pcr primer sequences in sequenom epityper sequencing  (Sequenom)

Journal: Clinical Epigenetics

Article Title: Casp8 hypomethylation and neural tube defects in association with polycyclic aromatic hydrocarbon exposure

doi: 10.1186/s13148-019-0673-6

Figure Lengend Snippet: Location and methylation levels of CpG sites in CASP8 examined in the discovery and validation stage in human subjects. a Locations of the CpG sites detected by HM450K and Sequenom EpiTYPER. The differentially methylated CpG units identified by HM450K Array are indicated as red dots above the black line. CpG sites detected in the validation stage are indicated as blue dots under the black line. b Methylation patterns of the CASP8 gene detected with Sequenom EpiTYPER in a larger sample of human subjects. Methylation levels for each CpG unit between NTD cases and controls within the amplicons were analyzed. HM450K, HumanMethylation450 BeadChip; NTD, neural tube defect. *Methylation levels of CpG sites were significantly different between the case and control groups (all p < 0.05)

Article Snippet: The PCR primer sequences in Sequenom EpiTYPER sequencing for mouse.

Techniques: Methylation

Journal: Biomolecules

Article Title: An Epigenomic Approach to Improving Response to Neoadjuvant Cisplatin Chemotherapy in Bladder Cancer

doi: 10.3390/biom6030037

Figure Lengend Snippet: HOXA9 promoter methylation as marker for sensitivity and resistance in bladder cancer cell lines. ( A ) Expression profiling and hierarchical clustering of top sensitive and top resistant bladder cancer cell lines identifies candidate genes to explain sensitivity and resistance to chemotherapy. The LIMMA package (version 3.28.20) was used for analyzing differential expression of RNA sequencing (RNAseq) data between sensitive and resistant cell lines; ( B ) The HOXA9 promoter is methylated in resistant cell lines ( p < 0.001). Methylation quantification of the HOX9A promoter was carried out using the EpiTYPER assay.

Article Snippet: EpiTYPER (Sequenom) primers were designed to cover CpG islands associated with the respective HpaII amplifiable fragments.

Techniques: Methylation, Marker, Expressing, Quantitative Proteomics, RNA Sequencing, EpiTYPER Assay

Journal: Biomolecules

Article Title: An Epigenomic Approach to Improving Response to Neoadjuvant Cisplatin Chemotherapy in Bladder Cancer

doi: 10.3390/biom6030037

Figure Lengend Snippet: HOXA9 promoter methylation is associated with chemoresistance of human muscle-invasive bladder cancer tissue. ( A ) CpG methylation at the HOXA9 promoter is increased in resistant compared to sensitive tumor samples. Methylation quantification of tumor samples was carried out using the EpiTYPER assay; ( B ) Based on methylation levels detected in the cisplatin sensitive cell lines, a cut-off methylation level of 12% was defined as predictive of cisplatin resistance. Resistant tumor samples ( n = 9) show methylation levels >12% ( p < 0.001).

Article Snippet: EpiTYPER (Sequenom) primers were designed to cover CpG islands associated with the respective HpaII amplifiable fragments.

Techniques: Methylation, CpG Methylation Assay, EpiTYPER Assay

Journal: Biomolecules

Article Title: An Epigenomic Approach to Improving Response to Neoadjuvant Cisplatin Chemotherapy in Bladder Cancer

doi: 10.3390/biom6030037

Figure Lengend Snippet: HOXA9 promoter methylation as marker for sensitivity and resistance in bladder cancer cell lines. ( A ) Expression profiling and hierarchical clustering of top sensitive and top resistant bladder cancer cell lines identifies candidate genes to explain sensitivity and resistance to chemotherapy. The LIMMA package (version 3.28.20) was used for analyzing differential expression of RNA sequencing (RNAseq) data between sensitive and resistant cell lines; ( B ) The HOXA9 promoter is methylated in resistant cell lines ( p < 0.001). Methylation quantification of the HOX9A promoter was carried out using the EpiTYPER assay.

Article Snippet: EpiTYPER assays (Sequenom, San Diego, CA, USA) were performed on bisulfite-converted DNA.

Techniques: Methylation, Marker, Expressing, Quantitative Proteomics, RNA Sequencing, EpiTYPER Assay

Journal: Biomolecules

Article Title: An Epigenomic Approach to Improving Response to Neoadjuvant Cisplatin Chemotherapy in Bladder Cancer

doi: 10.3390/biom6030037

Figure Lengend Snippet: HOXA9 promoter methylation is associated with chemoresistance of human muscle-invasive bladder cancer tissue. ( A ) CpG methylation at the HOXA9 promoter is increased in resistant compared to sensitive tumor samples. Methylation quantification of tumor samples was carried out using the EpiTYPER assay; ( B ) Based on methylation levels detected in the cisplatin sensitive cell lines, a cut-off methylation level of 12% was defined as predictive of cisplatin resistance. Resistant tumor samples ( n = 9) show methylation levels >12% ( p < 0.001).

Article Snippet: EpiTYPER assays (Sequenom, San Diego, CA, USA) were performed on bisulfite-converted DNA.

Techniques: Methylation, CpG Methylation Assay, EpiTYPER Assay

Journal: PLoS ONE

Article Title: Methylation of the SLC6a2 Gene Promoter in Major Depression and Panic Disorder

doi: 10.1371/journal.pone.0083223

Figure Lengend Snippet: Bisulphite primer sequences for SLC6a2 .

Article Snippet: Primers for EpiTYPER analyses were provided by Sequenom (San Diego, CA, USA).

Techniques: Sequencing, Bisulfite Sequencing

Journal: PLoS ONE

Article Title: Methylation of the SLC6a2 Gene Promoter in Major Depression and Panic Disorder

doi: 10.1371/journal.pone.0083223

Figure Lengend Snippet: Representation of the methylation percentages for CpG sites in Region A of the SLC6a2 gene determined by EpiTYPER analysis. CpG site. CpG sites are numbered 5’- 3’ along the X-axis, with percentage methylation on the Y-axis. Usable data could not be obtained for all CpG sites for all samples. All groups exhibited a similar methylation profile across the region, and no difference between groups for the region as a whole was determined to be significant by two-way ANOVA.

Article Snippet: Primers for EpiTYPER analyses were provided by Sequenom (San Diego, CA, USA).

Techniques: Methylation

Journal: PLoS ONE

Article Title: Methylation of the SLC6a2 Gene Promoter in Major Depression and Panic Disorder

doi: 10.1371/journal.pone.0083223

Figure Lengend Snippet: Representation of the methylation percentages for CpG sites in Region B of the SLC6a2 gene determined by EpiTYPER analysis. CpG sites are numbered 5’- 3’ along the X-axis, with percentage methylation on the Y-axis. Usable data could not be obtained for all CpG sites for all samples. The overall methylation of Region B in subjects with MDD was determined to be significantly greater than all other groups (p<0.05).

Article Snippet: Primers for EpiTYPER analyses were provided by Sequenom (San Diego, CA, USA).

Techniques: Methylation

Journal: PLoS ONE

Article Title: Methylation of the SLC6a2 Gene Promoter in Major Depression and Panic Disorder

doi: 10.1371/journal.pone.0083223

Figure Lengend Snippet: Representation of the methylation percentages for CpG sites in Region A of the NET gene determined by EpiTYPER analysis in human leukocytes pre- and post-SSRI treatment. CpG sites are numbered 5’- 3’ along the X-axis, with percentage methylation on the Y-axis. Usable data could not be obtained for all CpG sites for all samples. Samples pre- and post-SSRI treatment exhibited a similar methylation profile across the region, and no differences in average methylation of CpG sites in response to SSRI treatment were determined to be significant by paired t-test. *Statistically significant site-specific difference in methylation with SSRI treatment.

Article Snippet: Primers for EpiTYPER analyses were provided by Sequenom (San Diego, CA, USA).

Techniques: Methylation