methPrimer statistics

To access cutting-edge analytics on consensus tools, life science contexts and associated fields, you will need to subscribe to our premium service.

Subscribe
info

Citations per year

Citations chart
info

Popular tool citations

chevron_left File format conversion Bisulfite primer design File parsing-extraction chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

Protocols

To access compelling stats and trends, optimize your time and resources and pinpoint new correlations, you will need to subscribe to our premium service.

Subscribe

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 in pipelines

 (17)
2017
PMCID: 5502268
PMID: 28740500
DOI: 10.3389/fpls.2017.01178

[…] providing plant materials., http://bioinfo.ut.ee/primer3/ , http://genes.mit.edu/genscan.html , http://www.psc.edu/biomed/genedoc , http://www.arabidopsis.org/ , http://www.urogene.org/cgi-bin/methprimer/methprimer.cgi , http://linux1.softberry.com/berry.phtml , the supplementary material for this article can be found online at: […]

2017
PMCID: 5515838
PMID: 28720816
DOI: 10.1038/s41598-017-05961-2

[…] was isolated and treated with bisulfate using the epitect® bisulfite kit (qiagen, usa) according to the manufacturer’s instructions. the primers for detection of dna methylation were designed using methprimer (http://www.urogene.org/methprimer/) and modified using primer3web (http://primer3.ut.ee/). pcr products were cloned into a pgem-t vector (promega, usa) and subsequently sequenced using […]

2017
PMCID: 5560095
PMID: 28671686
DOI: 10.1038/ng.3906

[…] was utilized for fine-mapping of methylation patterns in cpcdh candidate sequences. genomic dna (1 μg) was bisulfite-converted using the epitect bisulfite kit (qiagen). primers were designed in methprimer and bisulfite-converted dna was amplified and multiplexed by high throughput pcr using a fluidigm accessarray instrument. pcrs were performed in duplicate and the duplicates pooled. […]

2017
PMCID: 5589591
PMID: 28903352
DOI: 10.18632/oncotarget.17081

[…] and co-expression information., phylogenetic tree was made using mega 6 after aligning the downloaded sequences in clustalw.we searchedwith interproscan [] in ebi, we identify cpg islands using methprimer [], and finally searched snps and cnvs from dbsnp and dgv respectively., molecular docking analysis were performed using moe (molecular operating environment) software []. protein […]

2017
PMCID: 5638567
PMID: 29023530
DOI: 10.1371/journal.pone.0186411

[…] corporation) and bioedit [] were employed for sequence alignment and visualization. the prediction of cpg islands was conducted using putative promoter regions sequences of arα with the online tool methprimer (http://www.urogene.org/cgi-bin/methprimer/methprimer.cgi) []., a 118 bp cdna fragment containing the heterozygous site (site 1947, []) was amplified with the same primers as used […]


To access a full list of citations, you will need to upgrade to our premium service.

methPrimer in publications

 (766)
PMCID: 5953930
PMID: 29765100
DOI: 10.1038/s41598-018-26049-5

[…] 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, […]

PMCID: 5951854
PMID: 29760437
DOI: 10.1038/s12276-018-0091-4

[…] next, we examined whether cd82 dna methylation directly influenced mtb-induced cd82 expression. portions of the cd82 gene, spanning positions −127 to −286 bp or −2194 to −2351 bp, were analyzed with methprimer, which is a cpg island prediction program (http://www.urogene.org/methprimer/). the results showed that this fragment contained several cpg-rich regions (fig. , upper). bisulfite […]

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 indivi […]

PMCID: 5921809
PMID: 29699590
DOI: 10.1186/s13046-018-0764-9

[…] pcr by amplified the genomic dna after standard sodium bisulfate modification. primer sequences which specifically recognized either the methylated or unmethylated tgfbr2 promoter were designed with methprimer (http://www.urogene.org/cgi-bin/methprimer/methprimer.cgi). the pcr conditions were: 95 °c for 5 min, followed by 40 cycles of 95 °c for 15 s, 57 °c for 30s, 72 °c for 30s; and a final […]

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 […]


To access a full list of publications, you will need to upgrade to our premium service.

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'.

methPrimer reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review methPrimer