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TranscriptomicsComprehensive genomic map of cytosine methylation for wild-type (WT) and Lsh-/- mouse embryonic fibroblasts
DNA methylation is critical for normal development and plays important roles in genome organization and transcriptional regulation. Although DNA methyltransferases have been identified, the factors that establish and contribute to genome-wide methylation patterns remain elusive. Here, we report a hi...
ORGANISM(S): Mus musculus 
2011-05-19 | E-GEOD-29394 | biostudies-arrayexpress
GenomicsHigh resolution transcriptome-wide RNA cytosine methylome of Mouse Embryonic Fibroblasts
We report high resolution transcriptome-wide RNA cytosine methylome of Mouse Embryonic Fibroblasts (MEFs) revealed by an optimized new RNA bisulfite sequencing approach. Comparison of RNA methylation profile from wild-type and Dnmt2 -/- MEFs shows that only C38 in three tRNAs (tRNA-Asp, Gly and Val...
ORGANISM(S): Mus musculus 
2013-04-21 | E-GEOD-44359 | biostudies-arrayexpress
ProteomicsMeasurement of deaminated cytosine adducts in DNA using a novel hybrid thymine DNA glycosylase
The hydrolytic deamination of cytosine and 5-methylcytosine drives many of the transition mutations observed in human cancer. The deamination-induced mutagenic intermediates are either uracil or thymine adducts mispaired with guanine. While a substantial array of methods exists to measure other type...
ORGANISM(S): Homo sapiens (Human) 
2022-02-15 | PXD030459 | Pride
Glycosylase Deamination Dna repair Mass spectrometry Dna damage Cytosine Mutation 
GenomicsGenome-wide mapping of cytosine methylation revealed dynamic DNA methylation patterns associated with rice centromeres
Specification and propagation of the centromeres of eukaryotic chromosomes is determined by epigenetic mechanisms. Unfortunately, the epigenetic characteristics of centromeric DNA and chromatin are difficult to define because the centromeres are composed of highly repetitive DNA sequences in most eu...
ORGANISM(S): Oryza sativa 
2010-04-22 | E-GEOD-21414 | biostudies-arrayexpress
TranscriptomicsIdentification of direct targets and modified bases of RNA cytosine methyltransferases
We report development of a mechanism-based technique, Aza-IP, that utilizes the stable covalent linkage formed in vivo between an RNA methyltransferase (m5C-RMT) and 5-azacytidine (5-aza-C) incorporated within the target RNA to enable specific target enrichment, coupled with high-throughput sequenci...
ORGANISM(S): Homo sapiens 
2013-04-21 | E-GEOD-38957 | biostudies-arrayexpress
GenomicsHuman embryonic stem cells HELP-tagging cytosine methylation data (Albert Einstein College of Medicine)
Background: To perform epigenome-wide association studies in human disease, assays need to be comprehensive and quantitative while remaining cost-effective. We explored how the strengths of prior tag-based cytosine methylation assays based on massively-parallel sequencing can be maximised analytica...
ORGANISM(S): Homo sapiens 
2010-04-12 | E-GEOD-19937 | biostudies-arrayexpress
TranscriptomicsGene expression array assay of Lsh WT and Knockout MEF cells
DNA methylation is critical for normal development and plays important roles in genome organization and transcriptional regulation. Although DNA methyltransferases have been identified, the factors that establish and contribute to genome-wide methylation patterns remain elusive. Here, we report a hi...
ORGANISM(S): Mus musculus 
2011-05-19 | E-GEOD-29392 | biostudies-arrayexpress
TranscriptomicsNSun2-mediated cytosine-5 methylation in Vault non-coding RNA determines its processing into small RNAs [iCLIP]
Autosomal-recessive loss of the NSUN2 gene has been recently identified as a causative link to intellectual disability disorders in humans. NSun2 is an RNA methyltransferase modifying cytosine-5 in transfer RNAs (tRNA). Whether NSun2 methylates additional RNA species is currently debated. Here, we a...
ORGANISM(S): Homo sapiens 
2013-07-23 | E-GEOD-44385 | biostudies-arrayexpress
TranscriptomicsNSun2-mediated cytosine-5 methylation in Vault non-coding RNA determines its processing into small RNAs [RNA-seq]
Autosomal-recessive loss of the NSUN2 gene has been recently identified as a causative link to intellectual disability disorders in humans. NSun2 is an RNA methyltransferase modifying cytosine-5 in transfer RNAs (tRNA). Whether NSun2 methylates additional RNA species is currently debated. Here, we a...
ORGANISM(S): Homo sapiens 
2013-07-23 | E-GEOD-44384 | biostudies-arrayexpress
TranscriptomicsGenome-wide variation of cytosine modifications between European and African populations and the implications for complex traits
Elucidating cytosine modification difference between human populations can enhance our understanding of ethnic specificity in complex traits such as disease predisposition and drug response. In this study, cytosine modification levels in 133 HapMap lymphoblastoid cell lines (LCLs) derived from indiv...
ORGANISM(S): Homo sapiens 
2013-07-01 | E-GEOD-39672 | biostudies-arrayexpress
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