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

Genome-wide microRNA transcriptome profiles in pluripotent mouse Embryonic Stem Cells and during Retinoic Acid-induced differentiation

ABSTRACT: We report the genome-wide microRNA expression levels in pluripotent mESC and as mESC differentiate towards a neuronal lineage in response to high levels of Retinoic Acid treatment in vitro. microRNA-seq was performed to identify all microRNAs expressed in both ESCs and neuronal cells. In total, 534 expressed microRNAs we identified, of which 18 were up-regulated and 6 were down-regulated (fold change (FC) > -/+2.0 and p-value < 0.05) during Retinoic Acid-induced neuronal differentiation. The top up-regulated microRNAs identified were Mir10a, Mir615, Mir217 and Mir219a-2. The top down-regulated microRNAs identifed were Mir211, Mir292, Mir302a and Mir302c. Examination, identification and comparision of microRNA expression profliles in two cellular states.

ORGANISM(S): Mus musculus

SUBMITTER: Michal Stachowiak

PROVIDER: E-GEOD-65696 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Genome-wide microRNA transcriptome profiles in pluripotent mouse Embryonic Stem Cells and during Retinoic Acid-induced differentiation

Project description:We report the genome-wide microRNA expression levels in pluripotent mESC and as mESC differentiate towards a neuronal lineage in response to high levels of Retinoic Acid treatment in vitro. microRNA-seq was performed to identify all microRNAs expressed in both ESCs and neuronal cells. In total, 534 expressed microRNAs we identified, of which 18 were up-regulated and 6 were down-regulated (fold change (FC) > -/+2.0 and p-value < 0.05) during Retinoic Acid-induced neuronal differentiation. The top up-regulated microRNAs identified were Mir10a, Mir615, Mir217 and Mir219a-2. The top down-regulated microRNAs identifed were Mir211, Mir292, Mir302a and Mir302c.

2015-05-01 | GSE65696 | GEO

Genome-wide transcriptome profiles in pluripotent mouse Embryonic Stem Cells and during Retinoic Acid-induced differentiation

Project description:We report the genome-wide RNA expression levels in pluripotent mESC and as mESC differentiate towards a neuronal lineage in response to high levels of Retinoic Acid treatment in vitro. RNA-seq was performed to identify all RNAs expressed in both ESCs and neuronal cells. In total, In total, 14,443 expressed genes were detected, of which 1,834 were up-regulated and 1,477 down-regulated (fold change (FC) > -/+2.0 and p-value < 0.035) during RA-induced neuronal differentiation. The top down-regulated genes included members of the pluripotency core transcriptional network, including Klf4, Sox2, Oct4, Nanog, Suz12, Esrrb, Stat3 and Tcfcp2l1. The top up-regulated genes are important for neuronal differentiation (e.g. Pax3, Irx3, Rest and Foxd3) and reside in the RA-pathway (e.g. various homeobox genes), the retinoic acid receptors and the RA-degradation enzyme Cyp26a1. Examination, identification and comparision of mRNA expression profliles in two cellular states.

2015-05-01 | E-GEOD-65697 | biostudies-arrayexpress

Genome-wide binding profiles of nuclear FGFR1, RXR? and Nur77 in pluripotent mouse Embryonic Stem Cells and during Retinoic Acid-induced differentiation

Project description:We report the genome-wide binding patterns of nuclear FGFR1, RXR? and Nur77 in pluripotenet mESC and as mESC differentiate towared a neuronal lineage in response to high levels of Retinoic Acid treatment in vitro. We also report the genome-wide incorporation of histone varant H3.3 into chromatin specifically during Retinoic Acid-induced differentiation. This study presents nuclear FGFR1 as a global factor that controls genomic function by binding within the promoters of thousands of genes, both alone and in cooperation with RXR, Nur77 and histone H3.3, by targeting consensus DNA sequences of diverse transcription factor families. As such, it identifies a previously unknown, multifaceted form of control of major ontogenic pathways and gene networks targeted by the nuclear form of FGFR1. Examination of nuclear FGFR1, RXR?, and Nur77 binding sites in 2 celluar states. Examination of H3.3 incorporation in 1 cellular state.

2015-05-01 | E-GEOD-65695 | biostudies-arrayexpress

Genome-wide transcriptome profiles in pluripotent mouse Embryonic Stem Cells and during Retinoic Acid-induced differentiation

2015-05-01 | GSE65697 | GEO

MicroRNA profiling of mouse embryonic stem cells during retinoic acid-induced differentiation

Project description:Changes in microRNA expression profile during retinoic acid-induced differentiation of mouse embryonic stem cells.

2007-04-01 | E-MEXP-977 | biostudies-arrayexpress

RNA-Seq profiling of mESCs and their neuronal derivatives overexpressing WT DNMT1 and DNMT1Y495C mutant form

Project description:To understand the molecular basis of neurodevelopmental abnormalities in HSAN1E disorder associated with DNMT1 Y495C mutation, we have developed transgenic mouse ES lines (R1Dnmt1 Y495C) that expresses mutant transcripts in addition to the endogenous wild-type transcripts. We also generated a transgenic cell line that overexpresses the wild-type transcripts (R1wt Dnmt1) to segregate the effects of mutant proteins. We performed transcriptome profiling of mESC lines and their neuronal derivatives using RNA-seq. Dysregulated transcripts in R1wt Dnmt1 and R1Dnmt1 Y495C mESCs and neurons were identified by comparisons with the wild-type counterpart (R1; wild-type mESC line). Gene ontology and pathway enrichment analysis were performed to identify potential pathways and key regulatory genes underlying the HSAN1E associated neurodevelopmental phenotypes.

2023-12-01 | E-MTAB-13337 | biostudies-arrayexpress

Wnt & LIF signalling in mESC

Project description:The molecular processes underlying the properties of ESC are yet unknown even when it's well established that LIF/STAT3 is neccesary for the maintenance of pluripotency. Other pathways as Wnt are may be implicated in the regulation of the biological mechanisms in mESC. Work model: D3-ES cultivated with or without LIF and treated with chronic (7 days) low doses (50nM) of GSK3 β inhibitor (lithium). We used microarrays to detail the global profile of gene expression to identified different groups of up and down-regulated genes in the work model. mESC cultivated as it has been defined in the work model were prepared for RNA extraction and hybridization on Affymetrix microarrays. We analyzed 3 independent experiments per replicate, and we did three replicates per sample.

2009-12-30 | E-GEOD-11628 | biostudies-arrayexpress

Homo sapiens

Project description:Characterization of retinoic acid-regulated microRNAs

| PRJNA106491 | ENA

FIREWACh: High-throughput Functional Detection of Transcriptional Regulatory Modules in Mammalian Cells

Project description:We report a new method called FIREWACh (Functional Identification of Regulatory Elements Within Accessible Chromatin), a high-throughput functional assay for directly identifying active promoter and enhancer elements. FIREWACh simultaneously assessed over 80,000 DNA fragments derived from M-bM-^@M-^\nucleosome-free regionsM-bM-^@M-^] within embryonic stem cell (ESC) chromatin to identify 6,364 new active regulatory elements. Many FIREWACh DNAs represent newly discovered ESC-specific enhancers and their analyses identified enriched binding site motifs for ESC transcription factors including SOX2, POU5f1 (OCT4), and KLF4. Thus FIREWACh identifies endogenous regulators of gene expression and can be used for the discovery of key cell-specific transcription factors. The application of FIREWACh to additional cultured cell types will facilitate functional annotation of the genome and expand our view of transcriptional network dynamics. Nucleosome free DNA (i.e. "open chromatin") is isolated enzymatically from cross-linked nuclei of cells (e.g. mouse embryonic stem cells, mESC) and cloned upstream of a minimal promoter driving GFP within a lentivral reporter construct. Virus is made from a pooled library of these plasmids, and used to transfect the target cell (mESC). GFP positive cells contain active NFRs and can be sorted by FACS. The loci of the NFR is determined using high throughput sequencing and mapping.

2014-03-22 | E-GEOD-54863 | biostudies-arrayexpress

RNA-binding protein repertoire of embryonic stem cells

Project description:RNA-binding proteins (RBPs) have essential roles in RNA-mediated gene regulation, and yet annotation of RBPs is limited mainly to those with known RNA-binding domains. To systematically identify the RBPs of embryonic stem cells (ESCs), we here employ interactome capture, which combines UV cross-linking of RBP to RNA in living cells, oligo(dT) capture and MS. From mouse ESCs (mESCs), we have defined 555 proteins constituting the mESC mRNA interactome, including 283 proteins not previously annotated as RBPs. Of these, 68 new RBP candidates are highly expressed in ESCs compared to differentiated cells, implicating a role in stem-cell physiology. Two well-known E3 ubiquitin ligases, Trim25 (also called Efp) and Trim71 (also called Lin41), are validated as RBPs, revealing a potential link between RNA biology and protein-modification pathways. Our study confirms and expands the atlas of RBPs, providing a useful resource for the study of the RNA-RBP network in stem cells.

2018-08-29 | PXD008914 | Pride

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