or cryopreserved cell suspensions, isolated nuclei, fixed cells or nuclei, tissue blocks, tissue sections, or prepared libraries. Requirements for quantity, concentration, volume, viability, purity, integrity, buffer, preservation, container, and delivery are assay-specific.
Should I contact the CoLab before preparing my samples?
Yes, particularly for single-cell, single-nucleus, Flex, ATAC-seq, CUT&RUN, CUT&Tag, Visium, Xenium, low-input, fixed, frozen, archived, or irreplaceable samples. Sample preparation choices can determine which assays remain possible, and requirements are not interchangeable among workflows.
Does submitting a sample mean that it has been accepted for processing?
Not necessarily. Samples may require intake review or quality control before final acceptance. We will discuss any material that falls outside the recommended criteria and whether it is preferable to stop, submit replacement material, modify the assay, or proceed with documented risk.
What happens if my samples do not meet the recommended quality criteria?
We will explain the concern, the likely consequences, and any reasonable alternatives. If an investigator asks us to proceed with material that does not meet the recommended criteria, the investigator generally assumes the financial risk of an unsuccessful or lower-quality result. The decision should be documented before additional work or costs are incurred.
How do I deliver samples?
Arrange delivery with the CoLab in advance. We will provide project-specific instructions for container, labeling, concentration, volume, temperature, packaging, and delivery timing. Do not leave samples without confirming that staff are available to receive and store them appropriately.
Should I keep backup material?
Yes, whenever possible. Many genomic workflows consume some or all of the submitted material, and a rerun may not be possible if no backup remains. This is especially important for valuable, limited, or irreplaceable samples.
Can the Genomics CoLab help in sample processing?
Potentially. We can isolate DNA and RNA from standardized cellular or tissue sources for an extra fee. This includes utilizing our Kingfisher Flex to perform magnetic bead based nucleic acid isolations. In some circumstances we may be able to take on column based isolations (Qiagen kits), but those are heavily dependent on bandwidth capabilities. We can also isolate nuclei from fixed tissue source for our single nuclei sequencing assays using the Flex kits.
Services, sequencing and timelines
Which parts of the project does the investigator perform?
Responsibilities depend on the assay. Investigators commonly provide the biological material, accurate sample metadata, experimental groups and covariates, organism and reference information, and relevant controls or investigator-supplied reagents. The CoLab performs the laboratory, sequencing-coordination, and analysis work defined in the approved project scope. Upstream tissue dissociation, nuclei isolation, fixation, sectioning, imaging, antibodies, probe design, or custom analysis may be separate components.
Can the Genomics CoLab process libraries made elsewhere or analyze externally generated data?
We may accept outside libraries or externally generated datasets after reviewing their format, quality, provenance, sample metadata, and compatibility with the requested service. Acceptance is project-dependent. Analysis-only projects require a complete sample key, experimental design, prior-processing information, reference details, and clearly defined questions and deliverables.
Does the CoLab perform sequencing?
The CoLab prepares and quality-controls libraries and coordinates sequencing through appropriate UCSF sequencing resources, predominately at the CAT core in Mission bay. Sequencing costs and timelines may depend on read configuration, required depth, available instrument formats, batching, and the sequencing provider.
How long will my project take?
Turnaround depends on assay complexity, sample readiness, project size, reagent availability, batching, sequencing queues, quality-control findings, and analysis scope. We provide an estimated schedule during project planning, but it is not a guaranteed completion date. Troubleshooting, replacement samples, custom work, or changes in scope can extend the timeline.
Are expedited and economy processing options available?
For some assays, compatible projects can share reagent or sequencing capacity to reduce costs, while a dedicated workflow may reduce waiting for a small project. Availability and the cost difference depend on the assay, sample number, reagent configuration, sequencing needs, and current schedule. Speeding projects up can be an option if teams are willing to accept full charge for a batch processing and potentially skipping QC checks prior to sequencing. Ask about these options when requesting an estimate.
Pricing, billing, and project changes
How much will my project cost?
Public prices provide a starting point. A complete estimate may include sample preparation, CoLab service fees, reagents, assay reactions or slides, sequencing, bioinformatic analysis, and optional or custom work. Some multiplexed assays have both a per-reaction cost and an effective per-sample cost that depends on how fully the reaction is used.
Why can the final cost differ from an initial estimate?
An estimate is based on the sample count, assay configuration, sequencing allocation, and analysis scope known at the time. Replacement samples, failed sample QC, investigator-requested additions, partially filled multiplexing reactions, additional sequencing, troubleshooting, or expanded analysis can change the final cost. We will discuss material scope changes before proceeding whenever possible.
Can I provide my own reagents?
Investigator-provided reagents may be possible for selected assays when the products, lot, quantity, storage history, expiration, and compatibility are confirmed in advance. Providing reagents does not remove CoLab labor, other consumable, quality-control, sequencing, or analysis charges.
When will my project be billed?
The CoLab bills monthly for completed work and may bill a project in stages as sample preparation, assay work, sequencing, or analysis is completed. UCSF investigators must provide a valid SpeedType that will remain active through the expected billing period. Soon to expire funds can be billed at the start of projects.
What if I cancel or change a project after work has begun?
Completed labor, opened or committed reagents, custom purchases, submitted sequencing, and other nonrecoverable costs remain billable. Changes in sample count, assay configuration, sequencing, or analysis may require a revised estimate.
Data and bioinformatic analysis
What data will I receive?
Deliverables depend on the assay and analysis scope. They may include raw sequencing or imaging data, quality-control reports, aligned files, count or peak matrices, spatial outputs, analysis-ready data objects, statistical result tables, annotations, figures, and a methods summary. The expected deliverables should be defined before work begins.
Does the CoLab provide bioinformatic analysis?
We offer experimental-design consultation, primary processing, standard assay-specific analysis, and separately scoped collaborative or custom analysis. Primary processing should not be confused with biological interpretation; the level of analysis included in a project will be stated in its scope and estimate.
View the Bioinformatic Analysis overview
View analysis services by assay
Can you help prepare publication figures or perform additional analysis?
Yes. Publication-oriented figures, advanced modeling, integration across datasets, and iterative biological interpretation are generally scoped separately from primary processing or standard analysis. Availability depends on the project, required expertise, staff capacity, and the investigator's participation ininterpretation.
How are data delivered and how long are they retained?
Data are delivered using an sftp server and/or UCSF Box. Investigators are responsible for downloading their data and maintaining long-term copies after delivery. Data retention timelines depend on the Genomic CoLab's involvement in analysis and availability of data storage space. We do not assure projects are stored longer than one year after completion if returned by the Genomics CoLab. If data is returned by a third party facility, such as the CAT core, and it is not required for the Genomics CoLab to retrieve them to complete the project, their data retention policies should be considered.
Can you help submit data to a public repository?
We can discuss the files and metadata needed for repositories such as the Gene Expression Omnibus or Sequence Read Archive. Repository submission and compliance with consent, privacy, and publication requirements remain the investigator's responsibility unless submission support is explicitly included in the project.
Facilities, collaboration and publications
What equipment and computational resources does the CoLab use?
The CoLab maintains specialized equipment for genomic library preparation, automation, quality control, single-cell workflows, and spatial transcriptomics, as well as computational resources for data processing and analysis. A current detailed
description is available for grant and project planning.
Download the 2026 facilities and equipment description
Can investigators use CoLab equipment directly?
Most instruments are operated by CoLab staff as part of an approved project. In certain cases, we may be willing to initiate collaborative efforts that allow access to Genomics CoLab equipment, but that will still require adequate training and machine, space and incidental consumable costs to be reimbursed to the Genomics CoLab.
How should I acknowledge the Genomics CoLab?
Please acknowledge the UCSF Genomics CoLab in publications, presentations, and other research products resulting from CoLab services. Include individual staff members as co-authors when their contributions meet the authorship standards used by the journal and research team. Staff who contributed but do not meet authorship criteria may be named in the acknowledgements.
Please notify us when work supported by the CoLab is published so that we can include it on our publications page.
When is a project considered a scientific collaboration rather than fee-for-service work?
Projects may be considered collaborative when they require substantial method development, experimental design, custom computation, iterative interpretation, embedded personnel, manuscript preparation, or other intellectual contributions beyond a defined standard service. Scope, responsibilities, funding, deliverables, and authorship expectations should be discussed at the beginning of the project.
Still have a question?
Contact the Genomics CoLab with your biological question, sample type, sample count, organism, project timeline, and the assay or analysis under consideration. Providing this information will help us respond with useful next steps.