methPrimer statistics

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Citations per year

Number of citations per year for the bioinformatics software tool methPrimer
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Tool usage distribution map

This map represents all the scientific publications referring to methPrimer per scientific context
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Associated diseases

This word cloud represents methPrimer usage per disease context
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Popular tool citations

chevron_left File format conversion Bisulfite primer design File parsing-extraction chevron_right
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Protocols

methPrimer specifications

Information


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

Taxon


  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus

Subtools


  • MethBlat
  • MethFasta
  • MethSequence

Maintainers


  • 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 http://www.urogene.org/methprimer/

Publications for methPrimer

methPrimer citations

 (476)
call_split

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

2018
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 (http://www.urogene.org/methprimer/) (see Supplementary Table ). BSP amplification products were purified using the MiniBest Agarose Gel DNA Extraction Kit (TaKaRa Bio Inc., Kusatsu, Shiga, […]

library_books

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

2018
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 (http://www.urogene.org/methprimer/, UCSF) [] and listed in Additional file : Table S1. The amplified PCR products were ligated into yT&A vector (Yeastern Biotech, Taiwan). Eight individual […]

library_books

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

2018
Oncotarget
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 (http://www.ncbi.nlm.nih.gov/). UCbase 2.0 (http://ucbase.unimore.it/) was also used for the identification of possible SNPs in Uc160, Uc283 and Uc3 […]

library_books

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

2018
PMCID: 5938046
PMID: 29674693
DOI: 10.1038/s12276-018-0067-4

[…] he mechanism of BASP1 down-regulation in A/E-positive AML, we analyzed the genomic sequence of the BASP1 promoter region (−2000 to −1 bp) by performing a bioinformatics search (http://www.urogene.org/methprimer/) and identified one CpG island with CpGs that were densely clustered close to the transcription start site (Fig. ). Bisulfite sequencing of the genome region from −179 to −400 bp of the BA […]

library_books

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

2018
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 […]

call_split

MeCP2 mediated epigenetic regulation in senescent endothelial progenitor cells

2018
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 (http://www.urogene.org/cgi-bin/methprimer/methprimer.cgi). 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.1.5.243.05 and G.0106.05, and a research grant from the Childhood Cancer Fund 'Kinderkankerfonds'.

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