Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA Sequencing Data in differentiating mouse embryonic stem cells

ABSTRACT: ES cell lines were established from mouse embryos, which were homozygous for the Trim33-flox allele and carried the UbcCreERT2 transgene. Cells were cultured without feeder cells in the presence of LIF and 2i. Embryoid bodies (EBs) were generated using the ATCC protocol on low attachment dishes under differentiating conditions. EBs were induced with Tamoxifen at day 4 and harvested at day 7.

ORGANISM(S): Mus musculus

PROVIDER: GSE80166 | GEO | 2016/11/14

SECONDARY ACCESSION(S): PRJNA318164

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

RNA Sequencing Data in differentiating mouse embryonic stem cells [day2 and 2.5 in differentiation]

Project description:ES cell lines were established from mouse embryos, which were homozygous for the Trim33-flox allele and carried the UbcCreERT2 transgene. Cells were cultured without feeder cells in the presence of LIF and 2i. Embryoid bodies (EBs) were generated using the ATCC protocol on low attachment dishes under differentiating conditions. EBs were induced with Tamoxifen at day 1 and harvested at days 2 and 2.5, respectively.

2017-01-01 | GSE81095 | GEO

Trascriptome profiling of murine Embryonic Stem cells under different culture conditions

Project description:Mouse Embryonic Stem (ES) cells have been cultured under chemically defined conditions in the absence of feeder cells on Gelatin coated dishes, for 5 passages under 4 different combinations of LIF and GSK3 or MEK inhibitors. Their trascriptome have been analysed by RNA sequencing. The ES cell line used, RexGFPd2, contains a destablised GFP protein in the Zfp42/Rex1 locus and was derived under 2i conditions, as described in Kalkan et al. 2017.

2018-11-21 | GSE111694 | GEO

Transcriptome profiles of mouse embryonic stem cells cultured in different conditions by RNA-seq analysis

Project description:Pluripotent mouse embryonic stem cells (ESCs) were originally derived and stably maintained on feeder cells such as inactivated mouse embryo fibroblasts, and can generate complete ESC-pups by tetraploid embryo complementation (TEC), the most stringent functional test of naive pluripotency. Remarkably, 2i (inhibitors of Mek and Gsk3β signaling) medium with LIF in the absence of serum and feeders was developed to achieve ground state of mouse ESCs, and also has been successfully used for derivation of germline competent ESCs in other species such as rat. Notably, 2i-culture gives rise to transcriptional profiles and epigenetic landscapes quite distinct from serum-based ESCs. To better understand transcriptional landscape and signal transductions, we performed RNA-seq analysis of ESCs cultured in four different conditions: serum without feeder, serum with feeder, serum with feeder and 2i, and N2B27+2i.

2018-01-20 | GSE109418 | GEO

Nodal signaling maintains H3K18ac landscape to promote mesendodermal differentiation through TRIM33

Project description:The epigenome of a cell is established and maintained by chromatin modifiers and remodelers, which are recruited to the chromatin by specific transcription factors. In this report, we show that nodal cross-talks with the epigenome through TRIM33-H3K18ac to mediate mesendodermal genes expression. The chromatin accessibility at mesendodermal genes depends on TRIM33. Moreover, histone acetylation is essential for TRIM33 recruitment to many nodal target genes involved in mesendodermal differentiation. The distribution pattern of the H3K18ac mark changes from foci to expanded domains at the mesendodermal genes promoter during embryonic stem cells (ESCs) differentiation to embryoid bodies (EBs). This could be the cue to facilitate TRIM33 colocalized with Smad2/3 at chromatin in EBs but not in ESCs. TRIM33 interacts with the H3K18ac “writer” p300 dependent on nodal signaling, providing a positive feedback to promote activation of mesendodermal genes and association with HDAC1 plays a negative role in activation of mesendodermal genes.

2019-06-01 | GSE115169 | GEO

Expression data from mouse embryonic stem cell differentiation experiment

Project description:We differentiated mouse embryonic stem (mES) cells spontaneously into embryoid bodies (EBs). Gene expression of biological replicates of undifferentiated ES cells (0-day), 4-day, 8-day and 14-day EBs were measured by Affymetrix microarrays. Keywords: time course

2010-02-25 | GSE12550 | GEO

Transcriptome profiles of differentiated mouse embryonic stem cells cultured in normal condition and static magnetic field condition by RNA-seq analysisanalysis

Project description:Embryonic stem cells (ESCs) have the ability to differentiate into cells of the three germ layers, and leukemia inhibitory factor (LIF) maintains the pluripotency and promotes the proliferation of ESCs. In the absence of LIF, ESCs spontaneously differentiate and form three-dimensional aggregates known as embryoid bodies (EBs). The differentiation of EBs mimics the process of embryonic development, that is, the differentiation of cells into the three embryonic germ layers (endoderm, mesoderm, and ectoderm), some of which differentiate into beating cardiomyocytes. Static magnetic fields have diverse effects on organisms, studies on the regulation of the differentiation of ESCs to cardiomyocytes by static magnetic fields are not sufficient. To better understand transcriptional landscape and signal transductions, we performed RNA-seq analysis of EBs cultured in two different conditions: conventional incubator, static magnetic field incubator.

2024-01-01 | GSE206413 | GEO

RNA-seq analysis of ES cell populations with different functional potentials in serum/LIF and 2i/LIF, as well as analysis of the transcriptional effect of LIF in ground state (2i) culture conditions.

Project description:We report that ES cells cultured in ground state (2i and 2i/LIF) culture conditions are heterogeneous and show heterogeneus expression of extraembryonic markers. Using a highly sensitive reporter for the endoderm marker Hex we can sort Hex high and low populations from either serum/LIF or 2i/LIF and demonstrate that they have different functional properties. Here we explored the transcriptional basis of these functional differences and noted that Hex low (HV-) and Hex high (HV+) populations showed more distinct expression profiles in 2i/LIF than in serum/LIF. Additionally in 2i/LIF the HV+ population showed an upregulation of extraembryonic markers (such as trophoblast stem cell specific genes) and also imprinted genes compared to the HV- population, which is not observed when these populations are sorted from serum/LIF. We also analysed the transcriptional effect of LIF in 2i by analysing unsorted ES cells cultured in either 2i alone or 2i with LIF. We observed that the addition of LIF led to an upregulation of extraembryonic markers but did not effect the expression of pluripotency genes, other than Klf4. Additionally, the most significantly upregulated genes from 2i/LIF cultured ES cells compared to 2i cultured ES cells showed the greatest correlation to placental tissue when compared to the GNF tissue specific expression database. This analysis, alongside functional experiments, suggested that HV+ ES cells in 2i/LIF corresponded to an extraembryonically primed population of cells and that the addition of LIF supported this population.

2013-06-11 | GSE45182 | GEO

In vitro modeling of primordial germ cell development

Project description:Transgenic StellaGFP ESCs were used to derive primordial germ cells during embryoid body (EB) differentiation, and microarry analysis used to compared FACS sorted Stella-positive cells of day 7 Ebs with the parental ESCs and Stella-negative cells of day 7 Ebs. Keywords: in vitro, primordial germ cells, embryonic stem cells, stella

2009-06-22 | GSE7948 | GEO

CLIP-seq of Csrp1 in mouse embryoid bodies of day 9

Project description:V6.5 mESCs over-expressing V5-tagged Csrp1 and wild-type mESCs were differentiated into embryoid bodies (EBs) and collected at day 9 for CLIP-seq.

2024-08-23 | GSE226213 | GEO

HP1β has distinct subnuclear localizations, chromatin binding features and functions in embryonic stem cells and differentiating cells [expression]

Project description:We used microarrays to identify the gene expression changes in Cbx1-/- (HP1beta) knockout embryonic stem cells (ESCs) and Cbx5-/- (HP1alpha) knockout ESCs compared to WT ESCs and in embryoid bodies (EBs) differentiated from those three ESC types.

2015-08-02 | GSE65121 | GEO

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