Performance of Evercode TCR in Activated Human T Cells

Key Takeaways

• Sensitive TCR paired chain detection in activated T cells
• Gene expression with TCR identity

Evercode TCR recovered paired TCR alpha and TCR beta chains in 82% of activated human T cells, along with their whole transcriptome.

Isolated T cells from human healthy donor PBMCs were placed in culture for 3 days and activated with CD3/CD28 beads and IL-2. Evercode Cell Fixation Kit v2 was used to stabilize the cell structure and protect the RNA transcriptome from degradation and fixed cells were stored at -80C prior to barcoding and library prep. The Evercode TCR kit generated whole transcriptome and TCR specific libraries that were sequenced on an Illumina Nextseq 550 using High Output and Mid Output Kits v2.5, respectively. The resulting data for 80,000 cells was processed with Parse Biosciences Analysis Pipeline v1.0.4.

Detection of individual TCR alpha chains (90% of cells) and beta chains (92% of cells) in activated T cells demonstrate high sensitivity of the assay. Median transcripts per cell were 2,016 while median genes per cell were 1,480 at a sequencing depth of 5,000 reads/cell.

A set of primary human T cells were assayed without activation for comparison. TCR detection rates from both the activated and primary T cells are shown below. The primary T cell dataset can be explored in detail here.

Figure 1: High TCR Chain Identification Rate. TCR detection from activated and primary T cells prepared using Evercode TCR. Among T cells with a detected TCR, the cells profiled with the TCR alpha (light pink), TCR beta (gray), or both for the same cell (purple) are represented in percentages.

Next Steps

• Download the data files generated from the preparation and analysis of the activated pan T cells. These datasets include the experimental summary report for all data, clonotype frequency file, TCR barcode report file, and AIRR file for TCR data, the digital gene matrix file, the cell metadata file, and genes file for whole transcriptome data.
• Explore the primary T cells dataset generated from 1M human T cells.
• Review a more comprehensive description of Evercode TCR in the Evercode TCR Technical Brochure.
• Visit the Evercode TCR product page for Evercode TCR product highlights.