Single-Base RNA Modification Sequencing
Seventeen workflows that resolve a modification to the individual nucleotide, so a study gets the position of a site and its level rather than a peak region.
01What this line is for
Single-base RNA modification sequencing resolves a modification to the individual nucleotide. Each method pairs one chemical or enzymatic reaction with the sequencing readout, so a site call traces back to a defined conversion rather than to an enrichment peak.
This is the line to use when the conclusion depends on where a modification sits. Because the signal reports position and level together, the same dataset supports site-level comparisons between conditions, between transcripts, and between a modified and an unmodified fraction of the same transcript.
The methods differ in chemistry, not in ambition. Some convert the unmodified base and leave the modification standing; others cut, enrich or misincorporate. Choosing between them is mostly a question of which modification is being studied and whether an antibody-based step is acceptable in the design.
02The sixteen methods
Every entry below is available as a standalone service. Open a method for its detection principle, workflow, analysis set and sample notes.
m6A Modification Seq (CAM-seq)
Cooperative catalysis deaminates unmodified adenosine to inosine while m6A resists, so the A-to-G signal gives both the site and its modification level.
Site-levelposition & level CAM_02m6A Modification Seq (GLORI2-seq)
Glyoxal-based deamination following the same A-to-G logic, applied to transcriptome-wide m6A mapping.
Site-levelposition & level CAM_03m5C Modification Seq (BS-seq)
Bisulfite conversion: unmethylated cytosine converts and is read as thymidine, while m5C resists and stays a cytosine read.
Site-levelposition CAM_04m1A Modification Seq (m1A-Quant-seq)
Mutation signatures from an engineered reverse transcriptase report absolute m1A stoichiometry.
Absolutestoichiometry CAM_05ac4C Modification Seq (RedaC:T-seq)
Reductive conversion marks acetylated cytidine as a thymidine read, resolving ac4C sites.
Site-levelposition CAM_06m7G Modification Seq (m7G-Quant-seq)
Targeted chemical conversion leaves a position-specific signature at m7G.
Site-levelposition & level CAM_07m3C Modification Seq (HAC-seq)
Hydrazine-aniline cleavage chemistry resolves m3C positions without an antibody.
Site-levelposition CAM_08m3C Modification Seq (m3C-IP-seq)
Antibody enrichment combined with reverse-transcription misincorporation to call m3C sites.
Site-levelposition CAM_09Pseudouridine (Ψ) Seq (BID-seq)
Bisulfite-induced deletion signatures mark pseudouridine positions across the transcriptome.
Site-levelposition CAM_10Pseudouridine (Ψ) Seq (BACS-seq)
Controlled bisulfite conversion reports Ψ positions from conversion signatures.
Site-levelposition CAM_11Ψ & Inosine Seq (BACS-seq)
Pseudouridine and inosine profiled from a single BACS-seq library.
Site-leveltwo marks CAM_122'-O-Me (Nm) Seq (NM-seq)
Periodate oxidation, elimination and dephosphorylation chemistry reports ribose methylation.
Site-levelposition CAM_13Dihydrouridine (D) Seq (CRACI-seq)
Chemical conversion signatures distinguish dihydrouridine from unmodified uridine.
Site-levelposition CAM_14O8G Modification Seq (O8G-miSeq)
Antibody enrichment with G>T mutation calling reports oxidative guanosine damage sites.
Site-levelposition CAM_15rRNA 2'-O-Me (Nm) Seq (RiboMeth-Seq)
Alkaline random fragmentation reads Nm on 18S, 28S and 5.8S rRNA, with a methylation level returned for every position.
Site-levelposition & level CAM_16m7G & m3C Seq (AlkAniline-Seq)
Heat and alkali open the abasic site at m7G and m3C; the aniline cut leaves a 5'-phosphate that becomes the adapter entry, so the cut marks the position.
Site-leveltwo marks CAM_17hm5C Seq (WO-Seq)
Peroxotungstate oxidizes hm5C to thT; TGIRT reads thT as T, so a C-to-T change marks the hydroxymethylated cytosine.
Site-levelposition & level03How the methods differ
Convert the unmodified base
Chemical deamination and bisulfite-type conversions change unmodified bases and leave the modification untouched, so the readout is a base change at each position. CAM-seq, GLORI2-seq, BS-seq and BID-seq sit here.
Cut at the modified base
Cleavage chemistry removes or breaks the RNA at a modified position, which is read as a gap or a truncation. HAC-seq, NM-seq and AlkAniline-Seq use this logic, and AlkAniline-Seq goes a step further by using the cut end itself as the entry point of the library.
Pull the modified fragment down
An antibody-based step enriches modified fragments before sequencing. It is the fastest route to a profile, and it is the only route in this line that depends on an antibody.
04FAQ
How do I choose between methods for the same modification?
Where two methods exist for one modification, they usually differ in how they convert. CAM-seq and GLORI2-seq both report m6A at single-base resolution but use different deamination chemistries; BS-seq, BID-seq and BACS-seq all build on bisulfite conversion but read it differently. For m7G, m7G-Quant-seq reads a conversion signature while AlkAniline-Seq reads the cut position and returns m3C from the same library.
Is antibody-based enrichment used in this line?
In m3C-IP-seq and O8G-miSeq. The remaining methods in this line are antibody-free.
What sample types are accepted?
Total RNA, cells, tissue or blood. Preparation and quality notes are listed on each method page.
How many samples can be handled together?
The design depends on the method and the comparison being made, so it is confirmed per project rather than quoted as a fixed number.
Where does the workflow start and end?
Sample QC, the modification-specific treatment or enrichment, library construction, sequencing and bioinformatics analysis are all part of the service.
05Related lines
| Line | Use it when | Request Quote |
|---|---|---|
| RNA Modification RIP-Sequencing | A transcript-level profile across many samples is the goal | |
| RNA Modification Arrays | Many targets need screening before site-level work |