Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Epigenetic biomarkers to track differentiation of pluripotent stem cells [methylation array]

ABSTRACT: Quality control of induced pluripotent stem cells remains a challenge. For validation of the pluripotent state, it is crucial to determine trilineage differentiation potential toward endoderm, mesoderm, and ectoderm. Here, we report GermLayerTracker, a combination of site-specific DNA methylation (DNAm) assays that serve as biomarker for early germ layer specification. CG dinucleotides (CpGs) were identified with characteristic DNAm at pluripotent state and after differentiation into endoderm, mesoderm, and ectoderm. Based on this, a pluripotency score was derived that may be indicative for differentiation capacity, as well as lineage-specific differentiation scores to monitor either directed differentiation, or self-organized multilineage differentiation in embryoid bodies. Furthermore, we established pyrosequencing assays for fast and cost-effective analysis. In the future, the GermLayerTracker could be used for quality control of pluripotent cells and to estimate lineage-specific commitment during initial differentiation events.

ORGANISM(S): Homo sapiens

PROVIDER: GSE207076 | GEO | 2022/12/06

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Epigenetic biomarkers to track differentiation of pluripotent stem cells [RNA-Seq]

Project description:Quality control of induced pluripotent stem cells remains a challenge. For validation of the pluripotent state, it is crucial to determine trilineage differentiation potential toward endoderm, mesoderm, and ectoderm. Here, we report GermLayerTracker, a combination of site-specific DNA methylation (DNAm) assays that serve as biomarker for early germ layer specification. CG dinucleotides (CpGs) were identified with characteristic DNAm at pluripotent state and after differentiation into endoderm, mesoderm, and ectoderm. Based on this, a pluripotency score was derived that may be indicative for differentiation capacity, as well as lineage-specific differentiation scores to monitor either directed differentiation, or self-organized multilineage differentiation in embryoid bodies. Furthermore, we established pyrosequencing assays for fast and cost-effective analysis. In the future, the GermLayerTracker could be used for quality control of pluripotent cells and to estimate lineage-specific commitment during initial differentiation events.

2022-12-06 | GSE207118 | GEO

SALL3 regulates propensity of human induced pluripotent stem cells to differentiate into distinct cell lineages [Affymetrix]

Project description:The expression of SALL3 in hiPSCs correlated positively with ectoderm differentiation capacity and negatively with mesoderm/endoderm differentiation capacity. We investigated reference gene expression in human iduced pluripotent stem cells infected shRNA to SALL3.

2019-03-12 | GSE114977 | GEO

MicroRNA expression data from differentiation of human H9 ESCs into definitive endoderm on MEF feeder layers

2010-07-30 | GSE16689 | GEO

MicroRNA expression data from differentiation of human Cyt49 ESCs into definitive endoderm on MEF feeder layers

2010-07-30 | GSE16687 | GEO

MicroRNA expression data from differentiation of human Cyt49 ESCs into definitive endoderm in feeder-free conditions

2010-07-30 | GSE16678 | GEO

MicroRNA expression data from differentiation of human H9 ESCs into definitive endoderm on MEF feeder layers

Project description:Pluripotent hESCs can differentiate into the three primary embryonic lineages (endoderm, mesoderm, ectoderm) as well as extraembryonic tissues. Definitive endoderm (DE) is the first step into the pathway to endoderm dreived tissues (pancreas, liver, gut, lung). We used microarrays to detail the changes in microRNA expression during the transition from pluripotent hESCs into definitive endoderm. hESCs (H9) were differentiated in the presence of Activin A and Wnt3A under low serum conditions to induce DE formation. Samples were collected at day 0 (hESCs), and day 4 (DE).

2010-07-30 | E-GEOD-16689 | biostudies-arrayexpress

MicroRNA expression data from differentiation of human Cyt49 ESCs into definitive endoderm on MEF feeder layers

Project description:Pluripotent hESCs can differentiate into the three primary embryonic lineages (endoderm, mesoderm, ectoderm) as well as extraembryonic tissues. Definitive endoderm is the first step into the pathway to endoderm dreived tissues (pancreas, liver, gut, lung) We used microarrays to detail the changes in microRNA expression during the transition from pluripotent hESCs into definitive endoderm hESCs (Cyt49) were differentiated in the presence of Activin A and Wnt3A under low serum conditions to induce DE. formation. Samples were collected at day 0 (hESCs), and day 4 (DE).

2010-07-30 | E-GEOD-16687 | biostudies-arrayexpress

MicroRNA expression data from differentiation of human Cyt49 ESCs into definitive endoderm in feeder-free conditions

Project description:Pluripotent hESCs can differentiate into the three primary embryonic lineages (endoderm, mesoderm, ectoderm) as well as extraembryonic tissues. Definitive endoderm is the first step into the pathway to endoderm dreived tissues (pancreas, liver, gut, lung). We used microarrays to detail the changes in microRNA expression during the transition from pluripotent hESCs into definitive endoderm. hESCs (Cyt49) were differentiated in the presence of Activin A and Wnt3A under low serum conditions to induce DE formation. Samples were collected at day 0 (2 samples), day 2 (3 samples) and day 4 (3 samples).

2010-07-29 | E-GEOD-16678 | biostudies-arrayexpress

mRNA expression data from differentiation of human ESCs into definitive endoderm, Cyt49 on matrigel

Project description:hESCs can differentiate into the three primary embryonic lineages (endoderm, mesoderm, ectoderm) as well as extraembryonic tissues. Definitive endoderm (DE) is the first step into the pathway to endoderm derived tissues: pancreas, liver, gut, lung. We used microarrays to detail the changes in mRNA expression during the transition from pluripotent hESCs into definitive endoderm.

2010-07-30 | GSE16681 | GEO

Transcriptomically-guided mesendoderm induction of human pluripotent stem cells using a systematically defined culture scheme

Project description:Human pluripotent stem cells (hPSCs) are an essential cell source in tissue engineering, studies of development, and disease modeling. Efficient and broadly amenable protocols for rapid lineage induction of hPSCs are of great interest in the stem cell biology field. We describe a simple yet robust method for differentiation of hPSCs into mesendoderm in defined conditions utilizing single-cell seeding and BMP4 and Activin A (BA) treatment. Gene sets and gene ontology terms related to mesoderm and endoderm differentiation were enriched after 48 hours of BA treatment. After 14 days of differentiation, BA-treated cells expressed genes indicative of mesoderm and endoderm-derived tissue types, including lung, kidney and adipose tissue. BA treatment was readily incorporated into existing protocols for chondrogenic and endothelial progenitor cell differentiation. Teratomas formed from BA-treated cells contained higher ratios of mesoderm and endoderm to ectoderm tissue compared to PSC-derived teratomas. Collectively, these data demonstrate that single-cell seeding with BA treatment is a powerful method for induction of mesendoderm that can be integrated into protocols for mesoderm and endoderm differentiation.

2019-04-11 | GSE129570 | 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