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CRISPR Cell Engineering Services


In partnership with editing service provider, Synthego, the UCSD IGM Genomics Center now offers iPSC and cell editing services to UCSD researchers and external research institutions. Researchers can choose to edit nearly any iPSC line or cell line, or choose to edit a line from the iPSC Collection for Omics Research (iPSCORE).

Cell editing services offered in iPSCs, ESCs and Cell Lines

  • Gene KO (single, or multi-gene, and conditional KOs)
  • Single Nucleotide Changes
  • Endogenous Gene Tags (GFP, HiBit, Flag, HA, His, etc.)
  • Other edits – just tell us what you need

The IGM Genomics Center has negotiated special discounted rates for UCSD researchers – up to 36% discount. Outside non-profit institutions are also supported with non-profit rates. Commercial organizations must work directly with Synthego.

For questions, pricing information, or a quote, please email kjepsen@ucsd.edu with a brief project description.


Guaranteed Edits or You Don't Pay

Type of Edit Description Deliverable Type Turn Around Time Guarantee Applies?
Gene Knockout Creating a gene KO using multi-guide sgRNA design strategy to make a functional protein knockout. Single or multi-gene KOs are supported. Pool 4-6 weeks Yes
Clone 8-12 weeks yes
SNV Change Changing a single nucleotide variant (SNV) or single nucleotide polymorphism. Can be either a nucleotide or amino acid change. Pool 6-8 weeks Partial
Clone 12-16 weeks Yes
Small Tag Insertion Insert a small tag (100 bp or less) into a region of the genome. Pool 6-8 weeks Partial
Clone 12-16 weeks Yes

    Standard Deliverables:
  • 2 independent biological clones or 1 cell pool (2 vials of each: 1M cells/vial)
  • 2 vials of wild type isogenic cells, passage matched and mock transfected (1M cells/vial)
  • Genotypic Analysis and Editing Summary Report
  • Certificate of Analysis

Service Rates

Rates vary depending on the iPSC line to edit, the type of edit (KO, SNV, Tag, other), desired deliverables, etc. Up to a 36% discount for UCSD researchers.

Only successfully completed projects will be billed to the investigator, and invoiced are only sent upon delivery of the completed project(s). Unsuccessful projects will not require payment of refundable fees.

For pricing information or a quote for a specific project(s), please email kjepsen@ucsd.edu with a brief project description.

For more information about iPSCORE lines, please email adc055@ucsd.edu


Instructions for starting a CRISPR editing project:

  • Download and Complete iPSC Cell Engineering Project Info
  • Email the completed form to kjepsen@ucsd.edu
  • Project details will be assessed for technical feasibility
  • Upon feasibility confirmation, the project will be priced according to edit type, deliverable type, and deliverables.

Process Overview

Project Start - Design and Synthesis of modified sgRNA and donor template (1-2 weeks)

Synthego will design several guides targeting the region of interest. Each guide will be required to meet strict off-target requirements of at least 2 mismatches. Donor designs will include the necessary homology arms of sufficient length to ensure knock-in efficiency. Unless otherwise requested, silent mutations will be included in the donor to modify the PAM site for each guide to reduce cutting post-editing and maximize the efficiency of the knock-in. Guides will be synthesized onsite by Synthego as chemically modified synthetic single-guide RNA. Donor templates either as ssODNs or plasmids will be manufactured.

Milestone 1- Transfection and genotyping of pool (2-4 weeks)

Your specific guide RNAs are complexed together with the spCas9 to form a ribonucleoprotein (RNP). RNPs and donors are then delivered to the cells via the optimized electroporation setting. The cells are then recovered for 2 days before the edits are evaluated. Positive control sgRNA (RELA) is always transfected at the same time. We rigorously assess the percentage of knock-in sequences of your genetic target. To achieve this, we PCR-amplify the edited site and Sanger sequence the amplicons. The sequence data are then analyzed using Synthego’s Inference of CRISPR Edits (ICE) software tool. ICE identifies the indel frequency (ICE Score) and the specific indels present in the pool. Additionally, ICE calculates the frequency of the desired knock-in, reported as the Knock-In (KI) Score.

Milestone 2 - Clonal isolation and initial genotyping (Clone workflow only) (5-9 weeks)

The edited pool is used to seed single cells for clonal expansion. Each well seeded is imaged every 2-3 days and rigorously tracked to ensure the population is truly clonal and only the progeny of a single cell. We do not use any selection agents to enrich or select for clonal populations. Resulting clones are verified using Sanger sequencing. Please note: Synthego only utilizes single cell dilution for clonal isolation.

Milestone 3 - Sequence validation of alleles (Clone workflow only) (1-2 weeks)

Colonies identified in Milestone 2 will be further screened and sequenced to precisely identify those that harbor the edits required. Two clones will be selected to be expanded to 1 million cells/vial for final QC. Our Quality Control process checks the viability of cells post-thaw, confirms genotype via Sanger sequencing and confirms the absence of mycoplasma. Additional QC includes karyotyping of the final clones to ensure genomic integrity and assessment of pluripotency via immunocytochemistry.