Journal: BMC Genomics

Article Title: Discrimination between human populations using a small number of differentially methylated CpG sites: a preliminary study using lymphoblastoid cell lines and peripheral blood samples of European and Chinese origin

doi: 10.1186/s12864-020-07092-x

Figure Lengend Snippet: Comparison of DNA methylation levels assessed using Illumina HM450K array and pyrosequencing assays (PyroAssays)

Article Snippet: Pyrosequencing assays (further referred as PyroAssays) were designed to validate candidate pop-CpG sites preselected in HM450K array experiment for which effective PyroAssays could be designed (Assay score in PyroMark Assay Design Software ≥75, no CpGs under PyroAssay primers); in some cases, PyroAssays covered additional CpGs located in the close proximity (less than 25 bp upstream or downstream) of the selected candidate pop-CpGs (see Table in section).

Techniques: DNA Methylation Assay, Methylation

Journal: BMC Genomics

Article Title: Discrimination between human populations using a small number of differentially methylated CpG sites: a preliminary study using lymphoblastoid cell lines and peripheral blood samples of European and Chinese origin

doi: 10.1186/s12864-020-07092-x

Figure Lengend Snippet: Results of the technical validation of eight PyroAssays. Twenty B-lymphocyte cell lines (10 from each population) were tested. The originally selected candidate pop-CpGs targeted in each PyroAssay are marked with *. Green – CEU population; blue – CHB population. Dots represent methylation levels in individual samples. Box plots denote mean value (lines inside the boxes) and standard deviation. Statistically significant ( p < 0.05) population differences in the methylation level are marked in red

Article Snippet: Pyrosequencing assays (further referred as PyroAssays) were designed to validate candidate pop-CpG sites preselected in HM450K array experiment for which effective PyroAssays could be designed (Assay score in PyroMark Assay Design Software ≥75, no CpGs under PyroAssay primers); in some cases, PyroAssays covered additional CpGs located in the close proximity (less than 25 bp upstream or downstream) of the selected candidate pop-CpGs (see Table in section).

Techniques: Methylation, Standard Deviation

Journal: BMC Genomics

Article Title: Discrimination between human populations using a small number of differentially methylated CpG sites: a preliminary study using lymphoblastoid cell lines and peripheral blood samples of European and Chinese origin

doi: 10.1186/s12864-020-07092-x

Figure Lengend Snippet: Validation of eight PyroAssays performed in the independent set of B-lymphocyte cell lines

Article Snippet: Pyrosequencing assays (further referred as PyroAssays) were designed to validate candidate pop-CpG sites preselected in HM450K array experiment for which effective PyroAssays could be designed (Assay score in PyroMark Assay Design Software ≥75, no CpGs under PyroAssay primers); in some cases, PyroAssays covered additional CpGs located in the close proximity (less than 25 bp upstream or downstream) of the selected candidate pop-CpGs (see Table in section).

Techniques:

Journal: BMC Genomics

Article Title: Discrimination between human populations using a small number of differentially methylated CpG sites: a preliminary study using lymphoblastoid cell lines and peripheral blood samples of European and Chinese origin

doi: 10.1186/s12864-020-07092-x

Figure Lengend Snippet: Correlation matrix showing the results of Pearson correlation analysis. Analysis was performed using data from PyroAssays performed in 20 B-lymphocyte cell lines ( n = 10 from CEU, n = 10 from CHB population). Pearson correlation coefficient values and directions are marked with different colors; positive correlation (from white to red on the color scale); negative correlation (from white to blue) (see color-bar next to the matrix)

Article Snippet: Pyrosequencing assays (further referred as PyroAssays) were designed to validate candidate pop-CpG sites preselected in HM450K array experiment for which effective PyroAssays could be designed (Assay score in PyroMark Assay Design Software ≥75, no CpGs under PyroAssay primers); in some cases, PyroAssays covered additional CpGs located in the close proximity (less than 25 bp upstream or downstream) of the selected candidate pop-CpGs (see Table in section).

Techniques:

Journal: Epigenetics & Chromatin

Article Title: Depletion of DNMT1 in differentiated human cells highlights key classes of sensitive genes and an interplay with polycomb repression

doi: 10.1186/s13072-018-0182-4

Figure Lengend Snippet: Loss of methylation at the protocadherin γ ( PCDHG ) cluster of neuroepithelial identity genes. a Structure of the PCDHG cluster showing the 5′ variable exons (A, B and C classes) which are spliced to the 3′ constant exons (right). The top track (amber) shows absolute β values in the WT fibroblast cells from the 450K array, which range from 1(fully methylated) to zero (unmethylated). Only the sites showing significant differences from WT (FDR < 0.05) in each cell line are shown in the three tracks below, with decreases in red representing loss of methylation, and gains in blue. The size of the bar is proportional to the magnitude of change: maxima and minima are indicated on the scales at left. The locations of CpG islands (CGI) are also shown. Pyroassay locations are boxed. b Median β values for all variable exons. Significant differences (Mann–Whitney U ) are indicated: * p < 0.05; ** p < 0.1; n.s., not significant. c Methylation at each exon in WT and d16 cells obtained by taking the median of the absolute β value for all probes at that exon. The variable class C exons are underlined. d Average methylation values in WT and KD cells obtained from a pyrosequencing assay (pyroassay) designed to cover CpGs in the A2 exon. Bars represent SEM; *** p < 0.001, t -test. e Methylation at the C4 variable exon by pyroassay, shown as a control

Article Snippet: Key to tracks as before; pyroassay locations ( UGT1A1 and UGT1A4 ) are boxed. b Median β values for all first exons: though medians are higher in KD lines these failed to reach statistical significance. c Median absolute β values at individual first exons in WT and d16 cells. d Average methylation values in WT and KD cells obtained from a pyrosequencing assay (pyroassay) designed to cover CpGs in the A4 exon. e Methylation by pyroassay at the A1 exon, shown as a control

Techniques: Methylation, MANN-WHITNEY, Pyrosequencing Assay, Control

Journal: Epigenetics & Chromatin

Article Title: Depletion of DNMT1 in differentiated human cells highlights key classes of sensitive genes and an interplay with polycomb repression

doi: 10.1186/s13072-018-0182-4

Figure Lengend Snippet: Gains in methylation on the X chromosome. a Sites reliably showing gain in methylation and located in promoters were analysed to identify those common to all three KD lines ( n = 201). Some of these sites showing the greatest change in methylation were located on the X chromosome including MAGEA12 and GABRQ . b Schematic showing the locations of the two genes adjacent to each other on X in a region showing gain in methylation. Tracks indicate the locations of all 450K probes and CGI; the positions of the pyroassays are also indicated; the scale bar pertains to the bottom part of the schematic; ∆ β , change in beta value. c Methylation as determined by pyroassay at the two genes indicated in a , b . d Clonal analysis of GABRQ in WT and d8. Filled circles represent methylated sites, open circles unmethylated. The CpG which were also analysed by the pyroassay (pyro) and the 450K array (asterisk) are indicated

Article Snippet: Key to tracks as before; pyroassay locations ( UGT1A1 and UGT1A4 ) are boxed. b Median β values for all first exons: though medians are higher in KD lines these failed to reach statistical significance. c Median absolute β values at individual first exons in WT and d16 cells. d Average methylation values in WT and KD cells obtained from a pyrosequencing assay (pyroassay) designed to cover CpGs in the A4 exon. e Methylation by pyroassay at the A1 exon, shown as a control

Techniques: Methylation

Journal: Epigenetics & Chromatin

Article Title: Depletion of DNMT1 in differentiated human cells highlights key classes of sensitive genes and an interplay with polycomb repression

doi: 10.1186/s13072-018-0182-4

Figure Lengend Snippet: Methylation loss is concentrated at regions normally repressed by polycomb. a Distribution of probes showing significant loss per chromatin state—numbers of probes are shown at left, chromatin states below: tcn, transcription; heterochrom/Lo, heterochromatin or low signal; repetitive, repeat DNA. b Region around the LEP gene: tracks as before, with the addition of data from cells treated with siRNA for 72 h (top). A track showing ChromHMM chromatin states from NHLF foetal lung fibroblasts is shown at bottom: grey, polycomb-repressed; green, transcriptionally active (full colour key at top right). c DNMT1 mRNA levels by qPCR following treatment with siRNA (+) for 72 h compared with scrambled control (Scr). ACTB is shown as a control; ladder as above. d Median β values for all regions (WT) compared to medians for polycomb-repressed regions (Polycomb), or all other regions (Other) in the cell lines indicated at top; remeth, remethylated. e Numbers of probes showing loss and gain in methylation in hTERT cells following treatment with siRNA for 72 h compared with the shRNA lines (averaged); #, number. f mRNA levels for the indicated genes in shRNA lines treated with the EzH2 inhibitor DZNeP; UNT, untreated; bars represent SEM, experiment carried out in duplicate. g Median β values for all variable exons at the PCDHG locus (left) and for fat/body mass genes (FBM, right): compare d16 shRNA lines with cells treated with siRNA. h DNMT1 mRNA levels in WT cells exposed to siRNA for 48 h, then allowed to recover in normal medium; comparisons were made to a scrambled siRNA negative control (Scr). i Methylation levels by pyroassay at the loci indicated during the transient KD and recovery shown in ( h ); timepoints are in days. All loci showed significant loss of methylation: LEP and SNRPN showed no significant gain versus lowest methylation level, while PCDHGA2 showed no significant gain between d22 and d36

Article Snippet: Key to tracks as before; pyroassay locations ( UGT1A1 and UGT1A4 ) are boxed. b Median β values for all first exons: though medians are higher in KD lines these failed to reach statistical significance. c Median absolute β values at individual first exons in WT and d16 cells. d Average methylation values in WT and KD cells obtained from a pyrosequencing assay (pyroassay) designed to cover CpGs in the A4 exon. e Methylation by pyroassay at the A1 exon, shown as a control

Techniques: Methylation, Control, shRNA, Negative Control