Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

DC3: Deconvolution and coupled clustering from bulk and single cell genomics data

ABSTRACT: HiChIP data generated for the retinoic acid-induced mESC differentiation at day 4.

ORGANISM(S): Mus musculus

PROVIDER: GSE127807 | GEO | 2019/08/14

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Integrative analysis of single cell genomics data by coupled nonnegative matrix factorizations (ATAC-Seq)

Project description:415 scATAC-seq samples generated for the retinoic acid-induced mESC differenation at day 4.

2018-06-19 | GSE115970 | GEO

Integrative analysis of single cell genomics data by coupled nonnegative matrix factorizations (RNA-Seq)

Project description:464 scRNA-seq samples generated for the retinoic acid-induced mESC differenation at day 4.

2018-06-19 | GSE115968 | GEO

Unsupervised clustering and epigenetic classification of single cells

Project description:96 scATAC-seq samples generated for the retinoic acid-induced mESC differentiation at day 4.

2018-04-20 | GSE107651 | GEO

DC3 is a method for deconvolution and coupled clustering from bulk and single-cell genomics data.

Project description:Characterizing and interpreting heterogeneous mixtures at the cellular level is a critical problem in genomics. Single-cell assays offer an opportunity to resolve cellular level heterogeneity, e.g., scRNA-seq enables single-cell expression profiling, and scATAC-seq identifies active regulatory elements. Furthermore, while scHi-C can measure the chromatin contacts (i.e., loops) between active regulatory elements to target genes in single cells, bulk HiChIP can measure such contacts in a higher resolution. In this work, we introduce DC3 (De-Convolution and Coupled-Clustering) as a method for the joint analysis of various bulk and single-cell data such as HiChIP, RNA-seq and ATAC-seq from the same heterogeneous cell population. DC3 can simultaneously identify distinct subpopulations, assign single cells to the subpopulations (i.e., clustering) and de-convolve the bulk data into subpopulation-specific data. The subpopulation-specific profiles of gene expression, chromatin accessibility and enhancer-promoter contact obtained by DC3 provide a comprehensive characterization of the gene regulatory system in each subpopulation.

| S-EPMC6787340 | biostudies-literature

DC3: Deconvolution and coupled clustering from bulk and single cell genomics data

Project description:DC3: Deconvolution and coupled clustering from bulk and single cell genomics data

| PRJNA525433 | ENA

Differentiation of entire complement of spinal sensory interneurons from mouse embryonic stem cells (mESCs) [10X]

Project description:By utilizing single-cell analysis of neurons that are produced at day 9 of mESC differentiation period (day 9) under the developmentally relevent signals- Retinoic acid and BMP4, we identified that our protocol can generate all major sensory neuron subtypes that are required for relaying sensation like pain, itch, heat and proprioception in the spinal cord. This analysis also identified functional features in each neuronal subtypes, confirming the bonafide status of the in vitro derived sensory neurons.

2022-07-09 | GSE185890 | GEO

Genome-wide microRNA transcriptome profiles in pluripotent mouse Embryonic Stem Cells and during Retinoic Acid-induced differentiation

Project description:We report the genome-wide microRNA expression levels in pluripotent mESC and as mESC differentiate towards a neuronal lineage in response to high levels of Retinoic Acid treatment in vitro. microRNA-seq was performed to identify all microRNAs expressed in both ESCs and neuronal cells. In total, 534 expressed microRNAs we identified, of which 18 were up-regulated and 6 were down-regulated (fold change (FC) > -/+2.0 and p-value < 0.05) during Retinoic Acid-induced neuronal differentiation. The top up-regulated microRNAs identified were Mir10a, Mir615, Mir217 and Mir219a-2. The top down-regulated microRNAs identifed were Mir211, Mir292, Mir302a and Mir302c.

2015-05-01 | GSE65696 | GEO

Genome-wide microRNA transcriptome profiles in pluripotent mouse Embryonic Stem Cells and during Retinoic Acid-induced differentiation

2015-05-01 | E-GEOD-65696 | biostudies-arrayexpress

Genome-wide binding profiles of nuclear FGFR1, RXR? and Nur77 in pluripotent mouse Embryonic Stem Cells and during Retinoic Acid-induced differentiation

Project description:We report the genome-wide binding patterns of nuclear FGFR1, RXR? and Nur77 in pluripotenet mESC and as mESC differentiate towared a neuronal lineage in response to high levels of Retinoic Acid treatment in vitro. We also report the genome-wide incorporation of histone varant H3.3 into chromatin specifically during Retinoic Acid-induced differentiation. This study presents nuclear FGFR1 as a global factor that controls genomic function by binding within the promoters of thousands of genes, both alone and in cooperation with RXR, Nur77 and histone H3.3, by targeting consensus DNA sequences of diverse transcription factor families. As such, it identifies a previously unknown, multifaceted form of control of major ontogenic pathways and gene networks targeted by the nuclear form of FGFR1. Examination of nuclear FGFR1, RXR?, and Nur77 binding sites in 2 celluar states. Examination of H3.3 incorporation in 1 cellular state.

2015-05-01 | E-GEOD-65695 | biostudies-arrayexpress

Genome-wide binding profiles of nuclear FGFR1, RXRα and Nur77 in pluripotent mouse Embryonic Stem Cells and during Retinoic Acid-induced differentiation

Project description:We report the genome-wide binding patterns of nuclear FGFR1, RXRα and Nur77 in pluripotenet mESC and as mESC differentiate towared a neuronal lineage in response to high levels of Retinoic Acid treatment in vitro. We also report the genome-wide incorporation of histone varant H3.3 into chromatin specifically during Retinoic Acid-induced differentiation. This study presents nuclear FGFR1 as a global factor that controls genomic function by binding within the promoters of thousands of genes, both alone and in cooperation with RXR, Nur77 and histone H3.3, by targeting consensus DNA sequences of diverse transcription factor families. As such, it identifies a previously unknown, multifaceted form of control of major ontogenic pathways and gene networks targeted by the nuclear form of FGFR1.

2015-05-01 | GSE65695 | 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