Journal: BMC Genomics

Article Title: Genome-wide survey reveals dynamic widespread tissue-specific changes in DNA methylation during development

doi: 10.1186/1471-2164-12-231

Figure Lengend Snippet: Comparison of methylation data between MeDIP/NimbleGen Promoter + CpGi Array and Sequenom MassArray: Stk31 CpGi promoter region . The Stk31 gene region with a CpGi promoter region that is methylated in the liver, but not in ES or testis cells. The box indicates the position of the methylation peak in the liver that overlaps with the CpGi promoter region analyzed by Sequenom. In the epigram of Sequenom methylation analysis shown at the bottom panel, the blue circles indicate 100% methylation, green circles indicate around 50%methylation and yellow circles indicate 0% methylation. The results from biological duplicate samples are shown. The bottom lane (Sequenom Methylation Analysis) shows the results of analysis of testis DNA after in vitro methylation using M. Sss1 methylase (New England Biolabs).

Article Snippet: Sequenom MassArray quantitative methylation analysis of bisulfite treated DNA was performed as an additional means to confirm DNA methylation peaks obtained by MeDIP/NimbleGen Array for both selected and randomly chosen MeDIP methylated regions.

Techniques: Methylation, Methylated DNA Immunoprecipitation, In Vitro

Journal: Journal of Experimental & Clinical Cancer Research : CR

Article Title: Downregulation of lncRNA ZNF582-AS1 due to DNA hypermethylation promotes clear cell renal cell carcinoma growth and metastasis by regulating the N(6)-methyladenosine modification of MT-RNR1

doi: 10.1186/s13046-021-01889-8

Figure Lengend Snippet: ZNF582-AS1 expression was regulated by DNA methylation in ccRCC. a Detection of CpG islands in ZNF582-AS1 promoter and design of MSP primers. The horizontal axis of the curved lines represents the input sequence of ZNF582-AS1, and the vertical axis of the curved lines represents GC percentage. TSS: Transcription Start Sites. b MSP analysis of ZNF582-AS1 promoter DNA methylation status in ccRCC cell lines. c MSP analysis of ZNF582-AS1 promoter DNA methylation status in ccRCC tissues. d Detection of 38 CpG sites in ZNF582-AS1 promoter. e Quantitative detection of DNA methylation level of 38 CpG sites in ZNF582-AS1 promoter using Sequenom MassARRAY quantitative DNA methylation analysis. f and g Comparison of the DNA methylation levels of 38 CpG sites in ccRCC and adjacent normal renal tissues. h Treatment with 5-aza-dC and TSA demethylated ZNF582-AS1 promoter and increased ZNF582-AS1 expression in OSRC2 and Caki-1 cells. T refers to Tumor tissue of ccRCC, N refers to Adjacent normal kidney tissue. M = Methylated, U = Unmethylated

Article Snippet: TSS: Transcription Start Sites. b MSP analysis of ZNF582-AS1 promoter DNA methylation status in ccRCC cell lines. c MSP analysis of ZNF582-AS1 promoter DNA methylation status in ccRCC tissues. d Detection of 38 CpG sites in ZNF582-AS1 promoter. e Quantitative detection of DNA methylation level of 38 CpG sites in ZNF582-AS1 promoter using Sequenom MassARRAY quantitative DNA methylation analysis. f and g Comparison of the DNA methylation levels of 38 CpG sites in ccRCC and adjacent normal renal tissues. h Treatment with 5-aza-dC and TSA demethylated ZNF582-AS1 promoter and increased ZNF582-AS1 expression in OSRC2 and Caki-1 cells.

Techniques: Expressing, DNA Methylation Assay, Sequencing, Comparison, Methylation

Journal: BMC Genetics

Article Title: DNA methylation of CpG sites in the chicken KLF7 promoter and Exon 2 in association with mRNA expression in abdominal adipose tissue and blood metabolic indicators

doi: 10.1186/s12863-020-00923-6

Figure Lengend Snippet: DNA methylation analysis of chicken KLF7 in adipose tissues. a . The CpG density of the genomic region of chicken KLF7 analyzed by CpGplot (Version 6.6.0). b . The CpG loci analyzed in the promoter and Exon 2. c . The levels of DNA methylation of CpG loci analyzed. d . The comparison of DNA methylation levels between the promoter and Exon 2. Asterisks indicate a significant difference between the promoter and Exon 2 (Student’s t test, *** P < 0.001)

Article Snippet: The methylation level of individual units was measured by Quantitative Methylation Analysis (MassARRAY EpiTYOER, Sequenom, San Diego, CA).

Techniques: DNA Methylation Assay, Comparison

Journal: BMC Genetics

Article Title: DNA methylation of CpG sites in the chicken KLF7 promoter and Exon 2 in association with mRNA expression in abdominal adipose tissue and blood metabolic indicators

doi: 10.1186/s12863-020-00923-6

Figure Lengend Snippet: Datasets characteristics of DNA methylation of chicken KLF7 in abdominal adipose tissues

Article Snippet: The methylation level of individual units was measured by Quantitative Methylation Analysis (MassARRAY EpiTYOER, Sequenom, San Diego, CA).

Techniques: DNA Methylation Assay

Journal: BMC Genetics

Article Title: DNA methylation of CpG sites in the chicken KLF7 promoter and Exon 2 in association with mRNA expression in abdominal adipose tissue and blood metabolic indicators

doi: 10.1186/s12863-020-00923-6

Figure Lengend Snippet: Association analysis of DNA methylation with KLF7 transcripts and blood metabolic indicators. a . The r value of the Spearman correlation analysis. b . The P value of the Spearman correlation analysis. c . The number of samples used in the Spearman correlation analysis. d . The regression analysis between the DNA methylation of PCpG6 and KLF7 transcripts in chicken adipose tissue

Article Snippet: The methylation level of individual units was measured by Quantitative Methylation Analysis (MassARRAY EpiTYOER, Sequenom, San Diego, CA).

Techniques: DNA Methylation Assay

Journal: BMC Genetics

Article Title: DNA methylation of CpG sites in the chicken KLF7 promoter and Exon 2 in association with mRNA expression in abdominal adipose tissue and blood metabolic indicators

doi: 10.1186/s12863-020-00923-6

Figure Lengend Snippet: Schematic representation of the relationship of DNA methylation, KLF7 transcripts, glycaemia and abdominal fat content in chicken. The negative associations marked red and blue were confirmed by the reference [ , ], respectively

Article Snippet: The methylation level of individual units was measured by Quantitative Methylation Analysis (MassARRAY EpiTYOER, Sequenom, San Diego, CA).

Techniques: DNA Methylation Assay

Journal: BMC Genetics

Article Title: DNA methylation of CpG sites in the chicken KLF7 promoter and Exon 2 in association with mRNA expression in abdominal adipose tissue and blood metabolic indicators

doi: 10.1186/s12863-020-00923-6

Figure Lengend Snippet: Oligonucleotides used in the current study

Article Snippet: The methylation level of individual units was measured by Quantitative Methylation Analysis (MassARRAY EpiTYOER, Sequenom, San Diego, CA).

Techniques: Methylation

Journal: Chinese Journal of Cancer Research

Article Title: Stomatin plays a suppressor role in non-small cell lung cancer metastasis

doi: 10.21147/j.issn.1000-9604.2019.06.09

Figure Lengend Snippet: During transforming growth factor β1 (TGFβ1)-induced epithelial-to-mesenchymal transition (EMT), stomatin was downregulated through methylation-dependent transcription mechanism. (A) Real-time polymerase chain reaction (PCR) was performed to validate the transcriptional change of stomatin identified in the microarray. **, P<0.001; (B) Two CpG islands spanning from −768 to −223 bp and from −143 to +122 bp upstream of STOM gene were identified by EMBOSS cpgplot program (upper). Schematic representation of −768/−223 and −143/+122 (marked with the grey square) CpG islands in the upstream of stomatin gene (lower). Red box marked the exon. The translation start site was position +1; (C) Measuring stomatin promoter methylation levels by Sequenom MassARRAY assay; (D) Sequenom MassARRAY analysis of methylation percentages of CpG sites at the stomatin promoter. The top panel showed the methylation percentages of 30 sites in human bronchial epithelial (HBE) and A549 cells. Dots with different color depths represent different methylation status. Dark dots represent high degrees of methylation. Light dots represent low degrees of methylation. The methylation percentages of 30 CpG sites were compared by two-tailed paired Student’s t test. In line graph, each dot represents an individual CpG dinucleotide. Green dots represent CpG dinucleotides in HBE cells. Red dots represent CpG sites in A549 cells. The corresponding detection sites were connected in a straight line. Real-time PCR was performed to evaluate the expression of stomatin in HBE and A549 cells (P<0.01); (E) The same sequenom MassArray and statistical analyses were also implemented to assess the methylation status of the indicated promoter region of stomatin in A549 and A549-5Aza cells (P<0.01); (F) A549 cells were exposed to TGFβ1 (5 ng/mL) for 2 d or 5 d with or without 5-Aza. Expression of DNMT3A and stomatin was analyzed by western blotting. β-actin was used as a loading control; (G) Sequenom MassArray analysis was implemented to assess the stomatin promoter methylation levels in A549, A549-TGFβ1, and A549-TGFβ1/5-Aza cells (P=0.005, P=0.004, respectively).

Article Snippet: The methylation status of Stomatin promoter was detected using Sequenom MassARRAY quantitative methylation analysis platform (BGI tech, Shenzhen, China).

Techniques: Methylation, Real-time Polymerase Chain Reaction, Microarray, Sequenom Massarray Assay, Two Tailed Test, Expressing, Western Blot, Control