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Results: 5

1.
Figure 4

Figure 4. Apoptotic Breakpoints Associated with Genes.. From: Next-Generation Sequencing of Apoptotic DNA Breakpoints Reveals Association with Actively Transcribed Genes and Gene Translocations.

A. Diagram of the distinct categories of locations. B. Graph of locations of apoptotic DNA breakpoint peaks. C. Screenshot of apoptotic breakpoint peaks with regards to UCSC Gene exon density in chromosome 14.

Melissa J. Fullwood, et al. PLoS One. 2011;6(11):e26054.
2.
Figure 5

Figure 5. Characterisation of Apoptotic DNA Breakpoints.. From: Next-Generation Sequencing of Apoptotic DNA Breakpoints Reveals Association with Actively Transcribed Genes and Gene Translocations.

A. Association of apoptotic breakpoints with H3K4me3 marks, DNase I hypersensitivity marks, and CTCF marks. B. Transcription factor motifs found in apoptotic breakpoints from both AHH001 and AHH002 biological replicates. C. Examples of transcription factor motifs found in only one apoptoseq replicate, AHH002.

Melissa J. Fullwood, et al. PLoS One. 2011;6(11):e26054.
3.
Figure 2

Figure 2. Comparison of Apoptoseq Replicates.. From: Next-Generation Sequencing of Apoptotic DNA Breakpoints Reveals Association with Actively Transcribed Genes and Gene Translocations.

A. Genome-wide graphs of AHH001 and AHH002. B. Venn diagram of overlaps between AHH001 and AHH002. The number in the pink circle indicates AHH002 peaks that did not overlap with AHH001 peaks. The number in the blue circle indicates unique AHH001 peaks that did not overlap with AHH002 peaks. The top number in the purple or overlapping region indicates AHH002 peaks that overlap with AHH001 peaks and the bottom number indicates AHH001 peaks that overlapped with AHH002 peaks. C. Graph comparing the peak intensities of overlapping regions in AHH001 and AHH002.

Melissa J. Fullwood, et al. PLoS One. 2011;6(11):e26054.
4.
Figure 1

Figure 1. The Apoptoseq Method.. From: Next-Generation Sequencing of Apoptotic DNA Breakpoints Reveals Association with Actively Transcribed Genes and Gene Translocations.

A. Schematic of the Apoptoseq methodology is shown. B. Screenshot of the apoptotic DNA patterns for the CASP3 gene Track labels: 1 – AHH001 biological replicate 1 Apoptoseq sequence density. 2 – Peaks called from AHH001. 3 - AHH002 biological replicate 2 Apoptoseq sequence density. 4 – Peaks called from AHH002. 5 – UCSC Genes. 6 – DNase I hypersensitivity Sequencing Peaks (1 indicates a peak is present, 0 indicates no peak is present) [53]. 7 – H3K4me3 ChIP-Seq Peaks (1 indicates a peak is present, 0 indicates no peak is present) [53]. 8 – CTCF ChIP-Seq Peaks (1 indicates a peak is present, 0 indicates no peak is present) [53]. C. Screenshot of the apoptotic DNA patterns for the MYB gene. Track labels follow labels in Figure 1B.

Melissa J. Fullwood, et al. PLoS One. 2011;6(11):e26054.
5.
Figure 3

Figure 3. Apoptoseq Validation.. From: Next-Generation Sequencing of Apoptotic DNA Breakpoints Reveals Association with Actively Transcribed Genes and Gene Translocations.

A. Quantitative PCR validations were performed using primers against apoptotic peaks, with normalization against a pair of negative control primers that did not map to apoptotic peaks. In addition, the 180 bp apoptotic DNA was normalized against uncut genomic DNA. A second pair of negative control primers “NegCont” was used to set the threshold for calling sites that passed. From this analysis, all the sites passed. The columns represent the average of three replicates. Error bars indicate standard errors. B. Screenshot showing the apoptotic peak at a region that was validated, HECW2.

Melissa J. Fullwood, et al. PLoS One. 2011;6(11):e26054.

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