Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Single-nucleus single-nucleus assay for transposase-accessible chromatin with sequencing analysis of in vitro cardiac differentiations

ABSTRACT: Single-nucleus single-nucleus assay for transposase-accessible chromatin with sequencing analysis of in vitro cardiac differentiations

PROVIDER: PRJNA1028608 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR26400236_1.fastq.gz	Fastqsanger.gz
	SRR26400236_2.fastq.gz	Fastqsanger.gz
	SRR26400237_1.fastq.gz	Fastqsanger.gz
	SRR26400237_2.fastq.gz	Fastqsanger.gz
	SRR26400238_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 44

Similar Datasets

Single-nucleus single-nucleus assay for transposase-accessible chromatin with sequencing analysis of in vitro cardiac differentiations

Project description:Here, we utilize single-cell gene regulatory analysis to interrogate the gene expression within CMs generated from monolayer (2D) and embryoid body (3D) hPSC cardiac differentiation systems.

2024-09-06 | GSE245498 | GEO

Single nucleus ATAC-seq datasets for "Temporally Specific Gene Expression and Chromatin Remodeling Programs Regulate a Conserved Pdyn Enhancer"

Project description:This dataset contains single nucleus Assay for Transposase-Accessible Chromatin (ATAC) sequencing results from rat nucleus accumbens tissue. Rats received repeated cocaine injections (20mg/kg, intraperitoneal injection), or saline injections as a control. Single-nucleus ATAC-seq was carried out with FACS-sorted nuclei using the 10X Genomics Chromium single cell sequencing platform using the Chromium Next GEM Single Cell ATAC Kit v2.

2023-08-07 | GSE233754 | GEO

The gene regulatory landscape of kidney organoid differentiation revealed by single nucleus multiomic analyses [multi-omics]

Project description:We performed single nucleus RNA sequencing (snRNA-seq) and assay for transposase-accessible chromatin with sequencing (snATAC-seq) to map the epigenetic and gene expression signatures of human kidney organoids during the organoid differentiation time course.

2023-04-28 | GSE213151 | GEO

Assay for Transposase-Accessible Chromatin in E4BP4 overexpressed RAW264.7 cells

Project description:Assay for Transposase-Accessible Chromatin in E4BP4 overexpressed RAW264.7 cells

| PRJNA978597 | ENA

Single-nucleus analysis of accessible chromatin in developing mouse forebrain reveals cell-type-specific transcriptional regulation

Project description:Analysis of chromatin accessibility can reveal transcriptional regulatory sequences, but heterogeneity of primary tissues poses a significant challenge in mapping the precise chromatin landscape in specific cell types. Here we report single-nucleus ATAC-seq, a combinatorial barcoding-assisted single-cell assay for transposase-accessible chromatin that is optimized for use on flash-frozen primary tissue samples. We apply this technique on the mouse forebrain through eight developmental stages. Through analysis of more than 15,000 nuclei, we identify 20 distinct cell populations corresponding to major neuronal and non-neuronal cell types. We further define cell-type-specific transcriptional regulatory sequences, infer potential master transcriptional regulators and delineate developmental changes in forebrain cellular composition. Our results provide insight into the molecular and cellular dynamics that underlie forebrain development in the mouse and establish technical and analytical frameworks that are broadly applicable to other heterogeneous tissues.

2018-01-27 | GSE100033 | GEO

Liver Transposase-Accessible Chromatin signal changes related to fat content in pigs

Project description:The present work emplyed pigs as an animal model for recognition of molecular processes associated with fat deposition. The Transposase-Accessible Chromatin signal changes dependent on fat content were showed at the liver levels. In the experiment Złotnicka White pigs were used that were not under selection pressure, because they are included in to National Preservation Program.

2022-04-03 | GSE199870 | GEO

Tn5 transposase-mediated library preparation of single-cell cDNAs for RNA-seq

Project description:Deep sequencing of single cell-derived genomic DNA and/or cDNAs brings novel insights into oncogenesis and embryogenesis. However, traditional library preparation for RNA-Seq requires multiple steps, including shearing the target DNA/RNA and following sequential enzymatic reactions, which result in consequent sample loss and stochastic variation at each step. Such variation may significantly affect the output from sequencing. We have found that a new technique of library preparation using hyperactive Tn5 transposase for the next-generation sequencer of Illumina's platform provided high-quality libraries from 100ng of short-length (average 700~800 bp) single-cell level cDNA. This new method reduced the number of steps in the protocol, which resulted in improved reproducibility and reduced variation among the specimens. Two methods of library preparation (sonication, tagmentation with hyperactive Tn5 transposase) were compared in the case of RNA-Seq for single-cell level cDNA. Technical triplicates were used.

2012-05-25 | E-GEOD-38198 | biostudies-arrayexpress

Single-nucleus transcriptomics and chromatin accessibility of cell type-specific contributions to the epileptogenic cortex of focal cortical dysplasia type IIIa [snRNA-seq]

Project description:Focal cortical dysplasia (FCD) is a heterogeneous group of cortical developmental malformations that constitute a common cause of medically intractable epilepsy. Multiomic integration was conducted via single-nucleus RNA sequencing (snRNA-seq) and single-nucleus assays for transposase-accessible chromatin sequencing (snATAC-seq) to analyse cell type-specific alterations in chromatin accessibility and correlate them with gene expression changes in the epileptogenic cortex of FCD type IIIa (FCD IIIa).

2024-10-30 | GSE266305 | GEO

Single-nucleus transcriptomics and chromatin accessibility of cell type-specific contributions to the epileptogenic cortex of focal cortical dysplasia type IIIa [snATAC-seq]

2024-10-30 | GSE266303 | GEO

ATAC-Se1 to investigate the spatial choreography of the accessible genome

Project description:In order to completely understand the spatial choreography of the accessible genome in the 3D intact nucleus, we had developed a new technique termed assay of transposase accessible chromatin by visualization (ATAC-see). In brief, we had labeled the adaptor in hypersensitive Tn5 transposase with fluorophore dye and performed the Tn5 tagmentation on the fixed culture cells slide. We had performed ATAC-see in different types of cells and found out there are cell types specific spatial choreography of the accessible genome in the 3D intact nucleus, which is tightly linked to cell types specific function. Importantly, we could images the open chromatin distribution and do the sequencing on the exactly same sample, which offer a powerful tool to understand how the open chromatin organize in the 3D nucleus and how the open chromatin regulate gene expression.

2016-10-05 | GSE76006 | 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