Figure 1. (A) Number of 8-oxodGs per million of dGs (8-oxodg/10<sup>6</sup> dG) measured by LC-MS/MS in untreated (NT), UV-irradiated (UV) and NAC-treated.

Slides:

Advertisements

Similar presentations

Figure 3. (A) Effect of the ON length on the HTT mRNA knockdown efficiency. LNA/DNA CAG 10- to 19-mer PS ONs were transfected at 100 nM concentration into.

Advertisements

Figure 1. Schematic of the corA leader mRNA

Figure 2. BRCA2–RAD51 complexes organize into filament-like structures

Figure 1. Unified models predicting gene regulation based on landscapes of gene-regulating factors. For each gene, position specific combinatorial patterns.

Figure 1. Gene expression analysis

Figure 1. The scheme of RCAS

Figure 1. Overview of the Ritornello approach

Figure 1. AsCpf1 and LbCpf1-mediated gene editing in human cells

Figure 1. Annotation and characterization of genomic target of p63 in mouse keratinocytes (MK) based on ChIP-Seq. (A) Scatterplot representing high degree.

Figure 2. The graphic integration of CNAs with altered expression genes in lung AD and SCC. The red lines represent the amplification regions for CNA and.

Figure 1. A3B NTD mediates enzyme activity and oligomerization

From: Learning by Working in Big Cities

Fig. 1 Nodes in a conceptual knowledge graph

Figure 1: Pneumomediastinum and subcutaneous emphysema as indicated by the arrows. From: Pneumomediastinum and subcutaneous emphysema after successful.

From: DynaMIT: the dynamic motif integration toolkit

Scheme 1. Rotation around the glycosidic bond leads to the syn-conformation, that in turn, stabilizes the 8-oxoG:A basepair mismatch. Biophysical properties,

Figure 2. Force and concentration dependence of the rate at which ScTopA initiates DNA relaxation. (A) The initial time lag (ITL) for ScTopA activity displays.

FIG. 1.— Correlation of RPKM between (A) 1,509 TE families estimated from B73–104 and the in silico data with 5 outliers indicated in gray; (B) 1,514 TE.

Figure 1. PARP1 binds to abasic sites and DNA ends as a monomer

Fig. 1. RUbioSeq pipelines for exome variant detection and BS-Seq analyses. Dark gray boxes correspond to the main steps of the pipelines. Light gray boxes.

Figure 1. Motif 1 is required for RP gene transcription in cells

Figure 3: Full-body skeletal scintigraphy.

Figure 2. Ritornello captures the FLD from single-end sequencing data

Figure 1. The flow chart illustrates the construction process of anti-CRISPRdb, and the information that users can obtain from anti-CRISPRdb. From: Anti-CRISPRdb:

Figure 3. Schematic of the parameters to assess junctions in SpliceMap

Figure 1. Loss of H2Bub1 promotes mutagenesis under conditions of replicative stress. (A) The graph shows the rates of spontaneous Canr mutation.

Figure 1. Workflow of the LISH assay. Step 1

Figure 1. Distinct chromatin regions isolated by the N-ChroP strategy

Figure 1. Effect of acute TNF treatment on transcription in human SGBS adipocytes as assessed by RNA-seq and RNAPII ChIP-seq. Following 10 days in vitro.

Figure 1. Complete work-flow of the Scasat

Figure 2. Workflow of MethMotif Batch Query

From: Dynamic protein–RNA interactions in mediating splicing catalysis

Figure 3. Schematic representation of co-expression networks for BipA, SidD, and Erg11 encoding genes. Genes are represented by circles, with positive.

Figure 4. (A) Scatterplot of RPC4 T statistic (between TP0 and TP36) for the indicated groups of isolated tRNA genes (RPC4 peak only, n = 35; RPC4 + H3K4me3.

Figure 1. (A) The VEGF promoter PQS and scheme of G oxidation to OG, as well as (B) the proposed APE1-dependent pathway ... Figure 1. (A) The VEGF promoter.

Figure 1. A CRISPR/Cas9 synthetic lethal screen with PRMT5 inhibitor EPZ in H2171 cell line. (A) A pie chart ... Figure 1. A CRISPR/Cas9 synthetic.

Figure 1. Circular taxonomy tree based on the species that were sequenced in our study. Unless provided in the caption above, the following copyright applies.

Figure 1. Overview of the workflow of NetworkAnalyst 3.0.

Figure 7. Primary cells from prostate tumours are more sensitive to ML than adjacent non-cancerous cells from the ... Figure 7. Primary cells from.

Figure 4. (A) Venn diagram showing the overlap of peaks differentially changed in DHT as compared to NT with peaks ... Figure 4. (A) Venn diagram showing.

Figure 1. AML containing the t(8:21) are extremely sensitive to CDK inhibitors. (A–C) Alamar blue assays were used to ... Figure 1. AML containing the.

Figure 1. Effect of random T/A→dU/A substitutions on transcription by T7 RNAP using a 321 bp DNA transcription template ... Figure 1. Effect of random.

Figure 1. Position and number of NLS improves genome editing by AsCas12a, LbCas12a and FnoCas12a. (A) General schematic ... Figure 1. Position and number.

Figure 2. Ectopic expression of PLZF modulates H3K27ac at enhancer regions in myeloid cells. (A) Box plots showing ... Figure 2. Ectopic expression of.

Figure 1. BRCA1-associated R-Loop accumulation at a non-coding region upstream of ESR1 locus. (A) Alignment of DRIP-seq ... Figure 1. BRCA1-associated.

Figure 1. The 12 species in this study and details of the improved G4-seq method. (A) Phylogenetic representation of ... Figure 1. The 12 species in this.

Figure 1. Nanopore methylation calls are consistent with expected results and established technologies. (A) Metaplot of ... Figure 1. Nanopore methylation.

Point estimates with ... Point estimates with 95% CI. HR: hip replacement; KR: knee replacement. Unless provided in the caption above, the following copyright.

FIGURE 1 Participant flow diagram. Exercise Counseling Clinic (ECC).

Figure 6. The DNA lyase activity of hNTHL1 contributes to the processing of lesions in nucleosomes, even in the ... Figure 6. The DNA lyase activity of.

Figure 1. Analysis of human TRIM5α protein with Blast-Search and PhyML+SMS ‘One click’ workflow. (A) NGPhylogeny.fr ... Figure 1. Analysis of human TRIM5α.

FIGURE 1 Study consort diagram

Figure 1. Illustration of DGR systems and their prediction using myDGR

Figure 1. Prediction result for birch pollen allergen Bet v 1 (PDB: 1bv1), as obtained by comparison to the cherry ... Figure 1. Prediction result for.

Figure 1. PaintOmics 3 workflow diagram

Figure 1. Yvis platform overview

Figure 1. Accumulation kinetics of TC-NER factors reveal a CSA independent UVSSA recruitment. (A) Representative images ... Figure 1. Accumulation kinetics.

Fig. 1. —Synteny analysis of melon chromosome 1 (brown) and cucumber chromosome 7 (green) based on melon-cucumber ... Fig. 1. —Synteny analysis of melon.

Figure 4. MTase JHP1050 inactivation causes phenotypic effects that vary between strains: growth, viability and ... Figure 4. MTase JHP1050 inactivation.

Figure 1. Scheme of a phosphorothioated-terminal hairpin formation and self-priming extension (PS-THSP) for selection ... Figure 1. Scheme of a phosphorothioated-terminal.

Figure 1. Analysis of ERV expression dynamics in early embryogenesis by WGCNA. (A) Principal component analysis of ... Figure 1. Analysis of ERV expression.

Figure 1 Genetic results. No case had more than one diagnostic result

Figure 1. CSB does not affect the recruitment of OGG1 to oxidative DNA damage. (A) Representative stills of time-lapse ... Figure 1. CSB does not affect.

Figure 1. DNA-guided RNA cleavage activity

Figure 1 The workflow of CAR development from a hybridoma

Figure 1. Crystal structures of Rim1

Figure 1 Mechanisms of mitral regurgitation.

Figure 1. Removal of the 2B subdomain activates Rep monomer unwinding

Figure 5. The endonucleolytic product from PfuPCNA/MR activity is displaced from dsDNA. Results from real-time ... Figure 5. The endonucleolytic product.

Figure 1. (A) Overview of ENPD including data source, data processing and features. Transcriptomes from TSA, genomes ... Figure 1. (A) Overview of ENPD.

Presentation transcript:

Figure 1. (A) Number of 8-oxodGs per million of dGs (8-oxodg/10<sup>6</sup> dG) measured by LC-MS/MS in untreated (NT), UV-irradiated (UV) and NAC-treated (NAC) MCF10A cells, as indicated. (B) Efficiency of polyclonal anti-8-oxodG from Millipore (Ab M), or monoclonal anti-8-oxodG from Trevigen (Ab T), and of anti-IgG antibodies in immuno-precipitation assays of 8-oxodG-containing synthetic ssDNA or G4 structures, as indicated. (C) Anti-8oxodG immuno-precipitation assay (% of input DNA, measured by qPCR; y axis) with equal amount (64 pg) of both synthetic oligonucleotides (8-oxodG-100mer and dG-100mer) added to 1 μg of NAC-treated genomic DNA. C1 and C2 indicate the same genomic negative control regions as in panel G. (D) Screenshot from the UCSC genome browser of 3.7 Mb from human chromosome 19 showing (top to bottom): OxiDIP-Seq signal profile, 8-oxodG peaks (dots), Input DNA, CG%, and RefSeq genes. (E) Screenshot from the UCSC genome browser of 2.1 Mb from human chromosome 19 showing OxiDIP-Seq signal profiles of two independent experiments (Exp #1 and #2) and Input DNA. (F) Scatter plot showing the correlation of the OxiDIP-Seq signals obtained in two independent experiments (Exp #1 and #2). Pearson's correlation coefficient (r), as indicated. Figure inset shows magnification of the high-density region. (G) OxiDIP-qPCR showing 8-oxodG enrichments (% of Input DNA) at eight different positive (#1–8) and two negative (C1, C2) regions, in untreated (black bar), UV- (gray), or NAC-treated (white) MCF10A cells. Screenshots from the UCSC genome browser show genomic position, 8-oxodG signal intensity, and qPCR probes (black box) of the selected regions. Data from two independent OxiDIP-qPCR assays are shown (±S.D.; P< 0.05 for all comparisons except for NT versus UV of peaks #3–#5; Student's t-test). From: Genome-wide mapping of 8-oxo-7,8-dihydro-2′-deoxyguanosine reveals accumulation of oxidatively-generated damage at DNA replication origins within transcribed long genes of mammalian cells Nucleic Acids Res. Published online November 20, 2018. doi:10.1093/nar/gky1152 Nucleic Acids Res | © The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

Figure 2. Pie charts showing the annotation of 8-oxodG (panels A, B) and γH2AX (panels C, D) peaks. (E) Scatter plot showing the correlation between 8-oxodG and γH2AX signals within the RefSeq genes. Pearson's correlation coefficient (r), and P-value (p), as indicated. From: Genome-wide mapping of 8-oxo-7,8-dihydro-2′-deoxyguanosine reveals accumulation of oxidatively-generated damage at DNA replication origins within transcribed long genes of mammalian cells Nucleic Acids Res. Published online November 20, 2018. doi:10.1093/nar/gky1152 Nucleic Acids Res | © The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

Figure 3. (A) Heatmap showing GRO-Seq, Pol2-S2P, γH2AX ChIP-Seq, and 8-oxodG OxiDIP-Seq signals at the gene body, and within the 5 kb both upstream the TSS and downstream the TTS of the RefSeq genes. Gene clusters identified by SeqMINER unbiased k-means clustering (Cluster #1–#4), and the number of genes contained within each cluster, as indicated. (B) Read density profiles of 8-oxodG OxiDIP-Seq (red) and γH2AX ChIP-Seq (black) in Cluster #1–#4, as indicated. (C) Box plot showing the distribution of transcription levels (RPKM, measured by GRO-seq) of human genes within each cluster in MCF10A cells. (D) Box plot showing the length distribution of human genes within each cluster in MCF10A cells (P< 2.2e–16, ANOVA test; ***P< 2.2e–16, **P = 2.1e–3, *P = 2.4e–2, Bonferroni post hoc analysis for pairwise comparison). From: Genome-wide mapping of 8-oxo-7,8-dihydro-2′-deoxyguanosine reveals accumulation of oxidatively-generated damage at DNA replication origins within transcribed long genes of mammalian cells Nucleic Acids Res. Published online November 20, 2018. doi:10.1093/nar/gky1152 Nucleic Acids Res | © The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

Figure 4. (A) Screenshot from the UCSC genome browser of 2 Figure 4. (A) Screenshot from the UCSC genome browser of 2.6 Mb from mouse chromosome 19 showing (top to bottom): OxiDIP-Seq signal profiles of two independents OxiDIP-Seq experiments (Exp #1 and #2), Input DNA, and RefSeq genes. (D-E) Pie charts showing the annotation of 8-oxodG (panels B, C) and γH2AX (panels D, E) peaks. (F) Scatter plot showing the correlation of 8-oxodG and γH2AX signals within the RefSeq genes. Pearson's correlation coefficient (r), and P-value (p), as indicated. From: Genome-wide mapping of 8-oxo-7,8-dihydro-2′-deoxyguanosine reveals accumulation of oxidatively-generated damage at DNA replication origins within transcribed long genes of mammalian cells Nucleic Acids Res. Published online November 20, 2018. doi:10.1093/nar/gky1152 Nucleic Acids Res | © The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

Figure 5. (A) Heatmap showing γH2AX ChIP-Seq and 8-oxodG OxiDIP-Seq signals within the gene body, and the 5 kb both upstream the TSS and downstream the TTS of the RefSeq genes. Gene clusters identified by SeqMINER unbiased k-means clustering (Cluster #1–#4), and the number of genes contained within each cluster, as indicated. (B) Read density profiles of 8-oxodG OxiDIP-Seq (red) an γH2AX ChIP-Seq (black) in Cluster #1–#4, as indicated. (C) Box plot showing the length distribution of mouse genes within each cluster in MEFs (P < 2.2e–16, ANOVA test; ***P < 2.2e–16, **P = 2.9e–4, Bonferroni post hoc analysis for pairwise comparison). (D) Box plot showing the distribution of transcription levels (RPKM, measured by GRO-seq) of mouse genes within each cluster in MEFs (P< 2.2e–16, ANOVA test; ***P < 2.2e–16, **P = 2.9e–4, Bonferroni post hoc analysis for pairwise comparison). (E) Venn diagram showing the number of common (group a) and mouse- (MEFs, group b) or human- (MCF10A, group c) specific Cluster #3 genes; P< 2.2e–16 (Hypergeometric test). (F) Gene length distribution of the common (a), mouse-specific (b) or human-specific (c) genes in human (white bars) and mouse (grey bars), as indicated (P< 2.2e–16, ANOVA test; ***P< 2.2e–16, **P = 1.0e–5, Bonferroni post hoc analysis for pairwise comparison). From: Genome-wide mapping of 8-oxo-7,8-dihydro-2′-deoxyguanosine reveals accumulation of oxidatively-generated damage at DNA replication origins within transcribed long genes of mammalian cells Nucleic Acids Res. Published online November 20, 2018. doi:10.1093/nar/gky1152 Nucleic Acids Res | © The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

Figure 6. (A) Bar plot showing the distribution within the four cluster of the genes contained within molecularly mapped CFSs (P< 2.2e–16; X<sup>2</sup>-test). (B and C) Bar plots showing the frequency of the genes recurrently deleted in cancer within each cluster (Ref (51), panel B; COSMIC database, panel C). (D) Boxplots showing the ORI density (human ORC1 binding sites) within the four identified clusters, as indicated. (E) Boxplots showing the ORI density (mouse Short Nascent Strands sites) within the four identified clusters, as indicated (P< 2.2e–16, ANOVA test; ***P< 2.2e–16, Bonferroni post hoc analysis for pairwise comparison). (F, G) Violin plot showing the relative abundance of genes with the indicated number of ORIs within each gene cluster (only genes with ≥2 ORIs are shown) in MCF10A (panel F) and MEFs (panel G). From: Genome-wide mapping of 8-oxo-7,8-dihydro-2′-deoxyguanosine reveals accumulation of oxidatively-generated damage at DNA replication origins within transcribed long genes of mammalian cells Nucleic Acids Res. Published online November 20, 2018. doi:10.1093/nar/gky1152 Nucleic Acids Res | © The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com