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

ATACseq of TNG-A derived mESCs comparing WT to Dax1, Nr5a2 and Dax1/Nr5a2 knock-out clones

ABSTRACT: ATACseq in WT, Dax1, Nr5a2 and Dax1/Nr5a2 knock-out clones of mESCs in order to determine the role of the Dax1/Nr5a2 complex on chromatin accessibility and the activity of cis-regulatory elements during differentiation.
This experiment is part of the study: "Mechanistic framework of lineage restriction in embryonic stem cells" by Olivieri et al.

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Mus musculus

SUBMITTER: Panagiotis Papasaikas

PROVIDER: E-MTAB-9453 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

RNA-seq comparing WT to Dax1, Nr5a2 and Dax1/Nr5a2 knock-out clones in 2iLIF and SL differentiation conditions

Project description:Determine the transcriptomic effects that are associated with the knock-out of the inhibitor of PrE trans-differentiation Dax1 and the associated nuclear receptor Nr5a2.<br>This experiment is part of the study: "Mechanistic framework of lineage restriction in embryonic stem cells" by Olivieri et al.

2021-03-15 | E-MTAB-9447 | biostudies-arrayexpress

ATACseq of TNG-A derived mESCs comparing WT to Dax1, Nr5a2 and Dax1/Nr5a2 knock-out clones

Project description:ATACseq of TNG-A derived mESCs comparing WT to Dax1, Nr5a2 and Dax1/Nr5a2 knock-out clones

| PRJEB39929 | ENA

Single-cell RNA-seq comparing WT, HDAC3 and Dax1 knock-out clones in SL(RA) differentiation conditions

Project description:We performed single-cell RNA-seq in order to characterize in high resolution the transcriptomic profiles, differentiation fates and heterogeneity of wild-type, HDAC3 or Dax1 knock-out cells in SL(RA) differentiation conditions.

2021-03-15 | E-MTAB-10147 | biostudies-arrayexpress

RNA-seq comparing WT to Dax1, Nr5a2 and Dax1/Nr5a2 knock-out clones in 2iLIF and SL differentiation conditions

Project description:RNA-seq comparing WT to Dax1, Nr5a2 and Dax1/Nr5a2 knock-out clones in 2iLIF and SL differentiation conditions

| PRJEB39928 | ENA

RNA-seq comparing WT to HDAC3 and Dax1 knock-out clones in cell-sorted populations in 2iLIF and SL(RA) differentiation conditions

Project description:In order to determine the transcriptomic profiles of PrE-induced cells following HDAC3 or Dax1 knock-out in SL(RA) differentiation conditions, RNA-seq was performed on Gata6+ or Nanog+ sort-selected cells. Profiles are contrasted with WT cells in the same differentiation conditions as well as to mock-sorted populations of the three genotypes in 2iLIF conditions.

2021-03-15 | E-MTAB-10150 | biostudies-arrayexpress

Gene expression profile after Dax1 deletion in ES cells

2015-05-13 | GSE61152 | GEO

Pluripotency-state-dependent Role of Dax1 in Embryonic Stem Cells Self-renewal

Project description:DAX1 (also known as Nr0b1) is regarded as an important component of the transcription factor network in mouse embryonic stem cells (ESCs). However, the role and the molecular mechanism of Dax1 in the maintenance of different pluripotency states are poorly understood. Here, we constructed a stable Dax1 knockout (KO) cell line using the CRISPR/Cas9 system to analyze the precise function of Dax1. We reported that 2i/LIF-ESCs had significantly lower Dax1 expression than LIF/serum-ESCs. Dax1KO ES cell lines could be established in 2i/LIF and their pluripotency was confirmed. In contrast, Dax1-null ESCs could not be continuously passaged in LIF/serum due to severe differentiation and apoptosis. In LIF/serum, the activities of the Core module and Myc module were significantly reduced, while the PRC2 module was activated after Dax1KO. The expression of most pro-apoptotic genes and lineage-commitment genes were drastically increased, while the down-regulated expression of anti-apoptotic genes and many pluripotency genes was observed. Our research on the pluripotent state-dependent role of Dax1 provides clues to understand the molecular regulation mechanism at different stages of early embryonic development.

2021-07-21 | GSE168423 | GEO

Effect of EWS/FLI1 and DAX1 silencing on the gene expression profile of the A673 Ewing cell line

Project description:The molecular hallmark of the Ewing family of tumors is the presence of balanced chromosomal translocations leading to the formation of chimerical transcription factors (i.e. EWS/FLI1) that play a pivotal role in the pathogenesis of Ewing tumors by deregulating gene expression. We have recently demonstrated that DAX1 (NR0B1), an orphan nuclear receptor which was not previously implicated in cancer, is induced by the EWS/FLI1 oncoprotein and is highly expressed in Ewing tumors, suggesting that DAX1 is a biologically relevant target of EWS/FLI1-mediated oncogenesis. In this work we demonstrate that DAX1 is a direct transcriptional target of the EWS/FLI1 oncoprotein through its binding to a GGA-rich region in the DAX1 promoter and show that DAX1 is a key player of EWS/FLI1-mediated oncogenesis. DAX1 silencing using an inducible model of RNA interference induces growth arrest in the A673 Ewing cell line and severely impairs its capability to grow in semisolid medium and form tumors in immunodeficient mice. Gene expression profile analysis demonstrated that about ten percent of the genes regulated by EWS/FLI1 in Ewing cells are DAX1 targets, confirming the importance of DAX1 in Ewing oncogenesis. These findings indicate that DAX1 is an important player in the pathogenesis of the Ewing family of tumors, identify new functions for DAX1 as a cell cycle progression regulator and open the possibility to new therapeutic approaches based on DAX1 function interference.

2012-02-23 | GSE36007 | GEO

Gene expression profile after Dax1 deletion in ES cells

Project description:To investigate the function of Dax1 in mouse ES cells, whole genome microarray expression profiling was employed to identify genes that are potentially affected by the deletion of Dax1. An inducible knockout ES cell line of Dax1 with the Cre-loxP system was generated and gene expression was measured (i) without Dax1 deletion, (ii) after 4 days of Dax1 deletion, or (iii) after several passags of Dax1 deletion. Each sample was prepared in triplicate.

2015-05-13 | E-GEOD-61152 | biostudies-arrayexpress

ChIP-seq of SATB1-bound regions in human ESC-derived dopaminergic (DA) neurons at different time points. ATAC-Seq and RNA-Seq of DA and cortical neurons (WT and SATB1-KO)

Project description:SATB1 is a genetic master regulator in dopaminergic neurons. We try to identify the downstream regulated genes and pathways of SATB1 in human dopaminergic and CTX neurons. The RNA-Seq experiment was performed to investigate the role of the genetic master regulator SATB1 in human dopaminergic neurons in comparison to cortical neurons. We generated a human embryonic stem cell knockout clone for SATB1 and differentiated this clone into either dopaminergic or cortical neurons. Immature dopaminergic (day 30 of differentiation), mature dopaminergic (day 50 of differentiation) and mature cortical neurons (day 30 of differentiation) were subsequently subjected to RNA-Seq. We compared wild type and SATB1-KO neurons at the afore mentioned time points, to characterize the regulatory role of SATB1 in the different neuron subtypes.

2019-09-20 | E-MTAB-5965 | 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