The immune repertoire within a sample is represented in each spectratyping plot by the range of CDR3 lengths and their pattern of distribution. Reads for identified clones are arranged along the X‑axis according to the variable gene identity and the Y‑axis according to the CDR3 nucleotide length. The variable gene order reflects the gene position within the IGH locus. Dots are separated vertically along the Y‑axis by 3 nucleotides (one codon), the higher up the Y‑axis the longer the CDR3 region. Circle size indicates the frequency of a particular variable gene-CDR3 nucleotide length combination within the dataset. Circle color represents a fourth metric specific to each graph (for example, Shannon Diversity, evenness, clone frequency). Key repertoire metrics are displayed along the lower margin of the plot.
In Ion Reporter™ Software, the spectratyping plots are interactive, allowing you to adjust the data and access clone details. For more information, see Adjust data and access clone details in spectratyping plots.
Note: T-cell Leukemia (Jurkat) Total RNA is derived from a cell line consisting of a single T‑cell clonotype. Running the Oncomine™ TCR Beta‑LR Assay on Jurkat Total RNA should detect a single clonotype (a single spot on spectratyping plot).
Sequencing of a B cell line such as Ramos will reveal a single dominating clonal lineage, indicated by a single spot on the spectratyping plot.