Supporting code for the analysis of a single cell RNAseq (10XGenomics platform) benchmark dataset, named BE1, providing a controlled heterogeneity environment using lung cancer cell lines characterised by expressing seven different driver genes (EGFR, ALK, MET, ERBB2, KRAS, BRAF, ROS1). BE1 is part of the WP3 of Elixir Single Cell Omics implementation study. BE1 fastq data have been loaded on GEO: GSE243665 (access under embargo till Sept 1st 2024). 10XGenomics count matrices and annotated derivatives are available at 10.6084/m9.figshare.23939481. Further supporting information on genomics and transcriptomis data (CCLE) and on the drive genes targets (see below BE1 structure) are available at 10.6084/m9.figshare.23284748. BE1 includes scRNAseq for the following lung cancer cell lines:
- PC9, 4492 sequenced cells (EGFR Del19, activating mutation, PMID: Simonetti et al. (2010)
- A549, 6898 sequenced cells (KRAS p.G12S, growth and proliferation, PMID: Yoon et al. (2010)
- NCI-H596 (HTB178), 2965 sequenced cells (MET Del14 , enhanced protection from apoptosis and cellular migration PMID: Cerqua et al. (2022)
- NCI-H1395 (CRL5868), 2673 sequenced cells (BRAF p.G469A, gain of function, resistant to all tested MEK +/− BRAF inhibitors, PMID: Negrao et al. (2020))
- DV90, 2998 sequenced cells (ERBB2 p.V842I, increases kinase activity, PMID: Boese et al. (2013)
- HCC78, 2748 sequenced cells (SLC34A2-ROS1 Fusion, ROS1 inhibitors have antiproliferative effect PMID: Davies et al. (2012)
- CCL.185.IG, 6354 sequenced cells EML4-ALK Fusion-A549 Isogenic Cell
install.packages("devtools")
devtools::install_git("https://github.com/kendomaniac/BE1")