Computational Service
Cell Line Models
Scoped After Feasibility Review
Service Overview
Circular RNA work carries a specific methodological risk: the evidence for circularity is easy to produce and easy to misinterpret. Divergent primers amplify from template artefacts, linear readthrough is common, and overexpression constructs frequently produce far more linear product than circle. We design constructs that favour circularisation and, equally importantly, design the validation that distinguishes genuine circles from the artefacts that mimic them.
Key Features & Advantages
Circularisation-Favouring Architecture
Flanking intronic complementary sequences and repeat design are used to promote back-splicing, with construct architecture chosen for the expression system in use.
Junction Validation Designed In
Divergent primer design, RNase R treatment strategy and junction sequencing are specified together, since no single one of them is sufficient evidence.
Linear Product Quantified, Not Assumed Absent
The design includes how linear readthrough will be measured, because it is usually present and usually affects interpretation.
Downstream Analysis Supported
Where circRNA sequencing data exists, we detect and quantify back-splice junctions with methods appropriate to the library preparation used.
Where This Service Is Used
1Overexpressing a candidate circRNA to test a proposed function
2Building stable lines for circRNA functional studies
3Validating circRNA candidates identified from sequencing data
4Designing controls that distinguish circRNA effects from those of the linear transcript
5Analysing circRNA sequencing datasets for detection and differential abundance
How the Work Is Performed
1Candidate circRNA sequence analysis including exon composition and back-splice junction definition
2Flanking intron and complementary repeat design to promote circularisation
3Vector architecture selection appropriate to the host and expression strategy
4Divergent and convergent primer design for circular and linear quantification
5RNase R and junction sequencing validation strategy design
6CircRNA detection and quantification from sequencing data where such data is supplied
What We Need From You
1Candidate circRNA identity: back-splice junction coordinates or the exon composition
2Host cell line and the expression vector system available
3Existing sequencing evidence for the circle, if any
4The functional hypothesis being tested, which affects which controls matter most
What You Receive
1Annotated expression construct design with the circularisation elements explained
2Primer designs for junction detection and for linear transcript quantification
3Validation strategy covering RNase R resistance and junction sequencing
4Control design, including a linear-only construct where the comparison is informative
5Sequencing analysis results where circRNA data is part of the scope
Questions We Are Asked Before Scoping
How do we prove the circle formed?
▸Convergent and divergent PCR from both RNA and genomic DNA, RNase R resistance and junction sequencing, considered together. Any one of these alone can be produced by artefacts.
Will the construct produce only circular RNA?
▸Almost certainly not. Linear readthrough is usual and its level affects interpretation, so measuring it is part of the design rather than an optional extra.
Can you analyse existing circRNA sequencing data?
▸Yes — detection, junction quantification and differential analysis, with the limitations of the library preparation used stated explicitly.
Interpretation and Limitations
This is a computational (in silico) service. Designs and predictions prioritise hypotheses and direct experimental effort; they do not by themselves establish that an edit, construct, molecule or assay will perform as intended. Laboratory execution — editing, cloning, expression, synthesis and testing — is planned with you and carried out by your own team or a qualified partner. Deliverables are for research use only and are not intended for diagnostic or therapeutic use.
Is This the Right Service for You?
Choose this when
A candidate circular RNA needs overexpressing to test a proposed function
Existing circRNA sequencing candidates require validation
Controls must distinguish circular from linear transcript effects
Consider another service when
The linear transcript is the subject
Gene Knockdown Cell Line Design Discovery from sequencing data comes first
Bulk & Single-Cell RNA-Seq Analysis What Goes Wrong, and How We Handle It
These are the failure modes that produce confident-looking results which do not survive the next experiment. Each one is designed against rather than discovered afterwards.
Divergent PCR taken as proof of circularity
RNase R resistance, junction sequencing and genomic DNA controls are designed together, because any one of them can be produced by artefacts.
Linear readthrough ignored in interpretation
Quantification of the linear product is part of the design, since it is usually present and affects the conclusion.
No control separating circular from linear effects
A linear-only construct is designed as the comparator where the functional claim requires it.
A Worked Example
Validating a circRNA candidate from sequencing
The situation
A back-splice junction appeared in the data and the team wanted a functional overexpression system.
What the work involved
Flanking intronic complementary sequences were designed to promote back-splicing, divergent and convergent primers were designed, and an RNase R and junction sequencing strategy was specified.
What came back
A construct with the circularisation elements explained, plus the control set — linear-only comparator, genomic DNA control and RNase R protocol — needed for the result to be believable.
Illustrative of the shape this work takes. Details are generalised, no client or target is identified, and scope and outcome vary with the system in question.
Service Workflow
1
Scientific Consultation
We discuss the objective, the decision it supports and the material and data you already hold.
2
Feasibility Review
We check that the target, system and available information can support the approach, and say plainly where they cannot.
3
Technical Proposal
Scope, methods, deliverables, timeline and price are confirmed in writing, together with the limitations we expect to report.
4
Design and Analysis
The design work runs on documented tools and parameters, with quality checks and alternatives compared where that is informative.
5
Delivery and Follow-Up
You receive the designs, the supporting analysis and a validation plan, plus support interpreting the results once the experiments run.
Service Process
1
Online Consultation
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2
Solution Matching
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3
Service Contract
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4
Project Execution
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5
Data Delivery
Specifications & Turnaround
Note: ICDMO delivers computational (in silico) services. Results prioritise hypotheses for testing; they do not by themselves establish binding, biological activity, efficacy or safety. All deliverables are for research use only and are not intended for diagnostic or therapeutic use. Downstream experimental work is scoped separately and executed through qualified partners.
Get a Custom Quote
Our scientific team responds within 24 hours with a detailed technical proposal and pricing tailored to your project.
Contact Us Online ConsultationStandard Deliverables
✓Sequence-verified final product
✓Full QC documentation
✓Certificate of Analysis (CoA)
✓Electronic data files
✓Project completion report
Why ICDMO?
Computational CDMO Focus
Reproducible, Versioned Pipelines
Confidence & Limitations Reported
Experiment-Aware Recommendations
Response Within One Business Day