Analysis of transcriptome data in SS. (A) Schematic of experimental design. SC and patient-matched normal CD4⁺ T lymphocytes were purified by flow cytometry, with SC sorted using Vβ antibodies to the malignant clone, followed by paired-end RNA-Seq. Sequence reads underwent genome alignment followed by assembly into gene transcripts and determination of differential expression. Scripture was used as an orthogonal means of transcriptome assembly, while both Scripture and Trinity were used for novel transcript discovery. (B) RNA-Seq tracks over the T-cell receptor beta locus, with normalized read scale between each SC and normal matched CD4⁺ T-cell control. Clonal Vβ transcript peaks are off-scale in SC, with read number shown next to each. (C) Transcript distribution by category in SS. Transcripts were annotated using a conglomeration of UCSC, Gencode, RefSeq, and Ensembl as reference. An FPKM > 1.5 was required in either SC or control cells. (D) Differentially expressed protein-coding, noncoding, pseudogene, and unannotated novel transcripts in SS.