RNA modification solutions
Most studies reach modification data through the same three steps: decide which mark matters, choose a route by the resolution the conclusion needs, then confirm the interesting targets. These pages set out how that looks for common research questions, for individual marks and for the sample types the work is done on.
01By research question
A modification project usually starts from a question about either position or pattern. Position questions need site-level chemistry; pattern and comparison questions are usually served faster by an enrichment or array route, with site-level work reserved for the targets that matter.
Modification mapping and site-level profiling
Build a site-level map of a mark across transcripts in a model, a treatment series or a cohort.
Site-levelmap MECHANISMWriter, eraser and reader studies
Compare modification profiles after perturbing a modifying enzyme, to connect the enzyme to the sites it acts on.
Perturbationcomparison SCREENINGBiomarker discovery and clinical samples
Screen modification levels across many samples on the enrichment or array line, then confirm the candidates that move.
Cohortscreening RESPONSEStress response and disease models
Follow how modification patterns shift between conditions, stages or genotypes within a defined experimental system.
Conditionshift TRANSLATIONTranslational control and transcript fate
Connect a resolved site to transcript stability and translation, and compare the same transcript between modified and unmodified states.
Functionlinkage GLYCORNAGlycosylated RNA
GlycoRNA array, sequencing and blotting as one line, for studies where the mark is a glycan rather than a chemical modification.
Dedicatedglyco line DESIGNReading several marks in one study
When a project covers more than one mark: shared libraries against separate routes, and what has to be held constant for the comparison to mean anything.
Designmulti-mark02By modification
The pages below take one mark at a time and set out the processes it has been linked to, which service line reads it, and which readouts are normally run alongside. The last entry covers studies that read more than one mark from the same samples.
m6A and transcript fate
Splicing, nuclear export, translation and stability — the four levels a resolved m6A site is usually read against.
Mark-levelfour levels m6Amm6Am and the cap-proximal position
The same chemistry as m6A, one nucleotide behind the cap — read against transcript lifetime, translation and cap identity.
Mark-levelcap-proximal m5Cm5C, R-loops and the DNA damage response
Where m5C work meets R-loop and G-quadruplex biology, and what the design has to do to speak to both.
Mark-levelstructure overlap m7Gm7G, translation and biomolecular condensates
Internal m7G read against translation and against condensate biology.
Mark-leveltranslation ΨPseudouridine and translation reprogramming
Pseudouridine read against stability, splicing and the translation of the transcript that carries it.
Mark-leveltranslation A-to-IA-to-I editing and the proteome
Editing events that change the read, the codon and sometimes the protein, read at defined positions.
Mark-levelediting O8GOxidative RNA damage and the O8G mark
Oxidative damage on RNA read against translation and transcript turnover.
Mark-leveloxidative stress ac4C & m1Aac4C and m1A in translation control
Two marks usually read in the same sentence: translation efficiency and transcript stability.
Mark-leveltranslation 2'-O-Me2'-O-methylation and the ribose
Methylation of the sugar rather than the base, read through ribose chemistry and against structure, guide RNA and recognition.
Mark-levelribose EMERGINGEmerging modifications: 2'-O-Me, D and m3C
Three sparsely mapped marks, and what a first controlled study on them can claim.
Mark-levelfrontier03By sample type
What changes between sample types is not the chemistry but the handling: the input that has to be prepared, the quality checks that apply, and which route the material can support.
Cultured cells and tissue
Total RNA from cultured cells or from fresh or frozen tissue is the most common starting point. Pellets and frozen specimens are handled the same way at the RNA stage, so the preparation notes that matter are the ones about degradation and purity. Each service page states its own quality thresholds and the input it needs.
Blood and body fluids
Whole blood collected in EDTA tubes is accepted; heparin is not compatible with the downstream procedure. Body fluids are treated as a low-abundance source, so the route is chosen with the starting amount in mind. Handling and storage notes are given on each service page rather than generalised here.
Low-input and scarce samples
Sorted populations, small biopsies and rare material change which route is realistic: some methods tolerate less starting RNA than others, and a comparison across many samples usually starts on the higher-throughput line before site-level work on the targets that differ. Which route fits is decided per project.
04How a project runs
- Define the question. The mark of interest, the sample type and the comparison being made are discussed before a route is fixed.
- Check the sample. Input type and quality are reviewed against what the chosen workflow needs.
- Run the workflow. Sample QC, the modification-specific treatment or enrichment, library construction and sequencing.
- Analyze and report. Site calling or profile quantification, followed by the analysis set and tables described on the service page.
- Take it further. Where a screen flagged a target, a site-level or LC-MS readout confirms it independently.
| Stage | What happens | Request Quote |
|---|---|---|
| Scoping | Mark, sample type and comparison reviewed; route proposed | |
| Screening | Enrichment or array line across the sample set | |
| Resolution | Single-base method on the targets that moved |
05FAQ
My question is about a specific site — where do I start?
Start on the single-base line. Those methods report the nucleotide and its modification ratio, which is what a site-level conclusion needs, and the ratio is what can be compared between conditions. An enrichment or array readout describes a region, so it cannot supply the position the question is about.
I have a large sample set but no clear target yet.
The enrichment and array lines are built for that situation. They profile many samples or targets at lower resolution and point to where site-level work is worth doing, so the first pass is a screen rather than a final answer. The targets that differ are then taken into a single-base method or an independent readout.
Can a project use more than one line?
Yes, and most do. Screening narrows the field across the sample set, and site-level or LC-MS work confirms what the screen flagged. The later step is planned from the start rather than added at the end, because a screen returns levels and a confirmed conclusion usually needs either a position or an independent measurement.
What if the modification I care about is not listed?
The list of covered marks is on the modification types page, which also states which of them can be resolved to a single base. If yours is not there, ask — it is worth confirming availability rather than assuming, and where a mark has no single-base route the question has to be framed at region level.