Key Term
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Abbreviation(s)
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Definition
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8-oxo-7,8-dihydrodeoxyguanine
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OG, 8-oxoG, 8-oxodG
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An oxidized derivative of deoxyguanosine; a major product of DNA oxidation
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Abasic site
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AB
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Also: apurinic/apyrimidinic site; a location in DNA that has neither a purine nor a pyrimidine base, either spontaneously or due to DNA damage
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AP-seq
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Used to identify abasic (AP) sites genome-wide
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Apurinic/apyrimidinic site
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AP
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Also: Abasic site; a location in DNA that has neither a purine nor a pyrimidine base, either spontaneously or due to DNA damage
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Base excision repair
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BER
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Process of DNA repair during which a DNA glycosylase recognizes and removes the damaged base, leaving an abasic site that is further processed by enzymes that restore the correct base; corrects DNA damage from oxidation, deamination, and alkylation
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Benzo(a)pyrene
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BaP
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A well-studied pro-carcinogen that is metabolically activated by cytochrome P450 enzymes
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Bulky DNA adducts
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Markers of exposure to genotoxic aromatic compounds, which reflect an individual’s ability to metabolically activate carcinogens and to repair DNA damage
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ChIP-seq
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A method used to analyze protein interactions with DNA
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Chromatin immunoprecipitation
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ChIP
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An antibody-based technology used to selectively enrich specific DNA-binding proteins along with their DNA targets
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Cisplatin-seq
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Used to identify genome-wide cisplatin crosslinking sites at base resolution
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Click-code-seq
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Used for genome-wide mapping of oxidative DNA damage
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CPD-seq
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Used for genome-wide mapping of UV-induced DNA damage
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Cyclobutane pyrimidine dimer
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CPD
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A type of UV-induced helix-distorting DNA damage
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DNA damage signature
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A genome-wide map of chemically induced damage
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DNA mutational signature
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A genome-wide map of genetic sequence changes
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Endogenous
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Growing or originating from within an organism
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enTRAP-seq
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A method used to map genome-wide oxidative DNA damage
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Epigenetics
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The study of changes in gene activity caused by mechanisms other than DNA sequence changes: DNA methylation, DNA-protein interactions, chromatin accessibility, histone modifications
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Excision-seq
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A method used to map genome-wide modifications to DNA nucleobases
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Exogenous
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Growing or originating from outside an organism
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Gene expression
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The process by which the information encoded in a gene is used to direct the assembly of a protein molecule; quantified by assessing levels of transcript mRNA (RT-qPCR, RNA-seq) or protein (western blot)
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Genome
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The complete set of genes or genetic material present in a cell or an organism
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GLOE-seq
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A method for genome-wide mapping of DNA replication patterns, single-strand breaks, and lesions
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HS-damage-seq
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High sensitivity damage sequencing; used for single-nucleotide resolution damage mapping
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Immunoaffinity chromatography
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A method for separating target antibodies or antigens from a heterogenous solution
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Massively parallel sequencing technology
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A technology enabling the sequencing of many DNA strands at the same time instead of one at a time as with traditional Sanger sequencing; also called next-generation sequencing
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Next-generation sequencing
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NGS
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A technology for determining the sequence of DNA or RNA; initially called massively parallel sequencing
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Nick-seq
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A method for genome-wide mapping of DNA modifications at single-nucleotide resolution
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Nucleotide excision repair
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NER
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Pathway to remove bulky DNA lesions such as those formed by UV light, environmental mutagens, and some cancer chemotherapeutic adducts from DNA
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OG-seq
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A method for genome-wide mapping of 8-oxodG locations
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Pu-seq
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A method for genome-wide mapping of ribonucleotides in genomic DNA; polymerase usage sequencing
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Reactive oxygen species
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ROS
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A type of unstable molecule that contains oxygen and that easily reacts with other molecules in a cell
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Ribonucleotide excision repair
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RER
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Pathway to remove mis-incorporated ribonucleotides from DNA
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Ribonucleotides
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Nucleotide containing ribose as its pentose component; incorporated into the DNA as primers for lagging strand synthesis, after which they are removed by an exonucleolytic action
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Ribose-seq
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A method for genome-wide mapping of ribonucleotides in genomic DNA
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RNA-seq
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A method for quantification of mRNA in a biological sample using next-generation sequencing; allows for assessment of differential gene expression
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Sanger sequencing
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A method for determining the nucleotide sequence of DNA; also known as the chain termination method
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Single nucleotide polymorphisms
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SNPs
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A single base-pair difference in the DNA sequence
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SSB-seq
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A method for genome-wide mapping of in vivo DNA single-strand breaks (SSBs)
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SSiNGLe
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A method for genome-wide mapping of single-strand breaks (SSBs) at the nucleotide level
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Transcription factor
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TF
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A protein that controls the rate of transcription of genetic information from DNA to messenger RNA, by binding to a specific DNA sequence
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Transcriptome
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The sum total of all the messenger RNA molecules expressed from the genes of an organism
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Translesion DNA synthesis
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TLS
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Process by which specialized DNA polymerases can bypass DNA damage to replicate DNA
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XR-seq
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A method for genome-wide mapping of nucleotide excision repair
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