Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Joint epigenome profiling reveals cell-type-specific gene regulatory programs in human cortical organoids

ABSTRACT: Gene expression is regulated by multiple epigenetic mechanisms, which are coordinated in development and disease. However, current multiomic methods are frequently limited to one or two modalities at a time, making it challenging to obtain a comprehensive gene regulatory signature. Here, we describe a novel approach, 3DRAM-seq, which simultaneously interrogates spatial genome organization, chromatin accessibility, DNA methylation genome-wide and at high resolution. We combine 3DRAM-seq with immunoFACS and RNA-seq in cortical organoids to map the cell-type-specific regulatory landscape of human neural development across multiple epigenetic layers. Finally, we apply a massively parallel reporter assay (MPRA) to profile cell-type-specific enhancer activity in organoids and functionally assess the role of key transcription factors for human enhancer activation and function. More broadly, 3DRAM-seq can be used to profile the multimodal epigenetic landscape in rare cell types and different tissues.

ORGANISM(S): Mus musculus Escherichia coli Homo sapiens

PROVIDER: GSE211736 | GEO | 2023/08/23

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Multiomic (Joint snRNA/snATAC) sequencing data of intestinal crypts and epithelial only organoids derived from human fetal duodenum

Project description:Here, we used joint single-nuclei RNA-sequencing (snRNA-seq) and single-nuclei ATAC sequencing (scATAC) to profile freshly isolated crypts from the human fetal intestine and matched intestinal epithelial only organoids (also known as enteroids) derived from these crypts after one passage of in vitro growth. Organoids were grown in the standard 25% LWRN media with either 100 ng/ml of EGF or 1 ng/ml of EREG added. Fresh crypts were not placed in culture but rather immediately frozen for multiomic processing.

2022-07-16 | E-MTAB-11908 | biostudies-arrayexpress

Systematic dissection of regulatory motifs in 2,000 predicted human enhancers using a massively parallel reporter assay

Project description:We employ a massively parallel reporter assay (MPRA) to measure the ex vivo activities of hundreds of K562 and HepG2 enhancers with known transcription factor motif instances. For seven selected motifs that correspond to known or predicted activators and repressors in the two cell types, we make directed modifications of the bases corresponding to these motifs and observe the changes in enhancer activity. Reporter mRNA-seq from HepG2 and K562 cells transfected with a ~55,000-plex MPRA plasmid pool containing 5,418 mutated human enhancer sequences, each linked to 10 distinct 10-nt tags. The reporter mRNA tags facilitate quantitation of their abundances. The same tags were also sequenced from the transfected MPRA plasmid pool to facilitate normalization to plasmid copy numbers.

2013-03-15 | E-GEOD-33367 | biostudies-arrayexpress

Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay

Project description:We apply a massively parallel reporter assay (MPRA) that relies on mRNA and plasmid tag sequencing (Tag-Seq) to compare the regulatory activities of more than 27,000 distinct variants of two inducible enhancers in human cells: a synthetic cAMP-regulated enhancer and the virus-inducible interferon beta enhancer. The resulting data define accurate maps of functional transcription factor binding sites in both enhancers at single-nucleotide resolution and can be used the to train quantitative sequence-activity models (QSAMs). Reporter Tag-Seq from HEK293 cells transfected with each of six MPRA plasmid pools, with and without stimulation (forskolin or Sendai virus). The reporter mRNAs contain unique 10 nucleotide tags that facilitates quantitation of their abundances. The same tags were also sequenced from each ransfected plasmid pool to facilitate normalization to plasmid copy numbers. The reporter constructs were designed according to two different mutagenesis strategies: 'single-hit scanning' and 'multi-hit sampling'. The specific variants are included in the processed data files.

2012-02-26 | E-GEOD-31982 | biostudies-arrayexpress

The epigenetic landscape of human colorectal cancer

Project description:We characterized the epigenetic landscape of human colorectal cancer (CRC). To this extent, we performed gene expression profiling using high throughput sequencing (RNA-seq) and genome wide binding/occupancy profiling (ChIP-seq) for histone modifications correlated to transcriptional activity, enhancers, elongation and repression (H3K4me3, H3K4me1, H3K27Ac, H3K36me3, H3K27me3) in patient-derived organoids (PDOs), and in normal and tumoral primary colon tissues. We also generated ChIP-seq data for transcription factors YAP/TAZ in human CRC PDOs.

2021-02-23 | E-MTAB-8416 | biostudies-arrayexpress

The epigenetic landscape of human colorectal cancer

2021-03-10 | E-MTAB-8448 | biostudies-arrayexpress

Foxp3 exploits a preexistent enhancer landscape for regulatory T cell lineage specification

Project description:This SuperSeries is composed of the following subset Series: GSE40684: Foxp3 exploits a preexistent enhancer landscape for regulatory T cell lineage specification [ChIP-Seq] GSE40685: Foxp3 exploits a preexistent enhancer landscape for regulatory T cell lineage specification [Expression] Refer to individual Series

2012-09-28 | E-GEOD-40686 | biostudies-arrayexpress

Dynamic epigenetic enhancer signatures are predictive for key transcriptional regulators associated with cellular differentiation states

Project description:Cellular differentiation is orchestrated by lineage-specific transcription factors and associates with cell type-specific epigenetic signatures. Here, we utilized stage-specific, epigenetic "fingerprints" to deduce key transcriptional regulators of a cellular differentiation process. In the model of human macrophage differentiation, we globally mapped the distribution of epigenetic enhancer marks (histone H3 lysine 4 monomethylation, histone H3 lysine 27 acetylation, and the histone variant H2AZ) and show that cell type-specific epigenetic "fingerprints" correlate with specific, de novo derived motif signatures at all differentiation stages studied (hematopoietic progenitor cell, monocyte, macrophage). We validated the novel, de novo derived, macrophage-specific enhancer signature which included ETS, CEBP, bZIP, EGR, E-Box and NFkB motifs by ChIP-sequencing for a subset of motif corresponding transcription factors (PU.1, C/EBPbeta, and EGR2) which confirmed their predicted association with differentiation-associated epigenetic changes. This study highlights the power of genome-wide epigenetic profiling studies to reveal novel functional insights. It describes the dynamic enhancer landscape of human macrophage differentiation and provides a unique resource for macrophage biologists. ChIP-seq of 3 histone marks and 3 transcription factors in human blood monocytes and macrophages

2012-05-02 | E-GEOD-31621 | biostudies-arrayexpress

RNA-seq of two human and one cynomologous NPC line to assay activity of DNAse1 hypersensitive sites in the proximity of the Trnp1 gene

Project description:Homo sapiens and Macaca fascicularis neural progenitor cell lines were transduced with a lentiviral MPRA (Massively Parallel Reporter Assay) library. MPRA barcode sequencing and RNA-seq was performed on the extracted RNA. RNA-seq data was used to confirm transcription factor expression.

2021-05-12 | E-MTAB-9951 | biostudies-arrayexpress

MPRA of two human and one cynomologous NPC line to assay activity of DNAse1 hypersensitive sites in the proximity of the Trnp1 gene

Project description:Homo sapiens and Macaca fascicularis neural progenitor cell lines were transduced with a lentiviral MPRA (Massively Parallel Reporter Assay) library. MPRA barcode sequencing and RNA-seq was performed on the extracted RNA. MPRA data was used to compare activity of regulatory sequences across 75 mammalian species with a focus on primates and correlate these activities with the Phenotype of gyrencephaly.

2021-05-12 | E-MTAB-9952 | biostudies-arrayexpress

STARR-seq enhancer activity determined following hydrodynamic delivery of STARR-seq plasmid library to mouse liver using three different STARR-seq promoters: Super Core promoter, ORI promoter, and minimal Albumin promoter [G173]

Project description:Massively parallel reporter assays (MPRA) are widely used to discover functional enhancers but have largely been limited to transfected cell models. Here, we combine hydrodynamic injection with a modified STARR-seq-based MPRA to determine condition-specific enhancer activity in mouse liver at scale, and we examine how different promoters affect STARR-seq reporter activity. Strong liver enhancer activity was observed with STARR-seq libraries containing an Albumin minimal promoter but not when using a Super Core promoter or an origin of replication (ORI) promoter. This work is part of a larger study where we prepare a global STARR-seq library, comprised of ~50,000 genomic sequences released by DNase-I digestion of mouse liver nuclei, and where we identify condition-specific enhancers with strong correlations between liver enhancer activity and the chromatin state of the corresponding endogenous genomic regions.

2024-06-17 | GSE267075 | GEO

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