Extended Data Fig. 5: Brachyury is highly expressed in chordoma cell lines.
From: Small-molecule targeting of brachyury transcription factor addiction in chordoma
a, Immunoblot analysis of chordoma and chondrosarcoma cell lines. Chordoma cell lines selectively express high levels of the brachyury protein. The experiment was performed once. b, Expression of T and MAX, as measured by RNA-sequencing, across 935 non-chordoma cancer cell lines derived from diverse tumor types. Data were generated as part of the Broad Institute Cancer Cell Line Encyclopedia (quantified data obtained from: https://ocg.cancer.gov/ctd2-data-project/translational-genomics-research-institute-quantified-cancer-cell-line-encyclopedia). Boxplots depict the inner quartiles (boxes) and median value (horizontal line) with whiskers representing 1.5 × the interquartile range. c, Gene-expression levels of 115 super-enhancer- (SE-) associated transcription factors in five chordoma cell lines (points), ranked by mean expression (horizontal ticks). d, T is amplified in the JHC7 chordoma cell line. Genomic copy-number alterations, inferred from whole-exome sequencing data, in five chordoma cell lines. A region of 2.06 Mb around the T locus on chromosome 6 shows 26-fold amplification in JHC7. This finding is consistent with the 2.6-Mb amplicon inferred from ChIP-seq whole-cell extract.
