Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

XAB2 binds genome-wide on putative DNA elements (e.g. enhancers, promoters) that are known to regulate gene expression

ABSTRACT: XAB2 ChIP-Seq profile of mESCs treated with trans-retinoic acid (tRA), a pleiotropic factor known to activate transcription and regulate gene expression during cell differentiation and embryonic development and CHIP-Seq profile of the same cells untreated.

INSTRUMENT(S): Illumina HiSeq 2500

ORGANISM(S): Mus musculus

SUBMITTER: Pantelis Topalis

PROVIDER: E-MTAB-8033 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

The impact of XAB2 on gene expression and pre-mRNA splicing

Project description:Xab2 knock down followed by RNA-sequencing of oligo-dT selected transcripts

2020-08-19 | E-MTAB-8035 | biostudies-arrayexpress

The role of DNA repair endonuclease XPF in transcription

Project description:In this experiment we want to explore and compare the bindind of XPF in normal MEFs, in tRA treated MEFs and in UV radiated MEFs

2020-08-19 | E-MTAB-8154 | biostudies-arrayexpress

Transcriptional activity during NuRD complex induction

Project description:Molecular functions of the Nucleosome Remodeling and Deacetylation (NuRD) complex in the control of gene expression were investigated using an inducible system to direct its assembly in embryonic stem cells. This dataset profiles time-resolved transcriptional changes in response to NuRD induction.

2018-05-31 | E-MTAB-6806 | biostudies-arrayexpress

Transcription factor binding and epigenetic modifications during NuRD complex induction

Project description:Molecular functions of the Nucleosome Remodeling and Deacetylation (NuRD) complex in the control of gene expression were investigated using an inducible system to direct its assembly in embryonic stem cells. This dataset maps time-resolved DNA association of NuRD complex members, pluripotency factors, components of the RNA polymerase II machinery and changes to histone modifications.

2018-05-31 | E-MTAB-6804 | biostudies-arrayexpress

Nascent transcription during NuRD complex induction

Project description:Molecular functions of the Nucleosome Remodeling and Deacetylation (NuRD) complex in the control of gene expression were investigated using an inducible system to direct its assembly in embryonic stem cells. This dataset profiles nascent RNA transcription in response to NuRD induction.

2018-05-31 | E-MTAB-6805 | biostudies-arrayexpress

Global gene expression analysis in murine iPS cells derived with mouse, chick and zebrafish Nanog orthologs

Project description:Nanog null neural stem (NS) cells were reprogrammed to naive pluripotency in 2i/LIF conditions with chick (c) and zebrafish (z) Nanog orthologs. Global gene expression was compared to iPS cells derived with mouse (m) Nanog. Murine iPS cells derived with zebrafish nanog, chick nanog, and mouse nanog orthologs (2 replicates each).

2011-10-23 | E-GEOD-32650 | biostudies-arrayexpress

Global gene expression analysis in murine iPS cells derived with mouse and human Nanog orthologs

Project description:Nanog null neural stem (NS) cells were reprogrammed to naive pluripotency in 2i/LIF conditions with mouse (m) Nanog and human (h) Nanog. Global gene expression in resulting iPS cells was compared to embryonic stem (ES) cells and nanog null NS cells. Murine iPS cells derived with mouse nanog iPS and human nanog iPS and then compared to embryonic stem cells and nanog null neural stem cells (3 replicates each).

2011-10-23 | E-GEOD-32464 | biostudies-arrayexpress

Global gene expression analysis of PB-Oct4.2A.cherry iPS-/-, PB-Oct4.2A.cherry (low) iPS-/- and ES cells

Project description:We have generated iPS cell lines with constitutive Oct4 expression at ES-cell level or 3 times lower. The aim of the experiment was to compare the global gene expression profile between these two cell lines and also between each of them and wild type ES cells. We have analysed two biological replicates of each cell line

2013-04-30 | E-GEOD-45003 | biostudies-arrayexpress

NaÃ¯ve pluripotency is associated with global DNA hypomethylation

Project description:Naive pluripotent embryonic stem cells (ESCs) and embryonic germ cells (EGCs) are derived from the preimplantation epiblast and primordial germ cells (PGCs), respectively. We investigated whether differences exist between ESCs and EGCs, in view of their distinct developmental origins. PGCs are programmed to undergo global DNA demethylation; however, we find that EGCs and ESCs exhibit equivalent global DNA methylation levels. Importantly, inhibition of Erk and Gsk3b by 2i conditions leads to pronounced reduction in DNA methylation in both cell types. This is driven by Prdm14 and is associated with downregulation of Dnmt3a and Dnmt3b. However, genomic imprints are maintained in 2i, and we report derivation of EGCs with intact genomic imprints. Collectively, our findings establish that culture in 2i instills a naive pluripotent state with a distinctive epigenetic configuration that parallels molecular features observed in both the preimplantation epiblast and nascent PGCs. EGC lines were derived from E8.5 mouse embryos using three different protocols: FCS+LIF on MEFs (FCS, n = 4)), FCS+LIF on MEFs for 48 hours followed by 2i+LIF (2is, n = 4), and direct derivation into 2i+LIF (2i, n = 4). ESC lines were derived in either FCS+LIF on MEFs or in 2i+LIF conditions and once established the cell lines were also switched between the two culture environments (n = 5 for each culture condition). All cell lines were derived from genetically identical embryos.

2013-02-17 | E-GEOD-43398 | biostudies-arrayexpress

Myc Depletion in NaÃ¯ve ESCs Induces a Pluripotent Dormant State Mimicking Embryonic Diapause

Project description:Microarray expression analysis of mouse ESCs treated with the MYCi 10058-F4. Mouse ESCs were analysed after 60h of treatment with DMSO or 10058-F4 (MYCi). The MYCiâReleased (Resc) group was treated with 10058-F4 for 60h, followed by withdrawal of the inhibitor and culture in 2i medium for additional 48h.

2016-02-11 | E-GEOD-74337 | 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