SCLC HTGEdge RNAseq dataset

Published: 9 March 2021| Version 1 | DOI: 10.17632/7n6rk5zgjj.1
David Dora


Samples 64 FFPE samples were provided as unstained and H&E slides. Macrodissection was performed if indicated on the slide. Macrodissection is indicated in the "Samples" tab. Macrodissection marks were provided by the customer. Slides were scraped and lysed at 12.5 mm2/35 µl for all samples except those marked in column U in the "Samples" tab. Please see the "Samples" tab for more information on samples. Assay HTG EdgeSeq Oncology Biomarker Panel Each sample was run at 12.5 mm2/well, except for 26/I and 33/III (run at 6 mm2/well) and 134/III (run at 5 mm2/well). All samples were run as singletons. Samples were tagged and individually cleaned up, quantitated, and loaded onto an Illumina NextSeq Sequencing run designation is 15-Sep-2017 Data and QC All samples passed QC. Sample 271-I was close to the QC threshold, but still passed. Raw data, CPM standardized data, and Normalized data have been provided on separate tabs. The Sample Information tab shows the samples in this run and their associated information. We performed a second run of 271-I, but the QC threshold was in the same place. This second run had more reads and is available on request. Please address any questions to Debrah Thompson/HTG 26.szept.17 In this cohort 32 histologically confirmed, early stage SCLC primary tumor and matched metastases samples are included. Under the "normalized" spreadsheet patient samples are categorized to Neuroendocrine (NE)-low and NE-high according to gene expression data previously publised (Rudin et al, 2019) Rudin CM, Poirier JT, Byers LA, Dive C, Dowlati A, George J, Heymach JV, Johnson JE, Lehman JM, MacPherson D et al (2019) Molecular subtypes of small cell lung cancer: a synthesis of human and mouse model data. Nat Rev Cancer 19, 289–297.


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Semmelweis Egyetem


RNA, Expression Analysis