Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Chromosome conformation analysis of N1E115 cells by HiC

ABSTRACT: Chromosome conformation analysis of N1E115 cells by HiC

PROVIDER: PRJNA579925 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR10354691_1.fastq.gz	Fastqsanger.gz
	SRR10354691_2.fastq.gz	Fastqsanger.gz
	SRR10354692_1.fastq.gz	Fastqsanger.gz
	SRR10354692_2.fastq.gz	Fastqsanger.gz
	SRR10416994_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 12

Similar Datasets

Chromosome conformation analysis of N1E115 cells by HiC

Project description:Neuronal nitric oxide synthase 1 (NOS1) produces the gaseous signaling molecule nitric oxide (NO), which plays important roles in the development and function of the nervous system. The regulation of Nos1 gene expression is incompletely understood. Here, we explored the role of physiological hypoxia in the control of Nos1 transcription and the underlying mechanisms using N1E115 mouse neuroblastoma cells as a model. N1E115 cells were cultured for 3 days at high (20%) and low (4%) oxygen levels. Following the verification of upregulation of Nos1 mRNA and protein levels in response to 4% oxygen, we analyzed 3-dimensional chromosome conformation by HiC.

2024-02-14 | GSE139470 | GEO

Chromosome conformation capture by high thoughput sequencing (HiC) during Naïve CD4 T cell activation

Project description:Chromosome conformation capture by high thoughput sequencing (HiC) during Naïve CD4 T cell activation

| PRJNA503263 | ENA

Genome-wide analysis of histone marks in N1E115 cells

2024-02-14 | GSE139478 | GEO

Genome-wide analysis of HIF1A and ARNT binding in N1E115 cells

2024-02-14 | GSE139477 | GEO

HiChIRP reveals RNA-associated chromosome conformation

Project description:HiChIRP reveals RNA-associated chromosome conformation

| PRJNA475265 | ENA

Long-range epigenetic concordance revealed by simultaneous profiling of DNA methylation and chromosomal conformation changes in bulk and single cell Methyl-HiC

Project description:Genomic sequences, as well as its covalent epigenetic modifications, are spatially organized into three-dimensional structures. Here, we developed Methyl-HiC by combining in situ Hi-C and whole genome bisulfite sequencing (WGBS) to simultaneously capture genome-wide chromosome conformation changes and DNA methylation within the same DNA molecule. Methyl-HiC generated consistent information compared with in situ Hi-C and WGBS from the same cell line. We detected long-range DNA methylation concordance in general but varied in different chromatin states. We extended Methyl-HiC to single cell level and applied it on 103 primed and 47 naïve mouse embryonic stem cells (mESCs). We revealed the heterogeneity of chromosomal conformation changes by grouping cells in their DNA methylation level alone. We also observed increases of DNA methylation stochasticity and decreases of contact frequency together in late replication timing regions. Our method here paves the road to evaluate the direct long-range effect of epigenetic alterations in different pathological and healthy conditions at genome-wide and single cell level.

2018-11-16 | GSE119171 | GEO

Transcriptome analysis of N1E115 cells cultured in the presence of 20% or 4% O2

Project description:Neuronal nitric oxide synthase 1 (NOS1) produces the gaseous signaling molecule nitric oxide (NO), which plays important roles in the development and function of the nervous system. The regulation of Nos1 gene expression is incompletely understood. Here, we explored the role of physiological hypoxia in the control of Nos1 transcription and the underlying mechanisms using N1E115 mouse neuroblastoma cells as a model. N1E115 cells were cultured for 3 days at high (20%) and low (4%) oxygen levels. Following the verification of upregulation of Nos1 mRNA and protein levels in response to 4% oxygen, we performed transcriptome analysis using stranded total RNA-sequencing.

2024-02-14 | GSE139472 | GEO

Multiplexed analysis of chromosome conformation at vastly improved sensitivity

Project description:Current methods for analysing chromosome conformation in mammalian cells are either insensitive and low resolution or low throughput. Since the methods are expensive and relatively difficult to perform and analyse they are not widely used outside of specialised laboratories. Here we have re-designed the Capture-C method producing a new approach, called next generation (NG) Capture-C, which solves most of the current setbacks in analysing chromosome conformation. NG Capture-C produces unprecedented levels of sensitivity and reproducibility, which can be used to analyse any number of genetic loci and/or many samples in a single experiment. NG Capture is straightforward to perform, requiring only standard reagents and access to basic next generation sequencing platforms. The complete and detailed protocol presented here, with new publically available tools for library design and data analysis, will allow most laboratories to analyse chromatin conformation at levels of sensitivity and throughput that were previously impossible.

2015-11-16 | GSE67959 | GEO

Genome-wide analysis of POLR2, CTCF, RAD21, and H3K9ac binding in N1E115 cells

2024-02-14 | GSE139481 | GEO

Targeted high-resolution chromosome conformation capture at genome-wide scale in mouse erythroid cells

Project description:Chromosome conformation capture (3C) provides an adaptable tool through which to study diverse biological questions. Currently, 3C techniques provide either low-resolution interaction profiles across the entire genome, e.g. HiC, or high-resolution interaction profiles at up to several hundred loci, e.g. NG Capture-C and 4C-seq. Generation of high-resolution, genome-wide interaction profiles can feasibly be achieved through efficiency improvements to current high-resolution methods. To this end we systematically tested and removed areas inefficiency in NG Capture-C to develop a new method Nuclear Capture-C, which provides a 300% increase in informative sequencing content. Using Nuclear Capture-C we target 8,026 erythroid promoters in triplicate, showing that this method can achieve high-resolution genome-wide 3C interaction profiles at scale.

2020-10-28 | GSE160229 | 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