RNA Modification RIP-Sequencing
Nine enrichment workflows that profile a modification across transcripts and across sample sets, using an antibody-based step to pull down modified fragments before sequencing.
01What this line is for
RNA modification RIP-sequencing enriches modified RNA fragments with an antibody and then sequences them. It reports where a modification is enriched across transcripts, which makes it a workable route when the question is about a profile or a comparison rather than a single position.
The trade is deliberate. Enrichment-based workflows need less of the sample and scale more easily across conditions and cohorts than site-level chemistry does, and in return the readout is a region of enrichment rather than a resolved nucleotide. Sites that look interesting in a profile are usually followed up with a single-base method.
Nine modifications are covered on this line. Where the immunoprecipitation chemistry differs — the cap-proximal m6Am readout, for example — the method page describes what is being enriched and what the resulting profile can and cannot resolve.
02The nine methods
Each method is available as a standalone service, and each page states the modification, the enrichment step, the analysis set and the sample notes.
m6A Modification Seq (MeRIP-Seq)
Antibody enrichment of m6A-containing fragments followed by sequencing.
Transcriptprofile RIP_02m5C Modification Seq (MeRIP-Seq)
Antibody-based enrichment of m5C-modified fragments.
Transcriptprofile RIP_03m7G Modification Seq (MeRIP-Seq)
Antibody-based enrichment of m7G-modified fragments.
Transcriptprofile RIP_04m1A Modification Seq (MeRIP-Seq)
Antibody-based enrichment of m1A-modified fragments.
Transcriptprofile RIP_05ac4C Modification Seq (acRIP-Seq)
Antibody-based enrichment of ac4C-modified fragments.
Transcriptprofile RIP_06Pseudouridine (Ψ) Seq (Ψ-RIP-Seq)
Antibody-based enrichment of pseudouridine-containing fragments.
Transcriptprofile RIP_07m6Am Modification Seq (m6Am-Exo-Seq)
Exonuclease-based readout that separates m6Am at the capped 5′ end from internal m6A.
Cap-proximalm6Am RIP_08O8G Modification Seq (O8G-IP-Seq)
Immunoprecipitation of 8-oxoguanosine-containing fragments.
Transcriptprofile RIP_095hmC Modification Seq (hMeRIP-Seq)
Antibody-based enrichment for 5-hydroxymethylcytosine on RNA.
Transcriptprofile03RIP-sequencing against single-base sequencing
Profile versus position
RIP-sequencing reports enrichment over transcript regions. Single-base sequencing reports the individual nucleotide and its modification level. The right choice follows from whether the conclusion depends on a specific site.
Many samples, fewer demands
Because the workflow starts from enrichment rather than from a base-level conversion, it tolerates larger sample sets and is often used as the first pass across conditions or cohorts.
Screening then resolving
The two lines are designed to be used in sequence: a RIP-seq profile identifies the transcripts and regions that differ, and a single-base method resolves and quantifies the sites inside them.
04FAQ
Is RIP-sequencing single-base resolved?
No. The signal comes from enriched fragments, so the result is a profile across transcript regions rather than a resolved nucleotide. Where site-level resolution is needed, a single-base method is the next step.
What is the advantage of an enrichment-based workflow?
It scales. Larger sample sets and cohort designs are more practical when the workflow starts from enrichment, which makes RIP-sequencing a common first pass before site-level work.
Which modifications are covered?
m6Am, m6A, m7G, m5C, m1A, ac4C, O8G, pseudouridine and 5hmC. Each has its own method page.
What sample types are accepted?
Total RNA, cells, tissue or blood. Preparation notes are listed on each method page.
Can RIP-sequencing and single-base work share the same samples?
In most designs yes, which is why the two lines are usually planned together so that the material and the comparisons stay aligned.
05Related lines
| Line | Use it when | Request Quote |
|---|---|---|
| Single-Base RNA Modification Sequencing | The exact position and level are the conclusion | |
| RNA Modification Arrays | Many targets need screening before either line |