Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

8 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

High resolution nulceotide level methylation map of female mouse primary keratinocytes

ABSTRACT: We determined the high resolution methylation maps of female mouse primary keratinocytes and compared these maps at nucleotide level with the female mouse primary dermal fibroblasts. Single nucleotide level methylation maps led us to identify several additional features of CG methylation. We have detected that differentially methylated regions are epigenetically marked in other cells including embryonic stem cells and neuronal progeniator cells. Different new charecteristics and functions were also discovered with these methylation maps. Determinationof whole genome DNA methylation profiles (BS-seq) of primary mouse keratinocytes

ORGANISM(S): Mus musculus

SUBMITTER: Raghunath Chatterjee

PROVIDER: E-GEOD-44918 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

High resolution nulceotide level methylation map of female mouse primary keratinocytes

Project description:We determined the high resolution methylation maps of female mouse primary keratinocytes and compared these maps at nucleotide level with the female mouse primary dermal fibroblasts. Single nucleotide level methylation maps led us to identify several additional features of CG methylation. We have detected that differentially methylated regions are epigenetically marked in other cells including embryonic stem cells and neuronal progeniator cells. Different new charecteristics and functions were also discovered with these methylation maps.

2014-12-08 | GSE44918 | GEO

CG methylated microarrays identify novel methylated sequence bound by the CEBPB|ATF4 heterodimer that are active in vivo

Project description:To evaluate the effect of CG methylation on DNA binding of sequence-specific B-ZIP transcription factors (TFs) in a high-throughput manner, we enzymatically methylated the cytosine in the CG dinucleotide on protein binding microarrays. Using this novel technology, we show that CG methylation enhanced binding for CEBPA and CEBPB and inhibited binding for CREB, ATF4, JUN, JUND, CEBPD and CEBPG. The CEBPB|ATF4 heterodimer bound a novel motif CGAT|GCAA 10-fold better when methylated. EMSA confirmed these results. CEBPB ChIP-seq data using primary female mouse dermal fibroblasts with 50X methylome coverage for each strand indicate that the methylated sequences well-bound on the arrays are also bound in vivo. CEBPB bound 39% of the methylated canonical 10-mers ATTGC|GCAAT in the mouse genome. After ATF4 protein induction by thapsigargin which results in ER stress, CEBPB binds methylated CGAT|GCAA in vivo, recapitulating what was observed on the arrays. mRNA-seq of primary female mouse dermal fibroblasts with and without thapsigargin identified differentially expressed genes. Genes that are commonly bound by CEBPB and ATF4 to TGAT|GCAA (the best-bound 8-mer in the array) at the promoters were highly expressed and up-regulated or remained unchanged in the thapsigargin treated primary female mouse dermal fibroblasts. RNA-Seq: Examination of whole genome transcriptome profiles (RNA-seq) of primary mouse dermal fibroblasts with and without Thapsigargin treatment ChIP-Seq: Examination of transcription factor binding in dermal fibroblasts with and without Thapsigargin teratment BS-Seq: Determination of whole genome DNA methylation profiles (BS-seq) of primary mouse dermal fibroblasts

2013-03-08 | E-GEOD-44942 | biostudies-arrayexpress

Genome-wide DNA methylation map of Zebrafish liver

Project description:Using a pooled (n=10) zebrafish liver DNA, we generated base-resolution DNA methylation maps to document epigenetic landscape in zebrafish genome. Here we generated single-nucleotide resoultion DNA methylation map of zebrafish pooled liver sample using Reduced Representation Bisulfite Sequencing (RRBS)

2014-10-01 | E-GEOD-59917 | biostudies-arrayexpress

Mus musculus

Project description:High resolution nulceotide level methylation map of female mouse primary keratinocytes

| PRJNA192599 | ENA

Genome-wide DNA methylation map of Zebrafish male and female brain

Project description:Using 2 male and 2 female zebrafish (pool of 6) brain samples, we generated base-resolution DNA methylation maps to document sex-specific epigenetic differences. Here we generated single-nucleotide resoultion DNA methylation map of 4 zebrafish brain samples using Reduced Representation Bisulfite Sequencing (RRBS)

2014-10-01 | E-GEOD-59916 | biostudies-arrayexpress

Genome-wide maps of ΔNLef1 in primary mouse keratinocytes

Project description:Genome-wide maps of ΔNLef1 in primary mouse keratinocytes

| PRJNA484337 | ENA

Analysis of paired primary and metastatic cell lines identifies common DNA methylation changes in melanoma metastasis.

Project description:Using 1 melanocyte and 6 melanoma cell line (3 pair of primary and metastatic), we generated base-resolution DNA methylation maps to document DNA methylation drivers of melanoma metastasis. Here we generated single-nucleotide resoultion DNA methylation map of a total of 7 cell lines using Reduced Representation Bisulfite Sequencing (RRBS)

2017-05-17 | E-GEOD-70621 | biostudies-arrayexpress

Genome-wide maps of Gata6 in primary mouse keratinocytes

Project description:In adult K14Î?NLef1 mouse, the overexpression of â??NLef1, a Ã?-catenin dominat negative, in basal keratinocytes leads to the conversion of hair follicles into multilayered epithelial cysts and ectopic sebaceous gland. â??NLef1 transcriptional activity led to Gata6 overexpression in the pilosebaceous unit in transgenic mice. To uncover direct target genes of Gata6 we performed ChIP-Seq experiments in primary mouse keratinocytes. Examination of Gata6 genomic targets in mouse primary keratinocytes

2017-05-16 | E-GEOD-62607 | biostudies-arrayexpress

Nfatc1 promotes stem cell contribution to squamous skin tumors

Project description:We find that epithelial-specific deletion of Nfatc1 decreases skin tumor susceptibility in mice subjected to DMBA/TPA carcinogenesis. To probe the molecular mechanisms by which Nfatc1 may regulate tumorigenesis, we identify gene expression changes associated with constitutive NFATc1 activation in primary mouse keratinocytes. Constitutively active NFATc1 activity in primary mouse keratinocytes to investigate how Nfatc1 regulates tumor initiation in the skin. Primary mouse keratinocytes were infected with retroviruses encoding a recombinant human NFATc1 containing mutations in the autoinhibitory domain that render it constitutively active (CAC1). Keratinocytes infected with retroviruses generated from an empty MSCV reotroviral vector were used as a control. Three biological replicates were performed.

2014-05-06 | E-GEOD-57314 | biostudies-arrayexpress

microRNA profiling of primary human keratinocytes and primary human dermal fibroblasts

Project description:In search for factors, overexpression of which in human dermal fibroblasts causes direct conversion to cells similar to keratinocytes, micro RNA expression profiles of human primary keratinocytes and human primary dermal fibroblasts are investigated. Skin samples obtained from 3 different sites of 1 subject were used for establishment of 3 primary keratinocytes and 3 primary dermal fibroblasts. Thus obtained 3 primary keratinocytes and primary dermal fibroblasts underwent micro RNA profiling.

2016-09-30 | E-MTAB-5055 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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