Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genome wide 5hmC patterns in the mouse liver, embryonic fibroblasts and induced pluripontent stem cells.

ABSTRACT: We carry out hydroxymethyl DNA immunoprecipitation (hmeDIP) prior to sequencing on the Ion Proton semiconductor sequencing platform to demonstate the strategy as an alternative method to Illumina sequencing.

ORGANISM(S): Mus musculus

PROVIDER: GSE66889 | GEO | 2015/06/01

SECONDARY ACCESSION(S): PRJNA278274

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Genome-wide epigenetic maps in the liver from male and female Wistar and Sprague-Daley rats

Project description:We carry out methyl DNA immunoprecipitation (meDIP) and hydroxymethyl DNA immunoprecipitaion (hmeDIP) prior to sequencing on the Ion Proton semiconductor sequencing platform to report on the genome-wide epigenetic patterns in rat livers

2018-03-07 | GSE111442 | GEO

MEK and GSK3β inhibition drives ES cells into a naive pluripotent state irrespective of their global methylation status

Project description:We carry out methyl DNA immunoprecipitation (meDIP), hydroxymethyl DNA immunoprecipitaion (hmeDIP) and H3K27me3 chromatin imminoprecipitation (ChIP) prior to sequencing on the Ion Proton semiconductor sequencing platform to report on the genome-wide epigenetic patterns in J1 mESC and mutant mESCs (hyper active DNMT3b/3l or DNMT1/3a/3b triple knock out) grown under serum conditions or in 2i meadia for 14 days

2019-09-24 | GSE72555 | GEO

DNA IP for 5hmC modified CpGs in the liver of control and HFD fed mouse liver.

Project description:We carry out 5-hydroxymethylation DNA immunoprecipitation (hmeDIP) prior to sequencing Ion Proton P1 to report on the genome-wide 5hmC patterns of hepatic in murine hepatic steatosis.

2019-01-12 | GSE109138 | GEO

DNA IP for 5hmC modified CpGs in the liver of control mice and a Tet1 -/- mouse liver [hmeDIP-seq]

Project description:Through the analysis of mouse liver tumours promoted by distinct routes (DEN exposure alone, DEN exposure plus non-genotoxic insult with phenobarbital and non-alcoholic fatty liver disease); we report that the cancer associated hyper-methylated CGI events in mice are also predicated by silent promoters that are enriched for both the DNA modification 5-hydroxymethylcytosine (5hmC) and the histone modification H3K27me3 in normal liver. During cancer progression these CGIs undergo hypo-hydroxymethylation, prior to subsequent hyper-methylation; whilst retaining H3K27me3. A similar loss of promoter-core 5hmC is observed in Tet1 deficient mouse livers indicating that reduced Tet1 binding at CGIs may be responsible for the epigenetic dysregulation observed during hepatocarcinogenesis. Consistent with this reduced Tet1 protein levels are observed in mouse liver tumour lesions. As in human, DNA methylation changes at CGIs do not appear to be direct drivers of hepatocellular carcinoma progression in mice. Instead dynamic changes in H3K27me3 promoter deposition are strongly associated with tumour-specific activation and repression of transcription. Our data suggests that loss of promoter associated 5hmC in diverse liver tumours licences DNA methylation reprogramming at silent CGIs during cancer progression. We carry out 5-hydroxymethylation DNA immunoprecipitation (hmeDIP) prior to sequencing Ion Proton P1 to report on the genome-wide 5hmC patterns. Heterozygote pairs of Tet1 B6;129S4-Tet1tm1.1Jae/J mice were bought from The Jackson Laboratory (Maine USA). Heterozygotes were interbred to produce homozygous knock out males with colony mate wild type controls. Genome-wide 5hmC patterns were generated by hydroxymethyl-DNA immuoprecipitation (hmeDIP) followed by genome wide sequencing on the Ion Proton P1 sequencer.

2016-05-17 | E-GEOD-77730 | biostudies-arrayexpress

Comparative high density microarray analysis of global 5hmC patterns in mouse brain and liver following independent affinity based enrichment protocols.

Project description:On mouse tiled microarrays (GPL17802), we profile 5hmC in WT mouse livers and brains following fragment enrichment by one of three affinity based techniques: i- antibody (HmeDIP), ii- Chemical capture (hMeSeal) and iii-JBP-1 protein affinity (JBP). HmeDIP and hMeSeal both return similar patterns of 5hmC whilst JBP enriched patterns (carriedo out on brain only) resemble background noise. 5hmC is largely found to reside in the bodies of active genes as well as being enriched over enhancer and promoter proximal regions. WT C57BL/6 mice aged 30-32 days old at time of organ removal. Tissues taken and frozen in liquid nitrogen prior to DNA extraction. Genomic DNA was sonicated (Bioruptor, Diagenode) to produce DNA fragments ranging in size from 200 to 1,000 bp, with a mean fragment size of around 300 bp. i- HmeDIP: antibody enrichment carried out as previously reported by Thomson et al 2013 (doi:10.1093/nar/gkt232). ii- HmeSeal: Enrichment based on the hMe-Seal based techniques described by Song et al 2010 (doi: 10.1038/nbt.1732) and marketed by Active motif under the name hydroxymethyl-collector kit. iii- JBP-1 affinity purification: Enrichment carried out using the Quest 5hmC DNA enrichment kit marketed by Zymo research.

2013-12-01 | E-GEOD-51577 | biostudies-arrayexpress

Project description:Double-digest RAD Sequencing using Ion Proton semiconductor platform (ddRADseq-ion) with non-model organisms

| PRJNA276094 | ENA

Semiconductor based DNA sequencing of histone modification states

Project description:The recent development of a semiconductor-based, non-optical DNA sequencing technology promises scalable, low-cost and rapid sequence data production. The technology has previously been applied mainly to genomic sequencing and targeted re-sequencing. Here, we demonstrate the utility of Ion Torrent semiconductor-based sequencing for sensitive, efficient and rapid chromatin immunoprecipitation followed by sequencing (ChIP-seq) through the application of sample preparation methods that are optimized for ChIP-seq on the Ion Torrent platform. We leverage this method for epigenetic profiling of tumor tissues. Examination of histone modifications in mouse dendentic cells stimulated with LPS, matched melanoma derived cell line, melanoma tumor tissue

2013-10-25 | E-GEOD-49477 | biostudies-arrayexpress

Semiconductor based DNA sequencing of histone modification states

2013-10-25 | GSE49477 | GEO

MicroRNA sequencing of mouse soleus muscle

Project description:MicroRNA sequencing using Ion Torrent Proton platform

2015-03-31 | GSE63342 | GEO

MicroRNA sequencing of mouse soleus muscle

Project description:MicroRNA sequencing using Ion Torrent Proton platform Single run of a pool of m.soleus from 5 male mice

2015-03-31 | E-GEOD-63342 | biostudies-arrayexpress