Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Whole genome DNA methylation analysis with reduced representation bisulfite sequencing (RRBS) to identify Myod1 promoter methylation in brown adipose tissues of D1KO and their respective wild type control mice

ABSTRACT: Our RRBS profiling indicated that the methylation rate at the proximate promoter and 5’-region of Myod1 gene was significantly decreased in brown adipose tissues of D1KO mice compared to their respective wild type control mice

ORGANISM(S): Mus musculus

PROVIDER: GSE175607 | GEO | 2021/09/24

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

RRBS (Reduced Representation Bisulfite Sequencing) of HL60

Project description:We exploited the methylation genome-scale screening RRBS to correlate the RNA species physically associated with DNMT1 and proximal to the annotated genes to the methylation status of the corresponding loci. Out of 15275 non ambiguous gene loci identified by DNMT1 RIP-Seq, 9436 loci were covered by RRBS. These 9436 loci were clustered according to the fold of specific DNMT1 library peaks enrichment (defined as the ratio of the sum of the area under the curve of specific DNMT1 library peaks covering the gene loci). Genes were then stratified by the expression profile ultimately leading to the epitranscriptome map, a comprehensive map cross-referencing DNMT1-interacting transcripts to (i) DNA methylation and (ii) gene expression profile. Relationship between DNMT1-RNA interactions, DNA methylation and gene expression

2012-12-01 | E-GEOD-32168 | biostudies-arrayexpress

RRBS (Reduced Representation Bisulfite Sequencing) of HL60

2012-12-01 | GSE32168 | GEO

Whole genome DNA methylation analysis with reduced representation bisulfite sequencing (RRBS) to identify Myod1 promoter methylation in brown adipose tissues of D1KO and their respective wild type control mice

Project description:Whole genome DNA methylation analysis with reduced representation bisulfite sequencing (RRBS) to identify Myod1 promoter methylation in brown adipose tissues of D1KO and their respective wild type control mice

| PRJNA733066 | ENA

GENE-SWITCH Pig DNA methylation with Reduced representation bisulfite sequencing (RRBS)

Project description: Not available

| S-BSST615 | biostudies-other

GENE-SWITCH Chicken DNA methylation with Reduced representation bisulfite sequencing (RRBS)

Project description: Not available

| S-BSST613 | biostudies-other

Reduced representation bisulfite sequencing (RRBS) of haploid, diploid and triploid hESCs

Project description:To test the differences in genome-wide DNA methylation signatures of haploid, diploid and triploid hESCs, we extracted genomic DNA from these cells and performed RRBS.

2023-05-04 | E-MTAB-11478 | biostudies-arrayexpress

Methylation profile generated by reduced representation bisulfite sequencing (RRBS) of H2O2-treated and untreated HCT116 cells

Project description:DNA methylation is an important regulatory mechanism that contributes to transcriptional repression. To examine whether DNA methylation affects the transcriptional changes of DNA repair genes under H2O2-induced oxidative stress, we performed reduced representation bisulfite sequencing (RRBS) in H2O2-treated and untreated HCT116 cells.

2016-05-01 | GSE75963 | GEO

High concordance between Illumina HiSeq2500 and NextSeq500 for Reduced Representation Bisulfite Sequencing (RRBS)

Project description:Reduced representation bisulfite sequencing (RRBS) provides an efficient method for measuring DNA methylation at single base resolution in regions of high CpG density. This technique has been extensively tested on the HiSeq2500, which uses a 4-colour detection method, however it is unclear if the method will also work on the NextSeq500 platform, which employs a 2-colour detection system. We created an RRBS library and sequenced it on both the HiSeq2500 and NextSeq500, and found no significant difference in the base composition of reads derived from either machine. Moreover, the methylation calls made from the data of each instrument were highly concordant, with methylation patterns across the genome appearing as expected. Therefore, RRBS can be sequenced on the Nextseq500 with comparable quality to that of the HiSeq2500.

2017-02-09 | GSE87097 | GEO

Reduced representation bisulfite sequencing (RRBS) of brown adipose tissue from postnatal day 12 mice perinatally exposed to vehicle or DDT

Project description:The insecticide dichlorodiphenyltrichloroethane (DDT) and its persistent metabolite, dichlorodiphenyldichloroethylene (DDE), have been associated with increased adiposity and obesity in rodent and human studies. These lipophilic pollutants accumulate in adipose tissue and it is theorized that their exposure leads to decreased decrease energy expenditure through the impairment of thermogenesis in brown adipose tissue. We hypothesized that impaired thermogenesis is due to persistent epigenetic modifications of brown adipose tissue. To address this, we exposed C57BL/6J mice to DDT from gestational day 11.5 to postnatal day 5 and isolated brown adipose tissue for RRBS from one offspring per litter when mice reached postnatal day 12 (n=20 DDT litters and 22 vehicle litters). DNA methylation levels in brown adipose tissue of mice perinatally exposed to vehicle or DDT were determined using RRBS. Analyses of differential methylation and KEGG pathway enrichment were performed.

2024-10-05 | GSE255231 | GEO

Laser Capture Microdissection-Reduced Representation Bisulfite Sequencing (LCM-RRBS) maps changes in DNA methylation associated with gonadectomy-induced adrenocortical neoplasia in the mouse

Project description:DNA methylation is a mechanism for long-term transcriptional regulation and is required for normal cellular differentiation. Failure to properly establish or maintain DNA methylation patterns leads to cell dysfunction and diseases such as cancer. Identifying DNA methylation signatures in complex tissues can be challenging due to inaccurate cell enrichment methods and low DNA yields. We have developed a technique called Laser Capture Microdissection-Reduced Representation Bisulfite Sequencing (LCM-RRBS) for the multiplexed interrogation of the DNA methylation status of CpG Islands and promoters. LCM-RRBS accurately and reproducibly profiles genome-wide methylation of DNA extracted from microdissected fresh frozen or formalin-fixed paraffin-embedded tissue samples. To demonstrate the utility of LCM-RRBS, we characterized changes in DNA methylation associated with gonadectomy-induced adrenocortical neoplasia in the mouse. Compared to adjacent normal tissue, the adrenocortical tumors showed reproducible gains and losses of DNA methylation at genes involved in cell differentiation and organ development. LCM-RRBS is a rapid, cost-effective, and sensitive technique for analyzing DNA methylation in heterogeneous tissues and will facilitate the investigation of DNA methylation in cancer and organ development. Laser capture microdissection-reduced representation bisulfite sequencing and reduced representation bisulfite sequencing on human blood leukocyte, human endometrial tumor, mouse liver tissue, and mouse normal and neoplastic adrenal tissue

2013-03-21 | E-GEOD-45361 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data