Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

3D chromatin organizations of human pancreatic cells reveal cell-type specific regulatory architectures of diabetes risk

ABSTRACT: To understand the cell-type specific regulatory architectures of diabetes risk, we generated transcriptomic and 3D epigenomic profiles from sorted human pancreatic acinar, alpha, and beta cells using Arima Hi-C.

ORGANISM(S): Homo sapiens

PROVIDER: GSE188311 | GEO | 2022/09/06

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

(Epi)genetic risk architectures of opioid dependent brain

Project description:(Epi)genetic risk architectures of opioid dependent brain

| PRJNA787000 | ENA

(Epi)genetic risk architectures of opioid dependent brain

Project description:(Epi)genetic risk architectures of opioid dependent brain

| PRJNA787001 | ENA

Bioprinting of Injectable Centimeter-scale Architectures with a Visible-light Crosslinking Bioink

Project description:This study propose a novel visible-light crosslinking hydrogel bioink (termed GP) to fabricate injectable centimeter-scale architectures. Composed of GelMA with large molecular weight PEGDA, GP can form a reinforced dual-crosslinking network, presenting excellent superelasticity and stability, supporting injection pass nozzles with 1.5mm inner diameter after bioprinted as 15mm×15mm scale architectures. Moreover, when printing with living cells, even for sensitive cell lines like genome-edited cells, the transcriptome of cells after printing shows no difference, suggesting the high cell printing suitability of GP and the visible-light extrusion printing technique. The printed architectures can support long-term culture for at least 14 days, and GP provides cells with a biocompatible microenvironment, supporting cell survival, proliferation, and function maintenance.

2023-10-19 | GSE230068 | GEO

Multiplexed imaging of nucleome architectures in single cells of mammalian tissue

Project description:The three-dimensional architecture of the genome affects genomic functions. Multiple genome architectures at different length scales, including chromatin loops, domains, compartments, and regions associated with nuclear lamina and nucleoli, have been discovered. However, how these structures are arranged in the same cell and how they are correlated with each other in different cell types in mammalian tissue are largely unknown. Here, we developed Multiplexed Imaging of Nucleome Architectures that measures multiscale chromatin folding, copy numbers of numerous RNA species, and associations of numerous genomic regions with nuclear lamina, nucleoli and surface of chromosomes in the same, single cells. We applied this method in mouse fetal liver, and identified de novo cell-type-specific chromatin architectures associated with gene expression, as well as chromatin organization principles independent of cell type. Polymer simulation showed that both intra-chromosomal self-associating interactions and extra-chromosomal interactions are necessary to establish the observed organization. Our experiments and modeling provide a multiscale and multi-faceted picture of chromatin folding and nucleome architectures in mammalian tissue and illustrate physical principles for maintaining chromatin organization. Here we submit our bulk RNA-sequencing data on E14.5 mouse fetal liver, used in the study to validate image-based RNA profiling results.

2020-05-15 | GSE148072 | GEO

3D Chromosome Structure Can Reveal Stem Cell Signatures (RNA-Seq)

Project description:We use in situ Hi-C to report the most comprehensive survey to date of chromatin organization in stem cells

2022-01-20 | GSE126013 | GEO

3D Chromosome Structure Can Reveal Stem Cell Signatures (Hi-C)

Project description:We use in situ Hi-C to report the most comprehensive survey to date of chromatin organization in stem cells

2022-01-20 | GSE126011 | GEO

3D Chromosome Structure Can Reveal Stem Cell Signatures (ChIP-Seq)

Project description:We use in situ Hi-C to report the most comprehensive survey to date of chromatin organization in stem cells

2022-01-20 | GSE126010 | GEO

Comparative 3D Genome Architectures of Adipose Tissues Provide Insight into Human-specific Regulation of Metabolic Homeostasis

Project description:Elucidating the regulatory mechanisms of human adipose tissue (AT) evolution is essential for understanding human metabolic homeostasis. In this study, we compared the chromatin architectures of anatomically distinct ATs from humans and six representative mammalian models. We recognized evolutionarily conserved and human-specific chromatin conformation at multiple scales, including compartmentalization, topologically associating domain (TAD), and promoter-enhancer interactions (PEI). We found PEIs are more evolutionarily dynamic with respect to compartmentalization and TAD. Human-specific chromatin structure-related genes were involved in multiple biological processes, including energy metabolism and maintenance of metabolic homeostasis. The genes regulated by human-specific PEIs were depleted for diabetic variations, implying a beneficial role in metabolic homeostasis. Additionally, numerous human-specific chromatin structures were observed among subcutaneous and visceral ATs, indicating the diversified functions of ATs during evolution. Collectively, the presented data highlight the value of comparative 3D genome analyses in dissecting the regulatory mechanisms of different ATs and evolution.

2023-04-25 | GSE199968 | GEO

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

Project description:In this study, we analyzed transcriptome gene expression microarray, epigenomic miRNA microarray and methylome sequencing data simultaneously in PBMs from 5 high hip BMD subjects and 5 low hip BMD subjects. Through integrating the transcriptomic and epigenomic data, firstly we identified BMD-related genetic factors, including 9 protein coding genes and 2 miRNAs, of which 3 genes (FAM50A, ZNF473 and TMEM55B) and one miRNA (hsa-mir-4291) showed the consistent association evidence from both gene expression and methylation data, and 3 genes (TMEM55B, RNF40 and ALDOA) were confirmed in the meta-analysis of 7 GWAS samples and GEnetic Factors for OSteoporosis consortium (GEFOS-2) GWAS results. Secondly in network analysis we identified an interaction network module with 12 genes and 11 miRNAs including AKT1, STAT3, STAT5A, FLT3, hsa-mir-141 and hsa-mir-34a which have been associated with BMD in previous studies. This module revealed the crosstalk among miRNAs, mRNAs and DNA methylation and showed four potential regulatory patterns of gene expression to influence the BMD status, including regulation by gene methylation, by miRNA and its methylation, by transcription factors and co-regulation by miRNA and gene methylation. In conclusion, the integration of multiple layers of omics can yield more in-depth results than analysis of individual omics data respectively. Integrative analysis from transcriptomics and epigenomic data improves our ability to identify causal genetic factors, and more importantly uncover functional regulation pattern of multi-omics for osteoporosis etiology. 5 high hip BMD subjects and 5 low hip BMD subjects

2014-10-22 | E-GEOD-62588 | biostudies-arrayexpress

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

2014-11-19 | E-GEOD-63446 | 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