HF-VHF帯における生体等価ファントムを用いた電磁波と人体相互作用の検証

研究科: 千葉大学大学院工学研究科学位:千大院工博甲第工185号博士(工学)千葉大

Generation of a genomic tiling array of the human Major Histocompatibility Complex (MHC) and its application for DNA methylation analysis-2

Cot1 DNA. Two independent hybridizations were carried out using genomic DNA extracted from CD8lymphocytes. In both experiments total DNA was labelled with Cy5 dye. Only in one of them unlabelled Cot1 DNA was added. In the non-Cot1 hybridization, Cy5 intensity increases almost linearly with repeat density until it reaches a plateau (around 25,000 Cy5 intensity). In the presence of Cot1 DNA, Cy5 intensity of highly repetitive probes is comparable to those of repeat-free probes. Repeats were defined based on the 'All repeats' track in Ensembl browser [43].<p><b>Copyright information:</b></p><p>Taken from "Generation of a genomic tiling array of the human Major Histocompatibility Complex (MHC) and its application for DNA methylation analysis"</p><p>http://www.biomedcentral.com/1755-8794/1/19</p><p>BMC Medical Genomics 2008;1():19-19.</p><p>Published online 30 May 2008</p><p>PMCID:PMC2430202.</p><p></p

Additional file 20: Table S19. of DNA methylation analysis of paediatric low-grade astrocytomas identifies a tumour-specific hypomethylation signature in pilocytic astrocytomas

Differentially methylated CpG sites identified between diffuse astrocytomas and cerebral cortex controls. 1_ MethLAB analysis identified 90,249 CpG sites that are significantly differentially methylated in supratentorial pilocytic astrocytomas, diffuse astrocytomas, glial component of the cerebral cortex, neuronal component of the cerebral cortex, adult cerebral cortex and foetal cerebral cortex (Benjamini-Hochberg corrected p-value <0.05). The adult cerebral cortex controls (including the glial and neuronal components) were taken from [Guintivano et al, Epigenetics 8:290-302, 2013]. The number of differentially methylated sites (averaged beta values with a difference of δβ ≥ 0.3, Benjamini-Hochberg corrected p-value <0.05) identified in tumour and all controls was 58 CpG sites for the diffuse astrocytomas. 2_ CpG sites hypermethylated and 3_ hypomethylated in diffuse astrocytomas compared to controls. 4_ Expression analysis for the genes that show differentially methylated CpG sites. Highlighted genes show ≤ 2 fold change in expression compared to controls. (XLSX 37720 kb

Additional file 13: Table S12. of DNA methylation analysis of paediatric low-grade astrocytomas identifies a tumour-specific hypomethylation signature in pilocytic astrocytomas

Comparison of methylation and expression for genes associated with 315 differentially methylated sites in pilocytic and diffuse astrocytomas. Correlation coefficients are shown for differentially methylated CpG sites that show a difference of ≥2-fold in expression of the associated gene. Expression probes were only assessed if they were located within the mRNA transcript. A) CpG sites located within the promoter of the gene. B) CpG sites located within the gene body, 3’UTR and intergenic regions. As the CpG is not within a promoter, correlation was also calculated for a CpG site within the promoter (where possible within the TSS200; brown panel). For each correlation p-values and Benjamini-Hochberg corrected p-values are shown. The table is ordered by FDR-corrected p-values (sites with a p-value <0.05 are shown in blue). Positive correlation is highlighted in yellow. Up-regulated genes in diffuse astrocytomas are highlighted in green. When the expression probe was located in an exon, the probe for the full transcript was used for the correlation (indicated by the asterisk). (XLSX 85 kb

Generation of a genomic tiling array of the human Major Histocompatibility Complex (MHC) and its application for DNA methylation analysis-4

GMeDIP enrichment ratios of the indicated tissues/cell types. Black boxes represent tDMRs that are more methylated in sample 1 of the comparison and grey boxes represent tDMRs that are more methylated in sample 2 of the comparison. b). Absolute DNA methylation values of individual CpG sites in tDMRs based on bisulphite sequencing analysis. Because of assay and or technical limitations, bisulphite data could only be obtained for about 50% of the CpG sites involved in the putative tDMRs. Each square represents a CpG site. The colour code indicates methylation values as calculated by ESME (see Methods). Grey squares indicate CpG sites for which no data could be obtained. Based on this analysis, bisulphite data essentially agree with array data in all cases. Numbers of tDMRs correspond to tDMR numbers in table 2.<p><b>Copyright information:</b></p><p>Taken from "Generation of a genomic tiling array of the human Major Histocompatibility Complex (MHC) and its application for DNA methylation analysis"</p><p>http://www.biomedcentral.com/1755-8794/1/19</p><p>BMC Medical Genomics 2008;1():19-19.</p><p>Published online 30 May 2008</p><p>PMCID:PMC2430202.</p><p></p

Generation of a genomic tiling array of the human Major Histocompatibility Complex (MHC) and its application for DNA methylation analysis-1

Al tracks to the UCSC genome browser using the 'smooth' function. Regions enriched or depleted in DNA methylation are shaded in black and grey, respectively. Also shown are the locations of HEP amplicons [49] and a track of the C+G content (the darker the shading, the higher the C+G content). For orientation, the approximate positions of the MHC class I, II and II sub-regions and some landmark genes are indicated.<p><b>Copyright information:</b></p><p>Taken from "Generation of a genomic tiling array of the human Major Histocompatibility Complex (MHC) and its application for DNA methylation analysis"</p><p>http://www.biomedcentral.com/1755-8794/1/19</p><p>BMC Medical Genomics 2008;1():19-19.</p><p>Published online 30 May 2008</p><p>PMCID:PMC2430202.</p><p></p

Generation of a genomic tiling array of the human Major Histocompatibility Complex (MHC) and its application for DNA methylation analysis-0

The relative enrichment of the MeDIP versus input fractions was calculated based on qRT-PCR data. The graph shows a specific and efficient enrichment of methylated over unmethylated fractions. The error bars indicate the variance of two independent measurements. Methylated amplicons display an approximately linear dependency on CpG density (CpG density equals the number CpG sites per amplicon divided by the length of the amplicon multiplied by 100).<p><b>Copyright information:</b></p><p>Taken from "Generation of a genomic tiling array of the human Major Histocompatibility Complex (MHC) and its application for DNA methylation analysis"</p><p>http://www.biomedcentral.com/1755-8794/1/19</p><p>BMC Medical Genomics 2008;1():19-19.</p><p>Published online 30 May 2008</p><p>PMCID:PMC2430202.</p><p></p

Generation of a genomic tiling array of the human Major Histocompatibility Complex (MHC) and its application for DNA methylation analysis-6

E browser. Each vertical black line represents a putative tDMR. The high density of 18 tDMRs within the C4A and C4B complement region is clearly visible (boxed with red doted line). Tracks showing C+G content, Ensembl genes, CpG islands and conservation are also shown. b). Enlargement of the C4A and C4B complement region showing the 18 overlapping or adjacent tDMRs (delimited by red dotted lines) which could be part of one large tDMR spanning the entire C4 complement region.<p><b>Copyright information:</b></p><p>Taken from "Generation of a genomic tiling array of the human Major Histocompatibility Complex (MHC) and its application for DNA methylation analysis"</p><p>http://www.biomedcentral.com/1755-8794/1/19</p><p>BMC Medical Genomics 2008;1():19-19.</p><p>Published online 30 May 2008</p><p>PMCID:PMC2430202.</p><p></p

Generation of a genomic tiling array of the human Major Histocompatibility Complex (MHC) and its application for DNA methylation analysis-3

-value < 0.001 was used. In total 90 tDMRs were identified. Vertical axis shows the logratio of the two corresponding methylation profiles. Each line represents a tDMR (average size 2 kb). Black lines represent tDMRs that are more methylated in sample 1 of the comparison and grey boxes represent tDMRs that are more methylated in sample 2 of the comparison (the identities of the pair-wise comparisons are given on the right). The majority of tDMRs are present in comparisons with sperm. The locations of HEP amplicons, a track of the C+G content and the approximate positions of the MHC class I, II and II subregions and some landmark genes are also indicated. Class III region encoding for the C4 genes seems to be less methylated in liver.<p><b>Copyright information:</b></p><p>Taken from "Generation of a genomic tiling array of the human Major Histocompatibility Complex (MHC) and its application for DNA methylation analysis"</p><p>http://www.biomedcentral.com/1755-8794/1/19</p><p>BMC Medical Genomics 2008;1():19-19.</p><p>Published online 30 May 2008</p><p>PMCID:PMC2430202.</p><p></p

Generation of a genomic tiling array of the human Major Histocompatibility Complex (MHC) and its application for DNA methylation analysis-5

Grey lines indicate regions (average size 2 kb) that are less methylated in liver compared to the other samples (placenta, sperm, CD8). Known genes and Affy_U95 expression array probes within this region are also shown. b). Expression of C4A and C4B. Graph shows the mean expression values of the probe corresponding to C4A and C4B (Affy_ID: 40776_at) transcripts in three samples tested: CD8, liver, placenta. C4A and C4B transcripts are highly expressed in liver tissue only. Data were taken from the GNF SymAtlas [41].<p><b>Copyright information:</b></p><p>Taken from "Generation of a genomic tiling array of the human Major Histocompatibility Complex (MHC) and its application for DNA methylation analysis"</p><p>http://www.biomedcentral.com/1755-8794/1/19</p><p>BMC Medical Genomics 2008;1():19-19.</p><p>Published online 30 May 2008</p><p>PMCID:PMC2430202.</p><p></p