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Whole Transcriptome scRNAseq
Whole Transcriptome scRNAseq

Full Transcriptome Insight from Single Cell Sequencing

1’
Review

Why Single Cell Whole Transcriptome Sequencing

Standard single-cell RNA sequencing (scRNA-seq) provides only a partial view of cellular activity.

mRNA comprises only a few percent of the total RNA content in a cell. Moreover, traditional methods focus solely on counting the ends of mRNA molecules, overlooking critical information contained along the length of the mRNA.

Whole-transcriptome approaches allow you to move beyond simple mRNA “end-counting” to capture the full transcriptome, including:

  • Coding and Non-Coding RNA: Capture both poly(A) and non-poly(A) species, including lncRNA and microRNA, to map the complete regulatory landscape.
  • Full Gene Body Coverage: Access sequence information across the entire transcript. Identify expressed mutations, SNPs, and alternative splicing at the single cell level across the entire transcript.

What is the Difference between Whole Transcriptome Sequencing and Standard scRNA-seq

Standard Single Cell RNA-seq (scRNA-seq)

• Detects mRNA
• Requires Poly(A) tail
• Only the 3’ or 5’ end of the gene is counted
• Isoform analysis is limited to the 3’ or 5’ end of the transcript
• Variant calling near the 3’ or 5’ end only

Whole Transcriptome scRNA-seq

• Detects coding and non-coding RNA (lncRNA, miRNA)
• Detects non-Poly(A) or partially degraded mRNA
• Full-length RNA is sequenced
• Isoform detection across the entire transcript
• Variant calling across the entire transcript

Demo Data

Mouse bladder cancer whole transcriptome single-nucleus sequencing data
Figure 1: Mouse bladder cancer FFPE single-nucleus sequencing data clustered by gene expression and overlaid with non-coding RNA expression.

Get More data from your samples

As research moves toward more detailed multi-omic profiling, capturing the full transcriptome ensures your datasets remain relevant and comprehensive.
Whether you are investigating complex disease states or developmental pathways, you can now access the full breadth of RNA information without the limitations of panel-based or end-counting assays.

Contact us to learn about whole transcriptome scRNA-seq options

We help researchers move beyond standard transcriptomics to uncover deeper biological insights. Contact us to learn about our full suite of single-cell solutions.

Whole Transcriptome scRNAseq

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A post by Yingting Wang

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