Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Integrated transcriptomic and epigenomic analysis of primary human lung cell differentiation

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Rattus norvegicus Homo sapiens

PROVIDER: GSE38571 | GEO | 2013/04/15

SECONDARY ACCESSION(S): PRJNA168155

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Integrated transcriptomic and epigenomic analysis of primary human lung cell differentiation

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2013-04-15 | E-GEOD-38571 | biostudies-arrayexpress

Integrated transcriptomic and epigenomic analysis of primary human lung epithelial cell differentiation.

Project description:Elucidation of the epigenetic basis for cell-type specific gene regulation is key to gaining a full understanding of how the distinct phenotypes of differentiated cells are achieved and maintained. Here we examined how epigenetic changes are integrated with transcriptional activation to determine cell phenotype during differentiation. We performed epigenomic profiling in conjunction with transcriptomic profiling using in vitro differentiation of human primary alveolar epithelial cells (AEC). This model recapitulates an in vivo process in which AEC transition from one differentiated cell type to another during regeneration following lung injury. Interrogation of histone marks over time revealed enrichment of specific transcription factor binding motifs within regions of changing chromatin structure. Cross-referencing of these motifs with pathways showing transcriptional changes revealed known regulatory pathways of distal alveolar differentiation, such as the WNT and transforming growth factor beta (TGFB) pathways, and putative novel regulators of adult AEC differentiation including hepatocyte nuclear factor 4 alpha (HNF4A), and the retinoid X receptor (RXR) signaling pathways. Inhibition of the RXR pathway confirmed its functional relevance for alveolar differentiation. Our incorporation of epigenetic data allowed specific identification of transcription factors that are potential direct upstream regulators of the differentiation process, demonstrating the power of this approach. Integration of epigenomic data with transcriptomic profiling has broad application for the identification of regulatory pathways in other models of differentiation.

| S-EPMC3688557 | biostudies-literature

Epigenomic profiling of stemness, differentiation and primary tissues in human glioblastoma

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2014-04-11 | E-GEOD-54792 | biostudies-arrayexpress

Integrated epigenomic and transcriptomic profiling of terminal human erythropoiesis

Project description:This SuperSeries is composed of the SubSeries listed below.

2019-03-30 | GSE115684 | GEO

Epigenomic analysis of primary human T cells reveals novel enhancers associated with Th2 memory differentiation and asthma susceptibility

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2014-07-05 | E-GEOD-53646 | biostudies-arrayexpress

Integrated epigenomic analyses of enhancer as well as promoter regions in gastric cancer

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2016-03-29 | E-GEOD-46598 | biostudies-arrayexpress

Integrative Analysis of Transcriptomic and Epigenomic Data to Reveal Regulation Patterns for Osteoporosis Risk

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2014-10-22 | E-GEOD-62589 | biostudies-arrayexpress

Epigenomic profiling of stemness, differentiation and primary tissues in human glioblastoma

Project description:This SuperSeries is composed of the SubSeries listed below.

2014-04-11 | GSE54792 | GEO

Integrated expression profiles of mRNA and miRNA in polarized primary murine microglia

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2014-03-13 | E-GEOD-49331 | biostudies-arrayexpress

Integrated analysis of transcript level regulation of metabolism during human adipocyte differentiation

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2013-11-19 | E-GEOD-41578 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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