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  • br d METHODS DETAILS br B Cell culture

    2022-04-25


    d METHODS DETAILS
    B Cell culture and isolation of single FLAG tag Peptide B DNA extraction and amplification
    B Library preparation, sequencing and alignment B Genotyping of cell line samples
    B Mutation discovery
    B Mutational catalogs from stock cell lines and cell line clones
    B Clonality of the cell line clones
    B Mutational catalogs from single cells B Mutational catalogs from PDX models B Base substitution and indel classification B Kataegis quantification
    B Sequence context quantification and enrichment analysis
    B Doubling time measurements B Pathogen detection
    B Identification of L1 mobile element insertions acquired in vitro 
    B RNA sequencing and analysis
    B 1,001 cell line panel expression and methylation datasets
    d QUANTIFICATION AND STATISTICAL ANALYSIS B Mutational Signatures Analysis
    B Relationships between somatic retrotransposition and APOBEC-associated SBS2 and SBS13
    d DATA AND SOFTWARE AVAILABILITY
    SUPPLEMENTAL INFORMATION
    Supplemental Information can be found with this article online at https://doi.
    ACKNOWLEDGMENTS
    This work was supported by Wellcome grants 098051 and 206194; Cancer Research UK Grand Challenge Award C98/A24032 to L.B.A. and B.O.; the Li Ka Shing Foundation and National Institute for Health Research Oxford Biomedical Research Centre to D.C.W.; ED481A-2016/151 from Xunta de Ga-licia to B.R.–M. The use of pre-embargo PCAWG project mutational signatures data was approved by the PCAWG Steering Committee (excluding co-author P.J.C.) and the Mutational Signatures Working Group. Particular thanks to Jaegil Kim, Nicholas Haradhvala, Gaddy Getz, Steve Rozen, and other mem-bers of the PCAWG Working Group and to Graham Bignell for annotating mu-tation catalogs from 1,001 cell lines.
    AUTHOR CONTRIBUTIONS
    DECLARATION OF INTERESTS
    During manuscript revision, M.P. was employed at Vertex Pharmaceuticals. U.M. is employed at AstraZeneca. Both were full-time employees of the Well-come Sanger Institute at the time of the primary manuscript draft preparation. M.R.S. is a member of the Grail Scientific Advisory Board.
    REFERENCES
    Callahan, J., Pai, S., Cotter, M., and Robertson, E.S. (1999). Distinct patterns of viral antigen expression in Epstein-Barr virus and Kaposi’s sarcoma-associ-ated herpesvirus coinfected body-cavity-based lymphoma cell lines: potential switches in latent gene expression due to coinfection. Virology 262, 18–30.
    Cesarman, E., Moore, P.S., Rao, P.H., Inghirami, G., Knowles, D.M., and Chang, Y. (1995). FLAG tag Peptide In vitro establishment and characterization of two acquired immunodeficiency syndrome-related lymphoma cell lines (BC-1 and BC-2) containing Kaposi’s sarcoma-associated herpesvirus-like (KSHV) DNA se-quences. Blood 86, 2708–2714.
    Conticello, S.G. (2008). The AID/APOBEC family of nucleic acid mutators.
    Freitas, T.A., Li, P.E., Scholz, M.B., and Chain, P.S. (2015). Accurate read-based metagenome characterization using a hierarchical suite of unique sig-natures. Nucleic Acids Res. 43, e69.
    Petljak, M., and Alexandrov, L.B. (2016). Understanding mutagenesis through delineation of mutational signatures in human cancer. Carcinogenesis 37, 531–540.
    Pfeifer, G.P. (2006). Mutagenesis at methylated CpG sequences. Curr. Top.
    mutations in yeast and in human cancers can arise from damaged long sin-gle-strand DNA regions. Mol. Cell 46, 424–435.
    Schneider-Ga¨dicke, A., and Schwarz, E. (1986). Different human cervical car-cinoma cell lines show similar transcription patterns of human papillomavirus type 18 early genes. EMBO J. 5, 2285–2292.
    STAR+METHODS
    KEY RESOURCES TABLE
    REAGENT or RESOURCE
    SOURCE IDENTIFIER
    Biological Samples
    1,001 human cancer cell lines COSMIC Cell Line Project https://cancer.sanger.ac.uk/cell_lines
    Critical Commercial Assays
    Custom SureSelect Library Prep Kit
    Agilent
    SureSelect Targeted Enrichment kit
    Agilent
    illustra GenomiPhi V2 DNA amplification kit
    GE Healthcare
    Ribo-Zero rRNA Removal Kit
    Illumina
    KAPA Stranded mRNA-Seq Kit
    Kapa Biosystems
    ERCC RNA Spike-In Mix
    Deposited Data
    DNA sequence data
    This paper
    RNA sequence data
    This paper
    Software and Algorithms
    Mapping workflow
    Cancer, Aging and Somatic Mutation https://dockstore.org/containers/quay.io/
    group, Wellcome Sanger Institute
    wtsicgp/dockstore-cgpmap
    Mutation calling workflows
    Cancer, Aging and Somatic Mutation Whole-exome: https://dockstore.org/
    group, Wellcome Sanger Institute containers/quay.io/wtsicgp/dockstore-cgpwxs
    Whole-genome: https://dockstore.org/
    containers/quay.io/wtsicgp/dockstore-cgpwgs
    vafCorrect
    Cancer, Aging and Somatic Mutation https://github.com/cancerit/vafCorrect