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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.
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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.
Experimental Summary Report (HTML)
Clonotype Frequency (TSV)
Barcode Report (TSV)
The Adaptive Immune Receptor Repertoire (AIRR) File (TSV)
Whole Transcriptome Results
Digital Gene Expression (DGE) Matrix (1.5 GB)
All Gene (CSV)
Cell Metadata (CSV)
Primary T cells dataset