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CRISPR Cell Engineering Services


Cell editing services offered in iPSCs, ESCs and Cell Lines

  • Gene KO (single, multi-gene, and fragment deletions)
  • Single Nucleotide Changes or cassette insertions
  • Endogenous Gene Tags (GFP, HiBit, Flag, HA, His, etc)
  • Large KI casette
  • Other edits – just ask what you need and our team will assess feasibility!

In partnership with editing service provider, Synthego, the UCSD IGM Genomics Center now offers Immortalized and iPSC and cell editing services to UCSD researchers and external research institutions. Researchers can choose to edit over 400 pre-optimized immortalized cell lines or nearly any iPSC line, or choose to edit a line from the iPSC Collection for Omics Research (iPSCORE).


Guaranteed Edits or You Don't Pay

All projects are subject to a feasibility review. If a project passes review, the guarantee applies.

Type of Edit Description Deliverable Type Turn Around Time
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
Clone 14-18 weeks
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
Clone 14-16 weeks
Small Tag Insertion Insert a small tag (100 bp or less) into a region of the genome. Pool 8-10 weeks
Clone 16-18 weeks

Standard Deliverables:
  • 2 independent biological clones or 2 cell pools (2 vials of each: 0.5-1M cells/vial)
  • 2 vials of wild type isogenic cells mock-transfected pools, passage matched (0.5-1M cells/vial)
  • Genotypic Analysis and Editing Summary Report
  • Certificate of Analysis

Service Rates

Only successfully completed projects will be billed to the investigator, and invoiced are only sent upon delivery of the completed project(s). Please visit our Money Back Guarantees page for more details.

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

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


Instructions for starting a CRISPR editing project:

  • Enter project details in the following form: iPSC/Immortalized 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 For Clones

  1. Project Submission
  2. Guide, Donor, and Primer Design
  3. Reagent Synthesis
  4. Cell Optimization & Quantification
  5. Transfection
  6. Pool Analysis
  7. Clonal Isolation | Expansion | Imaging | Image Analysis
  8. Hit Picking | Clonal Genotyping
  9. Clonal Confirmation | Clonal Expansion
  10. Quality Control - Mycoplasma, Genotyping

Milestone 1a

Design and Synthesis of modified sgRNA and donor template (for knock-in projects).
Synthego will design several guides targeting the region of interest. Each guide will be required to meet strict off-target requirements of at least two mismatches, within an early exon and targeting a common exon present in the majority of annotated transcripts. Guides will be synthesized onsite by Synthego as chemically modified synthetic single-guide RNA. For knock-in projects only, donors will be designed and synthesized as single-stranded DNA molecules.
Communication: Completion of design & beginning of the synthesis.

Milestone 1b

Transfection and genotyping of the pool.
Your specific guide RNAs are complexed together with the sp Cas9 to form a ribonucleoprotein (RNP). RNPs and the donor template are then delivered to the cells via the optimized electroporation setting we have identified using our 200 point optimization. Please note: if we have not optimized your cells yet, this will take an additional ~2 weeks. The cells are then recovered for 2 days before the edits created are evaluated. Positive control sgRNA (RELA) is always transfected at the same time.
We rigorously assess the percentage of knock-out 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 editing frequency and the specific indels present in the pool. Additionally, ICE calculates the frequency of the desired knock-in, reported as the Knock-In Score.
Communication: Editing efficiency of the pool.

Milestone 2

Clonal isolation and initial genotyping
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. The resulting clones are verified using Sanger sequencing.
Delivery of Knockin Clones is dependent on the ability of the cell line to be isolated and grow from a single cell.
It is feasible that cell lines that fail to reach clonality using single-cell dilution can do so using other methods, such as fluorescence- activated cell sorting (FACS), however, we do not have these capabilities.
Communication: Genotype of the identified clones.

Milestone 3

Sequence validation of alleles
Sequence validation of alleles 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 for final QC. Our Quality Control process confirms genotype via Sanger sequencing and confirms the absence of mycoplasma.
Communication: Final Report.