MODIFICATIONS / 14 MARKS

RNA modification types

Q: Which marks can be resolved to a single base?

m6A, m5C, m1A, ac4C, m7G, m3C, pseudouridine, inosine, 2′-O-methylation, dihydrouridine and O8G. Each has at least one single-base method listed above, and those methods report the individual nucleotide and its modification ratio. Where the conclusion turns on a specific site, use the single-base route.

Q: Which marks are covered only by enrichment?

m6Am at the cap and 5hmC are covered on the RIP-Sequencing line. Those pages state explicitly that the readout is a profile rather than a resolved position, so the result is enrichment across transcripts and regions rather than a site and its level. GlycoRNA is read through its own line rather than through a single-base method.

Fourteen marks are covered across the three service lines. This page states what each mark is chemically, which method reads it, and whether that method reports a position or a profile.

Browse single-base methods

01All fourteen marks in one table

The table separates the two ways a mark can be read. A single-base method resolves the individual nucleotide and reports a modification ratio for it; an enrichment method reports where a mark is enriched across transcripts and does not resolve positions.

The two routes answer different questions, and the right one follows from whether the conclusion depends on a specific site. Where a mark has both, the single-base entry is the route for position-level work and the enrichment entry is the route for larger sample sets.

Mark	What it is chemically	Single-base method	Enrichment method
m⁶A	Methylation at the N6 position of adenosine	CAM-seq · GLORI2-seq	MeRIP-Seq
m⁶Am	Methylation at the N6 position of the cap-proximal adenosine	—	m6Am-Exo-Seq
m⁵C	Methylation at the C5 position of cytosine	BS-seq	MeRIP-Seq
m¹A	Methylation at the N1 position of adenosine	m1A-Quant-seq	MeRIP-Seq
ac⁴C	Acetylation at the N4 position of cytidine	RedaC:T-seq	acRIP-Seq
m⁷G	Methylation at the N7 position of guanosine	m7G-Quant-seq	MeRIP-Seq
m³C	Methylation at the C3 position of cytidine	HAC-seq · m3C-IP-seq	—
Ψ	Isomerisation of uridine to pseudouridine	BID-seq · BACS-seq	Ψ-RIP-Seq
2'-O-Me (Nm)	Methylation of the ribose 2′-O position	NM-seq	—
D	Reduction of the uracil ring to dihydrouridine	CRACI-seq	—
O⁸G	Oxidation at the C8 position of guanosine	O8G-miSeq	O8G-IP-Seq
5hmC	Hydroxymethylation of cytosine	—	hMeRIP-Seq
Inosine (I)	Deamination of adenosine to inosine	BACS-seq (Ψ & I)	—
GlycoRNA	Glycosylation of the RNA at the sugar rather than at a base	—	Array · sequencing · blotting

02Find the method for a mark

Every entry opens the service page for that method. The mark, the chemistry it depends on and the level of resolution are stated on the page itself.

m6A · 01

m⁶A Modification Seq (CAM-seq)

Chemical deamination of unmodified adenosine leaves m⁶A readable at base resolution.

Site-levelposition & level m6A · 02

m⁶A Modification Seq (GLORI2-seq)

Glyoxal-based deamination following the same A-to-G logic.

Site-levelposition & level m5C

m⁵C Modification Seq (BS-seq)

Bisulfite conversion: unmodified cytosine is converted, m⁵C is protected.

Site-levelposition m1A

m¹A Modification Seq (m1A-Quant-seq)

Engineered reverse transcriptase mutation signatures give absolute stoichiometry.

Absolutestoichiometry ac4C

ac⁴C Modification Seq (RedaC:T-seq)

Reductive conversion marks acetylated cytidine as a thymidine read.

Site-levelposition m7G

m⁷G Modification Seq (m7G-Quant-seq)

Targeted conversion separates internal m⁷G from the cap.

Site-levelposition & level m3C · 01

m³C Modification Seq (HAC-seq)

Hydrazine-aniline cleavage chemistry, no antibody involved.

Site-levelposition m3C · 02

m³C Modification Seq (m3C-IP-seq)

Antibody enrichment with reverse-transcription misincorporation.

Site-levelposition Ψ · 01

Pseudouridine (Ψ) Seq (BID-seq)

Bisulfite-induced deletion signatures mark Ψ positions.

Site-levelposition Ψ · 02

Pseudouridine (Ψ) Seq (BACS-seq)

Controlled bisulfite conversion reports Ψ from conversion signatures.

Site-levelposition Ψ & I

Ψ & Inosine Seq (BACS-seq)

Pseudouridine and inosine profiled from a single library.

Site-leveltwo marks 2'-O-Me

2'-O-Me (Nm) Seq (NM-seq)

Periodate oxidation-elimination-dephosphorylation chemistry.

Site-levelposition D

Dihydrouridine (D) Seq (CRACI-seq)

Chemical conversion distinguishes dihydrouridine from uridine.

Site-levelposition O8G

O⁸G Modification Seq (O8G-miSeq)

Antibody enrichment with G>T mutation calling.

Site-levelposition RIP LINE

RNA Modification RIP-Sequencing

Nine enrichment workflows, including m⁶Am and 5hmC, for transcript-level profiles.

Transcriptenrichment GLYCORNA

Glycosylated RNA (GlycoRNA)

Glycosylation is read through its own line: array screening, sequencing and lectin-based blotting.

Dedicatedglyco line

03Choosing marks by research context

Different research settings lead to different marks. The table maps the contexts we are asked about most often onto the marks that are usually worth starting with, and onto the solutions pages that take that kind of project further.

It is a starting point rather than a rule: the mark still has to fit the question, and a study that already has a candidate mark should start there.

Research context	Marks to start with	Solutions to start with
Oncology and metabolism	m⁶A ac⁴C m⁵C	Biomarker discovery m⁶A and transcript fate
R-loop and G-quadruplex biology	m⁶A m⁵C	m⁵C, R-loops and DNA damage
Biomolecular condensates	m⁷G m⁶A	m⁷G, translation and condensates
Canonical translational control	m⁶A m⁵C m⁷G ac⁴C m¹A	Translational control and transcript fate ac⁴C and m¹A in translation
Aberrant translation and tRNA-centred work	Ψ A-to-I (inosine)	Pseudouridine and translation A-to-I editing and the proteome
Oxidative stress and ROS	O⁸G	Oxidative RNA damage Stress response and disease models
Early-stage exploration	2′-O-Me m³C D	Emerging modifications Modification mapping

MARK BY MARKSolutions by modification

One page per mark: what the mark is read against, which route reads it, and what is normally measured alongside it.

BY QUESTIONSolutions by research question

Mapping, writer and eraser work, biomarker screening, stress response, translational control and the GlycoRNA line.

BY DESIGNReading several marks in one study

One library or two routes, which arrangement suits which question, and what has to stay constant across the sample set.

The combinations above are compiled from Arraystar’s internal application summary (September 2026). The recommendations point to the solutions pages on this site, which set out what each line reads and what is normally measured alongside it.

04Which line to use

SINGLE-BASE

When the answer is a position

Site-level chemistry reports where a mark sits and how much of it is present. This is the route for mechanism work and for any conclusion that turns on a specific nucleotide.

ENRICHMENT

When the answer is a profile

RIP-sequencing enriches marked fragments and reports enrichment across transcripts. It scales to larger sample sets and is normally followed by a single-base method on the targets that matter.

ARRAY

When the answer is a screen

Modification arrays report levels across a defined set of transcripts in parallel, which is the practical route when the first question is which targets changed across a large sample set.

05FAQ

Which marks can be resolved to a single base?

m⁶A, m⁵C, m¹A, ac⁴C, m⁷G, m³C, pseudouridine, inosine, 2′-O-methylation, dihydrouridine and O⁸G. Each has at least one single-base method listed above, and those methods report the individual nucleotide and its modification ratio. Where the conclusion turns on a specific site, use the single-base route.

Which marks are covered only by enrichment?

m⁶Am at the cap and 5hmC are covered on the RIP-Sequencing line. Those pages state explicitly that the readout is a profile rather than a resolved position, so the result is enrichment across transcripts and regions rather than a site and its level. GlycoRNA is read through its own line rather than through a single-base method.

A mark has two single-base methods — how do I choose?

Where two methods exist for one mark, they differ in chemistry rather than in ambition. m⁶A is read by CAM-seq or GLORI2-seq, both deamination-based but with different reaction conditions; m³C is read by cleavage chemistry (HAC-seq) or by antibody enrichment with misincorporation (m3C-IP-seq).

Is m⁶A on the single-base line the same as on the RIP line?

No. The single-base route resolves each site and reports its level; the RIP route enriches m⁶A-containing fragments and reports enrichment across regions. The RIP route is often the first pass, and an enrichment profile is what scales to a larger sample set. A conclusion that turns on one nucleotide needs the single-base readout.

What sample types are accepted?

Total RNA, cells, tissue or blood. The workflows differ in what they do to the RNA rather than in the material they accept, so the sample notes apply across the service lines, and preparation notes for one method are given on that method's own page. Quality expectations, storage and shipping are covered in the sample submission guide.