Precision RNA Profiling for Discovery and Translational Decisions

Epigenome Technologies deploys validated poly-A, total, and long-read RNA-seq protocols so your project teams receive superior transcript quantification, isoform resolution, and regulatory context without pausing internal research. We qualify inputs, run the benchwork, and return interpretable deliverables that plug directly into downstream decisions.

Median Turnaround

10 business days

Sample intake to sequence-ready library QC, with interim status updates.

Quality Gates

Replicate R > 0.95

Mapping rates > 80% and replicate concordance documented per batch.

Assay Modes

Bulk + single-cell

Poly-A, total RNA, and long-read playbooks for discovery and translational studies.

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RNA-seq for Focused Discovery

RNA-seq volcano plot
Quick-turnaround transcriptomic analysis.

RNA sequencing quantifies transcript abundance, isoform diversity, and regulatory RNA expression at genome-wide scale. We align poly-A selection, ribo-depletion, and long-read chemistries to specific biological questions and sample constraints, emphasizing when each approach delivers the highest signal-to-noise and interpretive clarity.

Long-read RNA-seq sashimi plot demonstrating read coverage and splicing junctions in HeLa cells
RNA-sequencing enables the quantification both of transcript abundance and the specific use of splicing configurations within insoforms.

Where teams use the program

  • Biomarker discovery and validation in limited clinical cohorts.
  • Rare transcript detection and low-abundance target quantification.
  • Fusion gene identification and structural variant profiling.
  • Microbiome transcriptomics and host-pathogen interaction studies.
  • FFPE rescue and archival sample analysis.
  • lncRNA regulatory network mapping.
RNA-seq boxplot showing 6 genes expression values across control and knockout cell lines
Bulk RNA-sequencing enables transcriptome-wide investigation of changes in gene expression without a-priori biases.

Collaboration model

  • Joint design sessions align sample availability, replicates, sequencing depth, and controls.
  • Project scientists remain embedded through QC reviews, data interpretation, and reporting.
  • Integration briefs consolidate RNA with ATAC, CUT&Tag, or third-party datasets on request.

Included interpretation

  • Differential expression analysis and pathway enrichment summaries.
  • Transcript isoform quantification and alternative splicing annotations.
  • Actionable slide-ready visualizations delivered alongside raw outputs.

Aligning Method to Objective

Method Best For Key Applications
Poly-A RNA mRNA quantification in eukaryotic systems; transcript-level abundance Differential expression with high replicate concordance; gene-level quantification
Total RNA Unbiased profiling of coding and non-coding RNAs Bacterial transcriptomes; degraded or FFPE specimens; lncRNA and circRNA discovery
Long-read RNA Full-length transcript isoforms; fusion events; alternative splicing Structural rearrangements; allele-specific expression; novel isoform discovery

Poly-A RNA-seq

Selectively captures mature, polyadenylated mRNA transcripts for efficient quantification of protein-coding gene expression. Integrates seamlessly with Multiome workflows combining ATAC and RNA-seq.

RNA-seq volcano plot subset to non-coding RNA species showing significance across lncRNA, miRNA, and snoRNA
Poly-A Capture RNA-seq enables transcriptome-wide quantification of protein-coding RNA species.
  • Optimized for differential expression across conditions
  • High replicate concordance and statistical power
  • Compatible with bulk and single-cell platforms

Total RNA-seq

Captures both coding and non-coding RNA species—including lncRNAs, miRNAs, and other regulatory transcripts—for a complete transcriptional view.

RNA-seq volcano plot subset to non-coding RNA species showing significance across lncRNA, miRNA, and snoRNA
Total RNA-sequencing enables transcriptome-wide investigation of changes in non-coding gene expression and unprocessed pseudogenes.
  • Profiles non-coding regulatory RNAs
  • Works with degraded or FFPE specimens
  • Bacterial and archaeal transcriptome profiling

Long-read RNA-seq

  • Full-length isoform characterization for therapeutic targeting
  • Alternative splicing and promoter usage mapping
  • Fusion gene and structural variant identification
  • Allele-specific expression and phasing

Reconstructs complete transcript structures for isoform-level analysis, alternative splicing discovery, and fusion gene detection.

IGV screenshot of full-length reads and splice junctions in KO and WT cells across CD44
Full-length RNA-sequencing enables complete quantification of isoforms, exon skipping, intron retention, and splice junction usage.

Transparent workflow and checkpoints

  1. Plan

    We confirm sample condition, RNA integrity, sequencing depth, and optional multiomic deliverables before kickoff.

  2. Prepare & construct

    RNA isolation and library construction with poly-A capture, ribo-depletion, or long-read protocols; QC on yield, fragment size, and library complexity.

  3. Sequence

    Paired-end or long-read sequencing on Illumina or PacBio platforms with depth monitoring against internal standards.

  4. Interpret

    Automated alignment, quantification, and differential expression analysis with pathway enrichment and data packages.

Quality Assurance Dashboards

  • Mapping rate and gene detection summaries with cohort medians and percentile bands.
  • RNA integrity and library complexity metrics reviewed prior to sequencing approval.
  • Differential expression concordance against published gold standards and your internal reference datasets.

Delivery package

  • Sequencing-ready libraries with concentration, sizing, and complexity documentation.
  • FASTQ, count matrices, and metadata formatted for immediate cloud or on-prem ingestion.
  • Interpretive report summarizing differential expression, pathway context, and recommended next steps.
Request Data Package Example
Plot of alignment metrics showing high (>90%) mapping rate and intragenic rate
High-quality library preparation generates libraries with high mapping and intragenic rates.
Pairwise plot of log-CPM showing very high replicate correlation.
Technical replicates of library preparation exceed 98% correlation of expression values.
Deliverable Summary SLA
Sequencing-ready libraries Yield, sizing, and complexity documentation. Day 10
FASTQ and count matrices Aligned reads, gene/transcript counts, metadata. Day 14
Interpretive report Differential expression, pathway enrichment, and isoform summaries. Day 16

Partner with our scientists

Share your targets, cohort size, and required timelines. We will return a scoped RNA-seq brief outlining assay mix, QC checkpoints, and downstream reporting.

  • Sample requirements: 100 ng total RNA preferred with low-input contingencies available.
  • Storage guidance: Fresh, cryopreserved, or FFPE submissions accepted with documented handling.
  • Data options: Raw, processed, and interpretive outputs available individually or bundled.
  • Support: Project scientists provide experimental planning and guidance, data reviews, and troubleshooting.
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