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Reveal capping, dsRNA, integrity, poly(A) tails, and identity in a single experiment
Direct RNA sequencing with Oxford Nanopore Technologies (ONT) reads RNA in its native form, with no reverse transcription and no amplification. eSTRAND RNA QC examines key attributes of IVT RNA quality including capping, dsRNA, and integrity. eSTRAND Transcriptome identifies the isoforms expressed in a sample and locates where modifications are deposited.
Contact usOverview
Use:
IVT RNA quality control, isoform and modification profiling
Typical samples:
IVT RNA, cellular RNA
Characterize with direct sequencing
Library prep, sequencing, and analysis are handled end to end. You get an interactive report, not a folder of files to interpret.
Start a projectPrepare libraries
Libraries are prepared directly from RNA, with no cDNA conversion.
Sequencing
As each RNA molecule is pulled through a pore, every base type produces a distinct signal.
Analyze
Our bioinformatics team turns the signal into quality attributes and delivers them in an interactive report.
eSTRAND RNA QC
Traditional analytical tools answer one question at a time. eSTRAND RNA QC is a multi-attribute assay: identity, integrity, poly(A) tail length, 5' capping, and dsRNA content, measured together at nucleotide-level resolution.
Measure dsRNA impurities
Nanopore RNA sequencing directly measures poly(A) tail lengths on IVT RNAs, providing insight into a key determinant of stability, translation efficiency, and overall therapeutic performance.
dsRNA coverage at each position along an IVT RNA (top), the share of total dsRNA reads attributable to each initiation site (middle), and the length distribution of the species initiating at the highlighted site (bottom). One site accounted for 48.5% of all dsRNA reads in this sample.
Detect truncated species
Standard direct RNA sequencing reads only fragments carrying a poly(A) tail, so the products of a break go uncounted and truncation gets inferred from what survives. eSTRAND RNA QC recovers fragments regardless of tail, resolving where molecules actually broke.
Distribution of 3' ends across an intact RNA sample spiked with two truncated transcripts. Both truncations resolve as discrete peaks, at the positions where those spike-in molecules end.
Measure poly(A) tail length
Poly(A) tail length drives stability and translation efficiency, and it varies between manufacturers and between batches. eSTRAND RNA QC measures the tail on each molecule as it is read, with no reverse transcription or amplification in between, so you see the full distribution across the sample rather than an average.
Poly(A) tail length distributions for the same RNA sequence synthesized by two manufacturers. Manufacturer A produced tails clustered at the expected length. Manufacturer B produced variable tails, which tracked with reduced ribosome association, an assessment of potency measured by eRibo Pro.
eSTRAND Transcriptome
eSTRAND Transcriptome sequences full-length isoforms across the entire transcriptome, rather than assembling them from short reads. One run returns gene-level expression, isoform-level usage, and RNA modifications called from the raw signal on native molecules.
Map RNA modifications
N6-methyladenosine, pseudouridine, inosine, 5-methylcytosine, and 2'-O-methylation of all four bases, all called from the same reads that produced the expression results. On a short-read platform each of these needs its own enrichment chemistry, which is a separate experiment per modification.
Modification calls along NCF4 in a reference sample, one track per modification type. All eight types were called from the same reads, with no modification-specific chemistry, and all tracks share a common scale.
Measure isoform usage
A gene can appear steady with traditional RNA-Seq while the balance between its isoforms moves. Full-length reads with eSTRAND Transcriptome assign each molecule to an isoform directly, so a usage shift is measured rather than inferred. Differential gene expression, differential isoform usage, and pathway enrichment on both are returned for every comparison.
Each point is one isoform tested for differential usage between two reference RNA samples, UHRR and HG002. Saturated points shifted isoform usage in genes that were not differentially expressed, which a gene-level analysis alone would not have found.