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Protocols

QUMA specifications

Information


Unique identifier OMICS_30603
Name QUMA
Alternative name QUantification tool for Methylation Analysis
Interface Web user interface
Restrictions to use None
Input data Some target genomic sequence and raw bisulfite sequences.
Computer skills Basic
Stability Stable
Maintained Yes

Maintainers


  • person_outline Masaki Okano
  • person_outline Yuichi Kumaki

Publication for QUantification tool for Methylation Analysis

QUMA citations

 (111)
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Accurate estimation of 5 methylcytosine in mammalian mitochondrial DNA

2018
Sci Rep
PMCID: 5895755
PMID: 29643477
DOI: 10.1038/s41598-018-24251-z
call_split See protocol

[…] ng cycle sequencing. Insert sequences were then aligned with reference sequences using ATGC Sequence Assembly Software (GENETYX Inc., Japan) and the methylation status of mtDNA was analysed using the QUMA programme. […]

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

[…] s were subcloned into pCR2.1 vector with the TopoTA cloning Kit (Invitrogen). Six colonies were picked, plasmid DNA was purified, and DNA was sequenced. The degree of methylated DNA was analyzed with QUMA (http://quma.cdb.riken.jp/top/index.html). […]

call_split

Comparison of whole genome bisulfite sequencing library preparation strategies identifies sources of biases affecting DNA methylation data

2018
Genome Biol
PMCID: 5856372
PMID: 29544553
DOI: 10.1186/s13059-018-1408-2
call_split See protocol

[…] final 72 °C for 10 min and sent for Sanger sequencing at Beckman Coulter Genomics. All oligonucleotides are listed in Additional file : Table S2. Methylation of the sequenced clones was analysed with QUMA [] and plotted with a custom made R script. […]

library_books

Epigenetic modulation of Fgf21 in the perinatal mouse liver ameliorates diet induced obesity in adulthood

2018
Nat Commun
PMCID: 5809372
PMID: 29434210
DOI: 10.1038/s41467-018-03038-w

[…] tors (#A1360, Promega, Madison, WI, USA), and more than 13 clones were sequenced per reaction. We used a web-based quantification tool for the bisulfite-sequencing analysis of CpG methylation (http://quma.cdb.riken.jp/). […]

library_books

Ribosome Incorporation into Somatic Cells Promotes Lineage Transdifferentiation towards Multipotency

2018
Sci Rep
PMCID: 5786109
PMID: 29374279
DOI: 10.1038/s41598-018-20057-1

[…] it (TAKARA, Shiga, Japan) and the product was immediately amplified by using EpiTaq HS (TAKARA) with OCT4, NANOG, and LMNA primer pairs, which are listed in Table . Sequence data were analyzed on the QUMA server in RIKEN CDB. […]

call_split

Transcriptional Regulation by CpG Sites Methylation in the Core Promoter Region of the Bovine SIX1 Gene: Roles of Histone H4 and E2F2

2018
Int J Mol Sci
PMCID: 5796162
PMID: 29337851
DOI: 10.3390/ijms19010213
call_split See protocol

[…] bcloned into the pMD19-T vector (Takara). Different positive clones for each subject were randomly selected for sequencing (Sangon, Shanghai, China). Finally, the sequences were analyzed using online QUMA software []. […]

Citations

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QUMA institution(s)
Laboratory for Mammalian Epigenetic Studies, Center for Developmental Biology, RIKEN, Kobe, Japan
QUMA funding source(s)
Supported in part by Grants-in-Aid from the Ministry of Education, Culture, Sports, Science and Technology of Japan.

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