Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

12 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genome-wide maps of KDM5A/JARID1A/RBP2 in mouse ES cells.

ABSTRACT: We report the identification of genomic regions bound by KDM5A in mouse embryonic stem (ES) cells and define the functional categories that these regions represent. KDM5A modifies methylated lysine residues on histone tails. We developed anti-KDM5A antibodies and set to detect genomic regions enriched with these antibodies using cells with normal Kdm5a or cells from Kdm5a knockout mice as a control. We found high enrichment with the KDM5A antibodies in normal cells when compared with the genomic background. We found striking identity in the regions enriched with these antibodies in normal cells when compared with the total genomic DNA or with KDM5A ChIP assays from Kdm5a KO cells, showing that the antibodies are specific. Examination of target genes in ES cells

ORGANISM(S): Mus musculus

SUBMITTER: Elizaveta Benevolenskaya

PROVIDER: E-GEOD-28343 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Changes in H3K4 methylation in KDM5A/JARID1A/RBP2 knockout cells.

Project description:We sought to determine H3K4me3 distribution in mouse embryonic stem (ES) cells deficient for RBP2 compared with wild-type cells. RBP2 modifies methylated lysine residues on histone tails. As a result of this analysis, we identified genomic regions with changed H3K4me3 status and described these in gene ontology (GO) categories. Examination of histone methylation in the absence of histone demethylase RBP2

2015-08-12 | E-GEOD-28348 | biostudies-arrayexpress

Arid3a modulates the first cell fate decision by direct regulation of both embryonic and extraembryonic gene expression (ChIP-Seq)

Project description:Arid3a, a transcription factor known for its requirement in B-lymphocyte development, has been recently identified as a member of ES cell pluripotency network. Arid3a is moderately expressed in ES cells, and its expression is gradually increased during differentiation. Since Arid3a shows the highest expression in placenta, we hypothesized that Arid3a may play important roles in TE development. We report that Arid3a is a central regulator of both TE-specific and pluripotency-associated gene expression during ES cell differentiation. While dispensable for self-renewal, we observed that knockdown of Arid3a delays differentiation of ES cells. Induction of Arid3a leads ES cells to promote differentiation, specifically towards TE lineage. Moreover, these Arid3a-overexpressing cells maintained in TE culture media are sufficient to generate functional trophoblast stem-like cells, suggesting roles of Arid3a in TE differentiation. By integrative analyses using the chromosomal targets of Arid3a with expression profiling, we revealed the dual roles of Arid3a, as a direct activator of TE-specific genes and a repressor of pluripotency-associated genes. We further revealed the repressive roles of Arid3a are mediated by histone deacetylases (HDACs). Taken together, our results demonstrate that Arid3a is a critical novel regulator in TE lineage specification. Arid3a ChIP was performed using bioChIP-sequencing. Control ChIP-sequencing was performed using BirA cells. HDAC1 ChIP was performed as native antibody ChIP-sequencing.

2014-10-16 | E-GEOD-56876 | biostudies-arrayexpress

Arid3a modulates the first cell fate decision by direct regulation of both embryonic and extraembryonic gene expression (microarray)

Project description:Arid3a, a transcription factor known for its requirement in B-lymphocyte development, has been recently identified as a member of ES cell pluripotency network. Arid3a is moderately expressed in ES cells, and its expression is gradually increased during differentiation. Since Arid3a shows the highest expression in placenta, we hypothesized that Arid3a may play important roles in TE development. We report that Arid3a is a central regulator of both TE-specific and pluripotency-associated gene expression during ES cell differentiation. While dispensable for self-renewal, we observed that knockdown of Arid3a delays differentiation of ES cells. Induction of Arid3a leads ES cells to promote differentiation, specifically towards TE lineage. Moreover, these Arid3a-overexpressing cells maintained in TE culture media are sufficient to generate functional trophoblast stem-like cells, suggesting roles of Arid3a in TE differentiation. By integrative analyses using the chromosomal targets of Arid3a with expression profiling, we revealed the dual roles of Arid3a, as a direct activator of TE-specific genes and a repressor of pluripotency-associated genes. We further revealed the repressive roles of Arid3a are mediated by histone deacetylases (HDACs). Taken together, our results demonstrate that Arid3a is a critical novel regulator in TE lineage specification. Arid3a overexpression and Arid3a knockdown Total RNA was isolated from cultured cells using RNeasy plus mini kit (Qiagen). cDNA were synthesized and labelled, followed by hybridization on Affymetrix GeneChip mouse genome 430A 2.0 arrays.

2014-10-16 | E-GEOD-56853 | biostudies-arrayexpress

Arid3a modulates the first cell fate decision by direct regulation of both embryonic and extraembryonic gene expression

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2014-10-16 | E-GEOD-56877 | biostudies-arrayexpress

CpG island-mediated global gene regulatory modes in mouse embryonic stem cells

Project description:In order to identify the regions occupied by transcription factors, we performed bio-ChIP followed by massive parallel sequencing (bioChIP-Seq) in mouse ES cells. A total of seven DNA transcription factors including Myc module (Myc, Max, E2F4, Tip60 and Dmap1) and Core module transcription factors (Nanog, Dax1; Kim et al., 2010) were identified. We show that the transcription factors can be classified into several classes according to their occupancies. Our data also show transcription factors in the same class co-occupy the same regulatory elements, share the common characteristics and act together. Identification of seven transcription factor binding sites in mES cells

2014-11-24 | E-GEOD-48666 | biostudies-arrayexpress

cis regulated role of lncRNA in transcriptional or developmental process

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2016-03-24 | E-GEOD-70420 | biostudies-arrayexpress

An interactive database for the assessment of histone antibody specificity

Project description:Commercially available histone antibodies were analyzed using peptide microarrays to assess specificity. For two H3K27me3 antibodies from different vendors, we performed ChIP-seq in WT and EED-null murine ES cells to assess specificity. Cell lines were generated from e3.5 blastocysts of EED fl/fl animals and transfected with plasmid CAG-CRE-ERT2. Null cells were generated by single cell clones from tamoxifen-treated parent cell line. Analysis of the specificity of two H3K27me3 antibodies using WT and EED (Embryonic Ectoderm Develepment)-null (mutants lacking H3K27me3) ES cells. The goal was to compare WT and KO for each antibody with the expectation that if the antibodies were specific, there would remain few peaks and little signal in the knockout. We sequenced 2 replicates of each condition (3 for WT input) and after comparing replicates, we merged data, called peaks, and calculated signal in bins centered on the wild type H3K27me3 peaks. As little to no signal remained either by direct comparison of peaks or looking at 'metagenes' of the peaks, we concluded that the antibodies were specific. Antibodies: Abcam H3K27me3 (ab6002, lot# GR130002-1) Upstate H3K27me3 (07-449, lot# 2455635)

2015-06-21 | E-GEOD-66902 | biostudies-arrayexpress

Derivation of rat induced pluripotent stem cells that share similarities with embryonic stem cells using a transposon system

Project description:Induced pluripotent stem (IPS) cells have attracted enormous attention due to their vast potential in regenerative medicine, pharmaceutical screening and basic research. The majority of prior established rat IPS cells were generated from somatic cells by retroviral and lentiviral transduction with expression of Oct4, Sox2, Klf4 and c-Myc and using chemical inhibitors of key differentiation pathways. A major difficulty in the application of this technology is the efficient delivery of reprogramming factors and the long-term maintenance of properties of stem cells. Here, we employed the PiggyBac (PB) transposon carrying four 2A peptide-linked reprogramming factors for generating rat IPS cells. These stable rat IPS cells are similar to embryonic stem (ES) cells in morphology, proliferation, teratoma formation, expression characteristic pluripotency markers, developmental potential, and germline transmission. Transcriptional profiling of the IPS cells revealed both pathways in common with ES cells from rat and unique signaling pathway to our cells, including Wnt, TGF and Notch. The cell lines and information obtained in this study will accelerate our understanding of the molecular regulation underlying germline pluripotency and pave the way for exploration of cell-based therapies using the rat. To compare the gene expression profiling between rat IPS cells and ES cells to show if the rat IPS cells had been reprogrammed into pluripotent status like rat ES cells at the gene expression level.

2012-02-16 | E-GEOD-35841 | biostudies-arrayexpress

cis regulated role of lncRNA in transcriptional or developmental process (ChIRP-Seq)

Project description:We report that long noncoding RNAs contribute to transcription and developmental process. Thousands of lncRNAs have been identified in the whole genome, and tend to located closely to protein-coding genes. To study position relationship between lncRNA and protein-coding genes, we classified all of lncRNA to several subgroups based on the genome position with their coding neighbors. XH, the head to head subgroup is associated with transcription and development in GO analysis. Here, we knockdown serveral XH lncRNA by shRNA in embryonic stem cells and induce nondirectional differnetiation by removing LIF or neural differnetiation by RA. Knockdown of XH lncRNAs led to uniform downregulation of nearby coding genes, and form regulatory circuits with its nearby coding genes to fine-tune embryonic lineage development. In addition, we also knockout one lncRNA-Evx1as and its nearby protein-coding gene-EVX1 by CRISPR, and get similar results as knockdown.We propose that XH lncRNA may function primarily as 'cis-regulators' of the expression of nearby protein-coding genes, and tend to participate in transcriptional or development regulations as their coding neighbors. All RNA-seq(s) were designed to reveal the differentially expressed genes between wild-type and XH lncRNA knockdown/knockout ESCs during differentiation.

2016-03-24 | E-GEOD-79541 | biostudies-arrayexpress

Evx1as and EVX1 knockouts by CRISPR

2016-03-24 | E-GEOD-70419 | 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