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Sequenom bisulphite massarray

Adaptation of the HELP assay to use massively parallel sequencing: HELP-seq. Instead of using microarrays to map the representations to their genomic source, we sequenced the ends of the fragments using massively parallel sequencing (Illumina). We show the promoter region of the KCNQ1 gene as an example of the concordant data obtained, with hypomethylated sites represented as an upward/positive peak and methylated as downward/negative, in both the microarray-based (HELP) and Illumina-based (HELP-seq) assays. The HELP data are represented by quantile-normalized HpaII/MspI log 2 ratios while the HELP-seq data are represented by the number of HpaII reads per locus normalised to MspI reads for the same locus as described in the main text. Both embryonic stem (ES, red) and derived in vitro -differentiated erythroid progenitor (blue) cells are shown. The upstream (left) promoter of KCNQ1 is hypomethylated in both cell types, with a broader region of hypomethylation in erythroid compared with ES cells in both the HELP and HELP-seq studies. The downstream promoter appears to be methylated in ES cells in both assays, but microarray-based HELP weakly indicates hypomethylation in erythroid cells, whereas HELP-seq shows a strong hypomethylated signal in these cells. To determine which technique was more accurate, we performed validation using <t>bisulphite</t> <t>MassArray</t> (bottom), confirming the underlying hypomethylation of this locus in the erythroid and not ES cells, and demonstrating that HELP-seq offers improved capacity to identify sites of hypomethylated DNA in the genome.

Bisulphite Massarray, supplied by Sequenom, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/massarray+sequenom/bisulphite+massarray/pmc02709560-98-11-13
Average 90 stars, based on 1 article reviews

bisulphite massarray - by Bioz Stars, 2026-11

90/100 stars

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1) Product Images from "High-resolution genome-wide cytosine methylation profiling with simultaneous copy number analysis and optimization for limited cell numbers"

Article Title: High-resolution genome-wide cytosine methylation profiling with simultaneous copy number analysis and optimization for limited cell numbers

Journal: Nucleic Acids Research

doi: 10.1093/nar/gkp260

Figure Legend Snippet: Adaptation of the HELP assay to use massively parallel sequencing: HELP-seq. Instead of using microarrays to map the representations to their genomic source, we sequenced the ends of the fragments using massively parallel sequencing (Illumina). We show the promoter region of the KCNQ1 gene as an example of the concordant data obtained, with hypomethylated sites represented as an upward/positive peak and methylated as downward/negative, in both the microarray-based (HELP) and Illumina-based (HELP-seq) assays. The HELP data are represented by quantile-normalized HpaII/MspI log 2 ratios while the HELP-seq data are represented by the number of HpaII reads per locus normalised to MspI reads for the same locus as described in the main text. Both embryonic stem (ES, red) and derived in vitro -differentiated erythroid progenitor (blue) cells are shown. The upstream (left) promoter of KCNQ1 is hypomethylated in both cell types, with a broader region of hypomethylation in erythroid compared with ES cells in both the HELP and HELP-seq studies. The downstream promoter appears to be methylated in ES cells in both assays, but microarray-based HELP weakly indicates hypomethylation in erythroid cells, whereas HELP-seq shows a strong hypomethylated signal in these cells. To determine which technique was more accurate, we performed validation using bisulphite MassArray (bottom), confirming the underlying hypomethylation of this locus in the erythroid and not ES cells, and demonstrating that HELP-seq offers improved capacity to identify sites of hypomethylated DNA in the genome.

Techniques Used: HELP Assay, Sequencing, Methylation, Microarray, Derivative Assay, In Vitro, Biomarker Discovery

Biomarker Discovery:

Article Title: DNA hypermethylation of CD3(+) T cells from cord blood of infants exposed to intrauterine growth restriction.
Article Snippet: .. Bisulfite MassARRAY validation Technical validation of HELP tagging assay data using primers for loci with a range of methylation scores and validation of DML forMARK2 and CDH12 were performed using bisulfite MassARRAY (Mass array nanodispenser, Sequenom, San Diego, CA, USA) [24] on Cohort 1. .. Primers were designed to cover loci with varying levels of DNAmethylation (ESMTable 1).Matched peak data were exported using EpiTYPER software (Sequenom, San Diego, CA, USA) and analysed for quality using analytical tools that we developed [25].

Article Title: In Utero Exposure to a High-Fat Diet Programs Hepatic Hypermethylation and Gene Dysregulation and Development of Metabolic Syndrome in Male Mice
Article Snippet: .. Bisulphite MassARRAY validation To validate HELP assay data, bisulphite MassARRAY (Sequenom, San Diego, CA) was performed using the company’s standard protocol ( 16 ). .. Bisulphite MassARRAY validation To validate HELP assay data, bisulphite MassARRAY (Sequenom, San Diego, CA) was performed using the company’s standard protocol ( 16 ).

Methylation:

HELP Assay:

Article Title: In Utero Exposure to a High-Fat Diet Programs Hepatic Hypermethylation and Gene Dysregulation and Development of Metabolic Syndrome in Male Mice
Article Snippet: .. To validate HELP assay data, bisulphite MassARRAY (Sequenom, San Diego, CA) was performed using the company’s standard protocol ( 16 ). .. Matched peak data were exported using EpiTYPER software (Sequenom, San Diego, CA) and quality analyzed using tools that we developed ( 15 ).

Article Title: In Utero Exposure to a High-Fat Diet Programs Hepatic Hypermethylation and Gene Dysregulation and Development of Metabolic Syndrome in Male Mice.
Article Snippet: .. To validate HELP assay data, bisulphite MassARRAY (Sequenom, San Diego, CA) was performed using the company’s standard protocol (16). .. Matched peak data were exported using EpiTYPER software (Sequenom, San Diego, CA) and quality analyzed using tools that we developed (15).

other:

Article Title: Prostate cancer markers
Article Snippet: Since it is not feasible to use MeDIP-Seq with extensive statistical analyses for every tumour patient we also investigated the applicability of the bisulphite-based mass spectrometry (BS-MS) approach (Sequenom) as a potential technology for routine diagnostic usage.

Article Title: Epigenomic changes associated with impaired norepinephrine transporter function in postural tachycardia syndrome.
Article Snippet: Accepted Manuscript Title: Epigenomic Changes Associated with Impaired Norepinephrine Transporter Function in Postural Tachycardia Syndrome Author: Abdul Waheed Khan Susan J. Corcoran Murray Esler Assam El-Osta PII: S0149-7634(15)30354-7 DOI: http://dx.doi.org/doi:10.1016/j.neubiorev.2016.06.015 Reference: NBR 2476 To appear in: Received date: 19-12-2015 Revised date: 5-6-2016 Accepted date: 15-6-2016 Please cite this article as: Khan, Abdul Waheed, Corcoran, Susan J., Esler, Murray, ElOsta, Assam, Epigenomic Changes Associated with Impaired Norepinephrine Transporter Function in Postural Tachycardia Syndrome.Neuroscience and Biobehavioral Reviews http://dx.doi.org/10.1016/j.neubiorev.2016.06.015 This is a PDF file of an unedited manuscript that has been accepted for publication.. As a service to our customers we are providing this early version of the manuscript.. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form.

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