Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Endoderm differentiation of human embryonic stem cells (hESCs) [RNA-Seq]

ABSTRACT: Endoderm differentiation of human embryonic stem cells (hESCs) [RNA-Seq]

PROVIDER: PRJNA535525 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR8957120.fastq.gz	Fastqsanger.gz
	SRR8957121.fastq.gz	Fastqsanger.gz
	SRR8957122.fastq.gz	Fastqsanger.gz
	SRR8957123.fastq.gz	Fastqsanger.gz
	SRR8957114.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 12

Similar Datasets

Endoderm differentiation of human embryonic stem cells (hESCs) [RNA-Seq]

Project description:Purpose: The goal of this study is to identify the whole-genome transcriptome profiling of differentially expressed genes during human embryonic stem cell differentiation. Methods: Triplicate RNA profiles were generated from hESCs and induced endoderm cells, by deep sequencing with Illumina NextSeq 500. Results: We identified 6320 genes differentially expressed between hESCs and induced endoderm cells, with foldchange  1.5 and P < 0.05. Conclusion: Our study confirms that endodermal gene were dramatically induced during endoderm differentiation.

2021-02-23 | GSE130340 | GEO

Dynamic proteomic profiling of extra-embryonic endoderm differentiation in mouse embryonic stem cells

Project description:During mammalian pre-implantation development, the cells of the blastocyst’s inner cell mass differentiate into the epiblast and primitive endoderm lineages, which give rise to the fetus and extra-embryonic tissues, respectively. Extra-embryonic endoderm differentiation can be modeled in vitro by induced expression of GATA transcription factors in mouse embryonic stem cells. Here we use this GATA-inducible system to quantitatively monitor the dynamics of global proteomic changes during the early stages of this differentiation event and also investigate the fully differentiated phenotype, as represented by embryo-derived extra-embryonic endoderm (XEN) cells. Using mass spectrometry-based quantitative proteomic profiling with multivariate data analysis tools, we reproducibly quantified 2,336 proteins across three biological replicates and have identified clusters of proteins characterized by distinct, dynamic temporal abundance profiles. We first used this approach to highlight novel marker candidates of the pluripotent state and extra-embryonic endoderm differentiation. Through functional annotation enrichment analysis, we have shown that the downregulation of chromatin-modifying enzymes, the re-organization of membrane trafficking machinery and the breakdown of cell-cell adhesion are successive steps of the extra-embryonic differentiation process. Thus, applying a range of sophisticated clustering approaches to a time-resolved proteomic dataset has allowed the elucidation of complex biological processes which characterize stem cell differentiation and could establish a general paradigm for the investigation of these processes.

2015-06-13 | PXD001901 | Pride

Gene expression of human embryonic stem cells during endoderm differentiation

Project description:Using a well-established human definitive endoderm differentiation system, we can analyze the gene expression dynamic of human embryonic stem cells (hESCs) during endoderm differentiation. Samples from hESCs, D2 cells and definitive endoderm cells (DE) were collected for deep sequencing with two replicates for each sample. Differentially expressed genes analysis showed that endodermal genes were induced during endoderm differentiation.

2022-01-21 | GSE168625 | GEO

Arginine methylation of METTL14 promotes RNA N6-methyladenosine modification and endoderm differentiation of mouse embryonic stem cells

Project description:m6A is the most abundant modification of mRNA in mammals and plays an important role in human development and disease. METTL14 is a key component of m6A methyltransferase complex. The project showed that its post-translational arginine methylation can regulate the generation of m6A and the endoderm differentiation of mouse embryonic stem cells, indicating its essential function in the normal development of embryos.

2021-05-17 | PXD018458 |

ChIP-seq of definitive endoderm differentiation of human embryonic stem cells in early G1 phase of the cell cycle

Project description:The experiment was designed to investigate histone modification changes during cell cycle progression of human embryonic stem cells (hESCs) during definitive endoderm differentiation. For this, FUCCI hESCs were sorted in Early G1 (EG1), and differentiation into endoderm was performed for up to 72 hours with a combination of cytokines as described in Pauklin and Vallier (2013) and Pauklin et al. (2016). ChIP-seq was generated at 12-hour and 36-hour time-points for H3K4me3, H3K27ac, H3K4me1, H3K36me3 and H3K27me3. Library preparation and sequencing were performed at the Wellcome Sanger Institute next-generation sequencing facility on Illumina HiSeq 2000, 2 x 75bp paired-end reads. ChIP-seq data from other time-points (0h, 24h, 48h and 72h) of the same experimental set-up is available elsewhere (GEO DataSet, accession PRJNA593217). All processed ChIP-seq data is publicly available at http://ngs.sanger.ac.uk/production/endoderm

2020-09-07 | E-MTAB-9276 | biostudies-arrayexpress

Transcriptional profiling by array of human cardiac progenitors and cardiomyocytes generated from embryonic bodies, directed differentiation of hESCs with PDGFa or co-culturing hESCs with END2 cell line.

Project description:Human cardiomyocytes can be generated from human embryonic stem cells (hESCs) in vitro by a variety of methods, including co-culture with visceral endoderm-like cell lines and growth factor directed differentiation as monolayers or three-dimensional embryonic bodies. To enable the identification, purification and characterisation of human embryonic stem cell derived cardiomyocytes (CMs) and cardiac progenitor cells (CPCs), we introduced sequences encoding GFP into the NKX2-5 locus by homologous recombination. We found that NKX2-5GFP hESCs facilitate quantification of cardiac differentiation, purification of hESC-derived committed cardiac progenitor cells and cardiomyocytes and the standardization of differentiation protocols.

2011-11-16 | E-MEXP-3371 | biostudies-arrayexpress

microRNA Profiling during endoderm differentiation from mouse embryonic stem cells

Project description:microRNA Profiling during endoderm differentiation from mouse embryonic stem cells

| PRJNA543309 | ENA

DNMT3B supports meso-endoderm differentiation from mouse embryonic stem cells

Project description:DNMT3B supports meso-endoderm differentiation from mouse embryonic stem cells

| PRJNA707326 | ENA

Gene expression of human embryonic stem cells during endoderm differentiation

Project description:Gene expression of human embryonic stem cells during endoderm differentiation

| PRJNA713297 | ENA

ATAC-seq of definitive endoderm differentiation of human embryonic stem cells in early G1 phase of the cell cycle

Project description:The experiment was designed to look into chromatin accessibility changes during cell cycle progression in human embryonic stem cells (hESCs) during definitive endoderm differentiation. For this, FUCCI hESCs were sorted in Early G1 (EG1), and differentiation into endoderm was performed for up to 72 hours with a combination of cytokines as described in Pauklin and Vallier (2013) and Pauklin et al. (2016). Samples at 0, 12, 24, 36, 48 and 72 hours were generated from two independent experiments, with 100,000 cells per sample, as previously described in Kumasaka et al. (2016). Library preparation and sequencing were performed at the Wellcome Sanger Institute next-generation sequencing facility. ATAC-seq libraries were prepared with one of i5 and i7 Nextera tags combination (see protocol details), and pooled equimolarly. Sequencing was performed on Illumina HiSeq 2000, 2 x 75bp paired-end reads.

2020-09-07 | E-MTAB-9124 | 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