What is whole transcriptome analysis?
Whole-transcriptome analysis is the sequencing and characterization of the total RNA within a sample. It is of growing importance in understanding how altered expression of genetic variants contributes to complex diseases such as cancer, diabetes, and heart disease. Analysis of genome-wide differential RNA expression provides researchers with greater insights into biological pathways and molecular mechanisms that regulate cell fate, development, and disease progression.
Thermo Fisher Scientific offers an extensive range of products, from RNA isolation and microarray labeling reagents to next-generation sequencing reagents and instrumentation, to help capture the complexity of whole-transcriptome analysis for your research.
Whole transcriptome analysis depends on RNA quality
RNA-seq typically consists of RNA isolation, conversion of RNA into complementary cDNA, preparation of the sequence library, and finally, NGS sequencing.
After RNA isolation, RNA quality is typically assigned an RNA Integrity Number (RIN). These RIN estimates, ranging between 1 (lowest quality) and 10 (highest quality), are essential for RNA-Seq experiments as low-quality RNA samples (RIN <6) have a high probability of affecting sequencing results, which can cause erroneous conclusions.
Read about methods to check RNA integrity
Prepare high-quality RNA for whole transcriptome analysis with one of Thermo Fisher Scientific’s RNA extraction kits
What is the difference between a whole exome and a whole transcriptome?
| Type of sequencing | Genetic regions targeted | Variant detection | Output |
| Whole transcriptome sequencing | Entire transcriptome: exons and introns | Yes | RNA transcripts converted to cDNA |
| Whole exome sequencing | Exons (coding regions of genes) | Limited to coding regions | DNA sequences of exons |
mRNA enrichment for transcriptome analysis
Because mRNA is a minor fraction of the total RNA in a cell, enrichment of RNA transcripts helps increase the amount of high-quality mRNA in the sample. Several methods are available including positive selection via poly-A beads or removal of ribosomal RNA.
Compare mRNA extraction and enrichment kits
Learn more about transcriptome enrichment by rRNA depletion
What is the difference between whole transcriptome sequencing and mRNA sequencing?
| Type of sequencing | RNAs targeted | Studies used for | Complexity and cost |
| Whole transcriptome sequencing | Coding and non-coding mRNA | Gene expression and regulation | High |
| mRNA sequencing | Coding mRNA | Gene expression | Less high |
Arrays or sequencing?
Are you leveraging the appropriate technology for your research? The scientific community is now widely acknowledging that there are specific applications best served by arrays and others by RNA sequencing (RNA-seq). Additionally, many see opportunities to harness the power of both technologies for expression studies.
Microarray analysis
Gene arrays have become a powerful approach for comparing complex sample RNA populations. Using array analysis, the expression profiles of normal and tumor tissues, treated and untreated cell cultures, developmental stages of an organism or tissue, and different tissues can be compared to gain a better understanding of the Transcriptome.
Learn more about transcriptome profiling with microarrays
Explore Applied Biosystems microarray solutions
Next generation sequencing
With a dynamic range to detect subtle changes in expression level in a hypothesis-neutral environment, next generation sequencing helps provide an understanding of biological response to stimuli or environmental changes. Perform whole transcriptome sequencing for identification and quantification of novel and known transcripts, or targeted transcriptome sequencing for simple, gene-level expression analysis.
Explore Ion Torrent RNA sequencing solutions
RNA sequencing sample preparation workflow
For Research Use Only. Not for use in diagnostic procedures.