Full-Length Transcriptome Profiling Combined with Long- and Short-Read Sequencing

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Full-Length Transcriptome Profiling Combined with Long- and Short-Read Sequencing

CD Genomics provides comprehensive transcriptome profiling services using both short-read (Illumina) and long-read RNA sequencing technologies (PacBio Iso-Seq and ONT nanopore RNA sequencing). Our integrated analysis will facilitate the discoveries of novel transcripts and genes, identification of alternative splicing, and detection of allele-specific expression.

Methodologies for Transcriptome Profiling

Single-stranded RNA.

Transcriptomics is the study of the transcript catalog of a cell, tissue, or organism under specific conditions (physiological condition, developmental stage, and external environment), involving protein-coding messenger RNA (mRNA) and non-coding RNA (ncRNA), such as transfer RNA (tRNA), ribosomal RNA (rRNA), and among others. Due to the complexity of the transcriptome, transcriptome analysis relies heavily on the availability of high-throughput tools. RNA sequencing using short-read sequencing (Illumina) is currently the standard and widely used approach for transcript profiling. This method is particularly suitable for large-scale, high-throughput studies. While the emerging long-read RNA-seq technologies, such as PacBio SMRT sequencing and nanopore cDNA/RNA sequencing, offer new ways to investigate the transcriptome and its function.

Methodologies for Transcriptome Profiling

Representative Technologies Read lengths Advantages Disavantages Main Applications
Short-read sequencing technologies  Illumina ~300bp

-High throughput.


-Effective in quantifying transcript abundance.

-Read length limitations.

-Need to amplify or fragment.

-Complex splicing.

-Amplification bias.

-Identification and quantification of transcripts.

-Detection of gene expression changes.

Thermo Fisher (Ion Torrent) ~600bp
MGI (DNBSEQ) ~400bp
Long-read sequencing technologies Pacific Biosciences (PacBio) ~15 kb

-Long-read length exceeds the lengths of most transcripts.

-Without the need to amplify or fragment.

-Direct cDNA/RNA sequencing(ONT).

-Relatively high cost.

-Relatively high error rate.

-Relatively lower throughput.

-Characterization of full-length transcript.

-Systematical characterization of the complexity of transcript isoforms.

-Identification of gene fusions.

-Identification of RNA base modifications. (ONT)

-Analysis of poly-A tail lengths. (ONT)

Oxford Nanopore Technologies (ONT) > 30 kb

Outstanding Advantages of Our Services

  • The short reads correct the long reads to produce more accurate transcriptome information.
  • The combination of short-read and long-read RNA-seq enables systematical characterization of the complexity of transcript isoforms.
  • The combination of short-read and long-read RNA-seq enables more comprehensive transcriptome analysis.

Workflow of Our Service

Workflow of Our Service-CD Genomics.

Sample Requirements

-Sample type: Blood, tissues, cells, RNA samples (total RNA or poly-A+ RNA), and more.
-RNA amount ≥ 2 μg, RNA concentration ≥ 50 ng/μL, OD260/280=1.8~2.0.
-All RNA samples are validated for purity and quantity.

Sequencing platforms

-Illumina NovaSeq and HiSeq platform.
-PacBio Sequel II sequencing system.
-Nanopore PromethION sequencing platform.

Analysis Pipeline and Contents

Analysis Pipeline and Contents-CD Genomics.

Why Do You Choose Us?

  • Advanced instruments and highly experienced analysts.
  • Proper methods of sample preparation and RNA extraction.
  • Customized service to customer satisfaction.
  • Complete analytical study reports.
  • Our customer service representatives are available 24 hours a day from Monday to Friday.

With multiple specialists and years of experience in RNA-seq, we guarantee you high-quality data and integrated bioinformatics analyses. If you are interested in our short-read and long-read RNA sequencing, please feel free to contact us. We are looking forward to working on your next project.


  1. Dong, X., et al. (2021). "The long and the short of it: unlocking nanopore long-read RNA sequencing data with short-read differential expression analysis tools." NAR genomics and bioinformatics, 3(2), lqab028.
  2. Zheng, X., et al. (2021). "Short-read and long-read RNA sequencing of mouse hematopoietic stem cells at bulk and single-cell levels." Scientific Data, 8(1), 1-10.
  3. Huang, K. K., et al. (2021). "Long-read transcriptome sequencing reveals abundant promoter diversity in distinct molecular subtypes of gastric cancer." Genome biology, 22(1), 1-24.
For Research Use Only. Not for use in diagnostic procedures.

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