Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

NEUROD1 intrinsically initiates differentiation of induced pluripotent stem cells into neural progenitor cells

ABSTRACT: We generated ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) data and Hi-C data for induced pluripotent stem cell (iPSC), neuronal progentior cell (NPC), and investigated cell type-specific open chromatin regions and related enhancers

ORGANISM(S): Homo sapiens

PROVIDER: GSE158382 | GEO | 2021/01/06

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

DNA methyation of intragenic CpG islands are required for differentiation from iPSC to NPC

Project description:We generated whole genome bisulfite sequencing (WGBS) data with high sequencing depth in induced pluripotent stem cell (iPSC), neuronal progentior cell (NPC) and Early Neuron (EN), and investigated the relationship between DNA methylation changes in CpG islands (CGIs) and corresponding gene expression during NPC differentiation

2021-01-06 | GSE156723 | GEO

NEUROD1 Intrinsically Initiates Differentiation of Induced Pluripotent Stem Cells into Neural Progenitor Cells.

Project description:Cell type specification is a delicate biological event in which every step is under tight regulation. From a molecular point of view, cell fate commitment begins with chromatin alteration, which kickstarts lineage-determining factors to initiate a series of genes required for cell specification. Several important neuronal differentiation factors have been identified from ectopic over-expression studies. However, there is scarce information on which DNA regions are modified during induced pluripotent stem cell (iPSC) to neuronal progenitor cell (NPC) differentiation, the cis regulatory factors that attach to these accessible regions, or the genes that are initially expressed. In this study, we identified the DNA accessible regions of iPSCs and NPCs via the Assay for Transposase-Accessible Chromatin sequencing (ATACseq). We identified which chromatin regions were modified after neuronal differentiation and found that the enhancer regions had more active histone modification changes than the promoters. Through motif enrichment analysis, we found that NEUROD1 controls iPSC differentiation to NPC by binding to the accessible regions of enhancers in cooperation with other factors such as the Hox proteins. Finally, by using Hi-C data, we categorized the genes that directly interacted with the enhancers under the control of NEUROD1 during iPSC to NPC differentiation.

| S-EPMC7772509 | biostudies-literature

ATAC-seq profiles of glioblastoma stem cells (GSCs), Non-stem tumor cells (NSTCs) and neural progenitor cell (NPC).

Project description:Both chromatin accessibility and histone modifications are known to influence transcriptional regulation. We investigated the differences of chromatin accessibility among GSCs, NSTCs and NPC using ATAC-seq (assay for transposase-accessible chromatin with high throughput sequencing).

2022-08-28 | GSE211724 | GEO

Promoter capture Hi-C of human SGBS (Simpson-Golabi-Behmel syndrome preadipocyte) cells and iPSC-derived hypothalamic cells

Project description:To identify distal chromatin contacts between promoters and their putative regulatory elements in SGBS preadipocytes and hypothalamic arcuate-like neurons derived from iPSC, we performed Hi-C with a capture step to enrich the library for contacts involving promoters. Hi-C with a capture step was performed according to PMID: 29988018

2021-03-20 | E-MTAB-10200 | biostudies-arrayexpress

Mapping cis-regulatory chromatin contacts in neural cells links neuropsychiatric disorder risk variants to target genes [ATAC-seq]

Project description:Mutations in gene regulatory elements have been associated with a wide range of complex neuropsychiatric disorders. However, due to their cell-type specificity and difficulties in characterizing their regulatory targets, the ability to identify causal genetic variants has remained limited. To address these constraints, we perform an integrative analysis of chromatin interactions, open chromatin regions and transcriptomes using promoter capture Hi-C, assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) and RNA sequencing, respectively, in four functionally distinct neural cell types: induced pluripotent stem cell (iPSC)-induced excitatory neurons and lower motor neurons, iPSC-derived hippocampal dentate gyrus-like neurons and primary astrocytes. We identify hundreds of thousands of long-range cis-interactions between promoters and distal promoter-interacting regions, enabling us to link regulatory elements to their target genes and reveal putative processes that are dysregulated in disease. Finally, we validate several promoter-interacting regions by using clustered regularly interspaced short palindromic repeats (CRISPR) techniques in human excitatory neurons, demonstrating that CDK5RAP3, STRAP and DRD2 are transcriptionally regulated by physically linked enhancers.

2019-06-15 | GSE113480 | GEO

Mapping cis-regulatory chromatin contacts in neural cells links neuropsychiatric disorder risk variants to target genes [CUT&RUN]

2019-06-15 | GSE126211 | GEO

Mapping cis-regulatory chromatin contacts in neural cells links neuropsychiatric disorder risk variants to target genes [RNA-Seq]

2019-06-15 | GSE113482 | GEO

Mapping cis-regulatory chromatin contacts in neural cells links neuropsychiatric disorder risk variants to target genes [PCHiC]

2019-06-15 | GSE113481 | GEO

K562 cell line LC-MSMS,Quantitative measurement of hydrophobicity dependent LLPS property of chromatin condensate

Project description:K562 cell line treated with 2,5-HD and proteins were captured via cross-linking. We quantified chromatin structure changes and chromatin binding proteins in K562 cell before and after 2,5-hexanediol treatment by Hi-C and Hi-MS, respectively.

2021-07-26 | PXD027565 | Pride

K562 cell lime LC-MSMS,Quantitative measurement of hydrophobicity dependent LLPS property of chromatin condensate

Project description:K562 cell line treated with 1,6-HD and proteins were captured via cross-linking. We quantified chromatin structure changes and chromatin binding proteins in K562 cell before and after 1,6-hexanediol treatment by Hi-C and Hi-MS, respectively.

2021-07-26 | PXD021434 | Pride

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