A streamlined solution for processing, elucidating and quality control of cyclobutane pyrimidine dimer sequencing data

Quanhu Sheng, Hui Yu, Mingrui Duan, Scott Ness, Jiapeng He, Huining Kang, Limin Jiang, John J. Wyrick, Peng Mao, Yan Guo

Published: 2021-03-16 DOI: 10.1038/s41596-021-00496-3

cyclobutane pyrimidine dimers

UV-induced DNA damage

CPD-Seq

data processing protocol

genome-wide analysis

AI 解读

Supplementary information

Supplementary Data 1

Inventory of pre-compiled resources files for CPDSeqer. Includes file name, download link, brief description and applicable steps of BED files and naked DNA normalization files.

Author Correction: Full-length sequencing of circular DNA viruses and extrachromosomal circular DNA using CIDER-Seq

Generation of heart-forming organoids from human pluripotent stem cells

Design and fabrication of wearable electronic textiles using twisted fiber-based threads

Activation of mechanoluminescent nanotransducers by focused ultrasound enables light delivery to deep-seated tissue in vivo

Chromatin accessibility profiling by ATAC-seq

Deoxyfluorination of phenols for chemoselective18F-labeling of peptides

Author Correction: cfSNV: a software tool for the sensitive detection of somatic mutations from cell-free DNA

Human primordial germ cell-like cells specified from resetting precursors develop in human hindgut organoids

An inexpensive semi-automated sample processing pipeline for cell-free RNA extraction

Application of CHyMErA Cas9-Cas12a combinatorial genome-editing platform for genetic interaction mapping and gene fragment deletion screening

查看全部

Sections

Figures

References

Supplementary information

Guy, G. P., Machlin, S. R., Ekwueme, D. U. & Yabroff, K. R. Prevalence and costs of skin cancer treatment in the US, 2002–2006 and 2007–2011. Am. J. Prev. Med. 48, 183–187 (2015).
Mouret, S. et al. Cyclobutane pyrimidine dimers are predominant DNA lesions in whole human skin exposed to UVA radiation. Proc. Natl Acad. Sci. USA 103, 13765–13770 (2006).
Mao, P., Smerdon, M. J., Roberts, S. A. & Wyrick, J. J. Chromosomal landscape of UV damage formation and repair at single-nucleotide resolution. Proc. Natl Acad. Sci. USA 113, 9057–9062 (2016).
Mao, P., Wyrick, J. J., Roberts, S. A. & Smerdon, M. J. UV-induced DNA damage and mutagenesis in chromatin. Photochem. Photobiol. 93, 216–228 (2017).
Mao, P. et al. ETS transcription factors induce a unique UV damage signature that drives recurrent mutagenesis in melanoma. Nat. Commun. 9, 2626 (2018).
Elliott, K. et al. Elevated pyrimidine dimer formation at distinct genomic bases underlies promoter mutation hotspots in UV-exposed cancers. PLoS Genet. 14, e1007849 (2018).
Premi, S. et al. Genomic sites hypersensitive to ultraviolet radiation. Proc. Natl Acad. Sci. USA 116, 24196–24205 (2019).
Lindberg, M., Bostrom, M., Elliott, K. & Larsson, E. Intragenomic variability and extended sequence patterns in the mutational signature of ultraviolet light. Proc. Natl Acad. Sci. USA 116, 20411–20417 (2019).
Brown, A. J., Mao, P., Smerdon, M. J., Wyrick, J. J. & Roberts, S. A. Nucleosome positions establish an extended mutation signature in melanoma. PLoS Genet. 14, e1007823 (2018).
Mao, P., Smerdon, M. J., Roberts, S. A. & Wyrick, J. J. Asymmetric repair of UV damage in nucleosomes imposes a DNA strand polarity on somatic mutations in skin cancer. Genome Res. 30, 12–21 (2020).
Duan, M., Selvam, K., Wyrick, J. J. & Mao, P. Genome-wide role of Rad26 in promoting transcription-coupled nucleotide excision repair in yeast chromatin. Proc. Natl Acad. Sci. USA 117, 18608–18616 (2020).
Mao, P. et al. Genome-wide maps of alkylation damage, repair, and mutagenesis in yeast reveal mechanisms of mutational heterogeneity. Genome Res. 27, 1674–1684 (2017).
Robinson, M. D. & Oshlack, A. A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biol. 11, R25 (2010).
Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).
Ramirez, F. et al. deepTools2: a next generation web server for deep-sequencing data analysis. Nucleic Acids Res. 44, W160–W165 (2016).
Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).
Ward, C. M., To, T. H. & Pederson, S. M. ngsReports: a Bioconductor package for managing FastQC reports and other NGS related log files. Bioinformatics 36, 2587–2588 (2020).
Guo, Y., Ye, F., Sheng, Q. H., Clark, T. & Samuels, D. C. Three-stage quality control strategies for DNA re-sequencing data. Brief. Bioinform. 15, 879–889 (2014).
Patel, R. K. & Jain, M. NGS QC Toolkit: a toolkit for quality control of next generation sequencing data. PLoS One 7, e30619 (2012).
Girardot, C., Scholtalbers, J., Sauer, S., Su, S. Y. & Furlong, E. E. Je, a versatile suite to handle multiplexed NGS libraries with unique molecular identifiers. BMC Bioinformatics 17, 419 (2016).
Andrews, S. A Quality Control Tool for High Throughput Sequence Data. Available at http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ (2010).
Guo, Y. et al. Multi-perspective quality control of Illumina exome sequencing data using QC3. Genomics 103, 323–328 (2014).
Yu, H. et al. Non-canonical RNA-DNA differences and other human genomic features are enriched within very short tandem repeats. PLoS Comput. Biol. 16, e1007968 (2020).

A streamlined solution for processing, elucidating and quality control of cyclobutane pyrimidine dimer sequencing data

Supplementary information

推荐阅读