Parse Biosciences - Scalable Single Cell Sequencing
Evercode Whole Transcriptome Datasets

Mouse Liver Performance Data for Whole Transcriptome v2 Products

Key takeaways 

  • Sensitivity improved in adult mouse liver samples
  • Unbiased gene expression
  • Higher number of differentially expressed genes detected

More genes with less sequencing

Evercode WT v2 detected substantially more genes and transcripts in an adult mouse liver sample compared to the Evercode WT v1 sample. The gene detection of the technology versions are plotted across a range of sequencing depths (Figure 1).

The increased sensitivity of the Evercode WT v2 product was pronounced in adult mouse liver - 79% more genes were detected at 150,000 reads/cell. The sensitivity improvement is rapidly appreciated, with 66% more genes at a targeted sequencing depth of 30,000 reads/cell.

Downsample-MouseLiverFigure 1. Gene Detection for Adult Mouse Liver Nuclei. Identical adult mouse liver samples were prepared in parallel with Evercode WT v1 and Evercode WT v2.  A sublibrary from each experiment was sequenced to saturation and processed using the Parse Biosciences data analysis pipeline.

Unbiased gene expression

A gene correlation plots confirms unbiased gene expression of the adult mouse liver sample prepared with Evercode WT v1 and Evercode WT v2 (r2=0.901) (Figure 2).  

Researchers can transition to Evercode Whole Transcriptome Solution v2 kits to benefit from greater gene sensitivity and improved sample robustness while integrating data with other studies.


Figure 2. Gene Expression Correlation Between Evercode WT v1 and Evercode WT v2 in Adult Mouse Liver Nuclei. The average gene expression (log average transcripts per million) between the Evercode WT v2 and Evercode WT v1 results was compared. The r2 value = 0.901 indicates a high degree of correlation in gene expression between the different Evercode WT chemistry versions.

Higher number of differentially expressed genes

An analysis of the differentially expressed genes across cell types confirms the uniformity of sensitivity improvements across the cell populations. Evercode WT v2 consistently detected more differentially expressed genes than Evercode WT v1, regardless of cell type (Figure 3). 


Figure 3. Differentially Expressed Gene Comparison Between Evercode WT v1 and Evercode WT v2 in Adult Mouse Liver Nuclei. Analysis of the cell types in the liver data showed consistently more differentially expressed genes detected across all cell types for Evercode WT v2.

Next Steps 

  • Download the data files generated from the preparation and analysis of the adult mouse liver nuclei samples. These datasets include the experimental summary report, the digital gene matrix file, the cell metadata file, and genes file.
  • Explore more by reviewing the full experimental plan and detailed results across multiple sample types in the bioRxiv paper.