Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

49 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Identify the downstream targets of CHIR99021 and XAV939 in EpiSC using microarray analysis

ABSTRACT: The requirements for self-renewal differ between EpiSCs and ES cells and the underlying mechanism is largely unknown. Here we show that mouse EpiSCs can be efficiently derived and robustly propagated even from single cells, using two small-molecule inhibitors: CHIR99021 and XAV939. To better define how CHIR and XAV act together to maintain EpiSC self-renewal, we performed microarray analyses to identify their downstream targets. The data show the genes regulated by addition of CHIR, XAV or both. EpiSCs starved in serum free growth medium (shown in growth protocol) for 12hrs were treated with CHIR (2hrs), XAV(4hrs), or both, after which total RNA was extracted for analysis.

ORGANISM(S): Mus musculus

SUBMITTER: chihi tai

PROVIDER: E-GEOD-31544 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Global gene expression profile of mouse ESC-2i, EpiSC-CHIR/XAV and EpiSC-FGF2/activin

Project description:The requirements for self-renewal differ between EpiSCs and ES cells and the underlying mechanism is largely unknown. Here we show that mouse EpiSCs can be efficiently derived and robustly propagated even from single cells, using two small-molecule inhibitors: CHIR99021 and XAV939. The whole-genome microarray analyses is performed to confirm the identity of EpiSC maintained in CHIR/XAV by comparing the expression profile in EpiSC-CHIR/XAV to those in ESC maintained in 2i and EpiSC maintained in FGF2/activin. Total RNA from ESC-2i, EpiSC-CHIR/XAV, and EpiSC-FGF2/activin were extracted for microarray analisys

2011-08-18 | E-GEOD-31461 | biostudies-arrayexpress

Identify the downstream targets of CHIR99021 and XAV939 in EpiSC using microarray analysis

Project description:The requirements for self-renewal differ between EpiSCs and ES cells and the underlying mechanism is largely unknown. Here we show that mouse EpiSCs can be efficiently derived and robustly propagated even from single cells, using two small-molecule inhibitors: CHIR99021 and XAV939. To better define how CHIR and XAV act together to maintain EpiSC self-renewal, we performed microarray analyses to identify their downstream targets. The data show the genes regulated by addition of CHIR, XAV or both.

2011-08-25 | GSE31544 | GEO

Global gene expression profile of mouse ESC-2i, EpiSC-CHIR/XAV and EpiSC-FGF2/activin

2011-08-19 | GSE31461 | GEO

Genome-wide profiles of gene expression levels in mouse nephron progenitor cells

Project description:During embryonic kidney development, nephron progenitor cells (NPCs) self-renew and differentiate into all cells in mature nephrons. The Wnt signaling components Wnt9b and β-catenin are required for both NPC self-renewal and differentiation. A low level of Wnt/β-catenin are associated with NPC self-renewal while a high level with differentiation. To investigate the transcriptional mechanisms behind Wnt/β-catenin-driven regulation of NPCs states, we modeled NPC self-renewal and differentiation in vitro with NPEM (Brown et al., 2015) supplemented with low (1.25 μM) or high (5 μM) concentration of CHIR22091 (CHIR), a small molecule GSK3β inhibitor that stabilizes β-catenin. To investigate change of NPC chromatin landscape under influence of CHIR treatment, here we generated ATAC-Seq data from primary NPC, as well as NPC cultured in low and high CHIR concentration.

2021-01-07 | GSE131118 | GEO

Genome-wide map of open chromatin in mouse nephron progenitor cells

2021-01-07 | GSE131116 | GEO

Genome-wide profiles of chromatin interaction in mouse nephron progenitor cells [HiC]

Project description:During embryonic kidney development, nephron progenitor cells (NPCs) self-renew and differentiate into all cells in mature nephrons. The Wnt signaling components Wnt9b and β-catenin are required for both NPC self-renewal and differentiation. A low level of Wnt/β-catenin are associated with NPC self-renewal while a high level with differentiation. To investigate the transcriptional mechanisms behind Wnt/β-catenin-driven regulation of NPCs states, we modeled NPC self-renewal and differentiation in vitro with NPEM (Brown et al., 2015) supplemented with low (1.25 μM) or high (5 μM) concentration of CHIR22091 (CHIR), a small molecule GSK3β inhibitor that stabilizes β-catenin. To investigate change of higher-order chromatin structure of NPC under influence of CHIR treatment, here we generated HiC data from primary NPC, as well as NPC cultured in low and high CHIR concentration.

2021-01-07 | GSE132057 | GEO

Genome-wide map of Tcf/Lef transcription factors, β-catenin, Six2 and chromatin marks in mouse nephron progenitor cells

Project description:During embryonic kidney development, nephron progenitor cells (NPCs) self-renew and differentiate into all cells in mature nephrons. The Wnt signaling components Wnt9b and β-catenin are required for both NPC self-renewal and differentiation. A low level of Wnt/β-catenin are associated with NPC self-renewal while a high level with differentiation. To investigate the transcriptional mechanisms behind Wnt/β-catenin-driven regulation of NPCs states, we modeled NPC self-renewal and differentiation in vitro with NPEM (Brown et al., 2015) supplemented with low (1.25 μM) or high (5 μM) concentration of CHIR22091 (CHIR), a small molecule GSK3β inhibitor that stabilizes β-catenin. We have found the Tcf/Lef family repressors Tcf7l1 and Tcf7l2 are enriched in low CHIR condition, while the activators Tcf7 and Lef1 in high CHIR condition, correlating with the NPC differentiation program transiting from being repressed to activated. To identify direct transcriptional targets of Tcf/Lef factors and β-catenin, here we generated ChIP-Seq data from primary NPC, as well as NPC cultured in low and high CHIR concentration.

2021-01-07 | GSE131117 | GEO

EpiSC RNAseq

Project description:EpiSCs were transfected with different TET1 constructs or empty vector controls. RNA was collected using All prep Qiagen kit and ran on gel to check for RNA integrity.

2015-01-14 | E-ERAD-325 | biostudies-arrayexpress

ZHBTc4 ES cells stably expressing EGFP vs Nr5a2-EGFP or Oct4-EGFP vs Nr5a2-EGFP

Project description:Gene expression profiles of ZHBTc4 ES cells expressing EGFP, Oct4-EGFP, Nr5a2-EGFP under CAG promoter. Monoclonal cell lines selected by Puromycin were used for analysis. Each of the cell lines was cultured in doxycycline containing media for endogenous Oct4 knock-down. Pupose of this experiment is to investigate the possibility that forced expression of Nr5a2 can replace Oct4 function in the self-renewal of ES cells. Monoclonal ZHBTc4 ES cells expressing EGFP vs Nr5a2-EGFP, Oct4-EGFP vs Nr5a2-EGFP, no replication

2013-11-05 | E-GEOD-52034 | biostudies-arrayexpress

RNA-seq experiment of mouse embryonic stem cells (mESCs), comparing TCF/LEF quadruple knock-out cells with wild type cells

Project description:Mouse embryonic stem cells (mESCs), derived from pre-implantation blastocyst cells, can be maintained in vitro in defined N2B27 medium supplemented with two chemical inhibitors for GSK3 and MEK (2i) and the cytokine leukemia inhibitory factor (LIF), which act synergistically to promote self-renewal and pluripotency. Many efforts have been devoted to identify genes that promote exit from the pluripotent state and the transition to a primed state of differentiation. One of the first identified players in this process was the Wnt/b-catenin effector TCF7L1 (previously referred to as TCF3), belonging to the family of four TCF/LEF transcription factors, which acts as pro-differentiation factor by repressing pluripotency genes. Of note, there is little evidence that the genetic abrogation of the mechanisms required for the exit from the pluripotent state is sufficient to enable self-renewal in the absence of 2iL. Here, we found that complete loss-of-function of Tcf7, Lef1, Tcf7l1 and Tcf7l2, the genes encoding for the four TCF/LEF transcription factors, (refered to as qKO) allows mESCs to become fully 2iL-independent and to propagate in basal N2B27. To understand the genetic program that allows qKO cells to achieve 2iL-independent self-renewal, we performed RNA sequencing (RNA-seq) of qKO and wild type mESCs.

2021-06-15 | E-MTAB-10564 | 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