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Data availability
RNA-seq data from H-STS replicates were downloaded from Gene Expression Omnibus, via accession code GSE96760. Raw RNA-seq data from Sahlgrenska University Hospital small-intestinal GEPNET tumors have been deposited in the European Genome-phenome Archive under accession code EGAS00001003358. Restrictions for download include submission of a data access application to a local data-access committee. The agreement met requires that the data be used for cancer research only and that variants cannot be cross-searched in other databases.
Code availability
Code used for transcriptomic classification is available at http://bitbucket.org/jowkar/gepnet_classification/.
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Acknowledgements
The results published here are based partly on previously processed data generated with the TCGA database (http://cancergenome.nih.gov/). E. Larsson (Lekholm) is acknowledged for previous funding and supervision of J. Karlsson. The groups are also funded by the Swedish Cancer Society, Vetenskapsrådet, Familjen Erling-Persson Foundation, Knut and Alice Wallenberg Foundation, Sjöberg Foundation, Assar Gabrielsson Foundation and Wilhelm and Martina Lundgren’s Foundations.
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Supplementary information
Supplementary Information
Supplementary Note and Supplementary Figure 1
Supplementary Table 1
Six-nearest-neighbor classification of H-STS replicates, based on Spearman correlation. The cancer types of the top six correlating TCGA cancer samples and their respective frequency and average correlation.
Supplementary Table 2
Six-nearest-neighbor classification of small intestinal GEPNETs from Sahlgrenska University Hospital patients. The cancer types of the top six correlating TCGA samples and their respective frequencies are shown.
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Hofving, T., Karlsson, J., Nilsson, O. et al. H-STS, L-STS and KRJ-I are not authentic GEPNET cell lines. Nat Genet 51, 1426–1427 (2019). https://doi.org/10.1038/s41588-019-0490-z
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DOI: https://doi.org/10.1038/s41588-019-0490-z