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methPrimer specifications


Unique identifier OMICS_01841
Name methPrimer
Alternative name methPrimerDB
Interface Web user interface
Restrictions to use None
Input data An original DNA sequence.
Computer skills Basic
Version 2.0
Stability Stable
Maintained Yes


  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus


  • MethBlat
  • MethFasta
  • MethSequence


  • person_outline Jo Vandesompele
  • person_outline Filip Pattyn
  • person_outline Jasmien Hoebeeck
  • person_outline Piet Robbrecht
  • person_outline Evi Michels

Additional information

methPrimer 1.0 is available at

Publications for methPrimer

methPrimer citations


Non thermal plasma treatment improves chicken sperm motility via the regulation of demethylation levels

Sci Rep
PMCID: 5953930
PMID: 29765100
DOI: 10.1038/s41598-018-26049-5
call_split See protocol

[…] erted DNA (50 ng/μl), 10 μl of 2× Prime Taq Premix, 1 μl of upstream primer (5 pmol/μl), 1 μl of downstream primer (5 pmol/μl), and 7 μl of DEPC-treated water. Primers for BSP were designed using the MethPrimer ( (see Supplementary Table ). BSP amplification products were purified using the MiniBest Agarose Gel DNA Extraction Kit (TaKaRa Bio Inc., Kusatsu, Shiga, […]


Inactivation of the tight junction gene CLDN11 by aberrant hypermethylation modulates tubulins polymerization and promotes cell migration in nasopharyngeal carcinoma

PMCID: 5946489
PMID: 29747653
DOI: 10.1186/s13046-018-0754-y

[…] 1.8 μg DNA was treated with sodium bisulfite by using a Zymo DNA Modication Kit (Zymo Research, Hornby, Canada) and amplified by specific bisulfite sequencing (BS) primers that were designed by using Methprimer (, UCSF) [] and listed in Additional file : Table S1. The amplified PCR products were ligated into yT&A vector (Yeastern Biotech, Taiwan). Eight individual […]


Deregulation of methylation of transcribed ultra conserved regions in colorectal cancer and their value for detection of adenomas and adenocarcinomas

PMCID: 5940382
PMID: 29765549
DOI: 10.18632/oncotarget.25115

[…] (qMSP). Bisulfite treated-based methylation-specific primers and relevant Locked Nucleic Acid (LNA) dual labeled hydrolysis probes specific for methylated T-UCRs 160, 283 and 346 were designed using MethPrimer [], following the NCBI library sequences ( UCbase 2.0 ( was also used for the identification of possible SNPs in Uc160, Uc283 and Uc3 […]


Methylation associated silencing of BASP1 contributes to leukemogenesis in t(8;21) acute myeloid leukemia

PMCID: 5938046
PMID: 29674693
DOI: 10.1038/s12276-018-0067-4

[…] manufacturer’s instructions supplied with the EpiTect Bisulfite Kit (Qiagen, Hilden, Germany). The bisulfite sequencing PCR (BSP) and methylation-specific PCR (MSP) primer sequences were designed by Methprimer and are shown in Supplementary Table . For BSP, amplified PCR products were purified and cloned into pGEM-T vectors (Promega, Madison, WI, USA), and five positive clones were sequenced for […]


Exposure to the gut microbiota drives distinct methylome and transcriptome changes in intestinal epithelial cells during postnatal development

Genome Med
PMCID: 5899322
PMID: 29653584
DOI: 10.1186/s13073-018-0534-5

[…] DNA (EpiTect Bisulfite Kit, QIAGEN) followed by PCR-amplification of target differentially methylated position (DMP)-containing regions (EpiMark Hot Start Taq, NEB). Primer pairs were designed using “MethPrimer” [] and target specificity was evaluated using “BiSearch” []. PCR amplicons were normalized using SequalPrep plates (ThermoFisher), pooled sample-wise, and subjected to NGS library preparat […]


MeCP2 mediated epigenetic regulation in senescent endothelial progenitor cells

PMCID: 5883541
PMID: 29615114
DOI: 10.1186/s13287-018-0828-y
call_split See protocol

[…] ini Preparation Kit with Spin Column (Beyotime) and bisulfite converted with the EpiTect Kit (Qiagen). Primers of a CpG island within 2 kb upstream of the initiation codon of SIRT1 were designed with MethPrimer ( Sequences of primers were: forward, 5′-AAGGTTAAGGTAGGTTAGGTGT-3′; and reverse, 5′-CCAACTACCTCTCTAACCCT-3′. PCR products were subc […]


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methPrimer institution(s)
Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium; Belgian EMBnet Node, Université libre de Bruxelles, Campus de la Plaine, Brussels, Belgium
methPrimer funding source(s)
Supported by GOA-grant 12051203, FWO-grant G.0185.04, G. and G.0106.05, and a research grant from the Childhood Cancer Fund 'Kinderkankerfonds'.

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