Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Human palindrome P8

ABSTRACT: Disclosing complex mutational dynamics at a Y chromosome palindrome evolving through intra- and inter-chromosomal gene conversion

PROVIDER: PRJEB52142 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR9526730.fastq.gz	Fastqsanger.gz
	ERR9526730_1.fastq.gz	Fastqsanger.gz
	ERR9526730_2.fastq.gz	Fastqsanger.gz
	ERR9526740.fastq.gz	Fastqsanger.gz
	ERR9526740_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 471

Similar Datasets

Hi-C Calibration by Chemically Induced Chromosomal Interactions

Project description:The genome-wide chromosome conformation capture method, Hi-C, has greatly advanced our understanding of genome organization. However, its quantitative properties, including sensitivity, bias, and linearity, remain challenging to assess. Measuring these properties in vivo is difficult due to the heterogenous and dynamic nature of chromosomal interactions. Here, using Chemically Induced Chromosomal Interaction (CICI) method, we create stable intra- and inter-chromosomal interactions in G1-phase budding yeast across a broad range of contact frequencies. Hi-C analysis of these engineered cell populations demonstrates that static intra-chromosomal loops do not generate Topologically Associated Domains (TADs) and only promote 3D proximity within ~50kb flanking regions. At moderate sequencing depth, Hi-C is sensitive enough to detect interactions occurring in a few percent of cells. It also shows no inherent bias toward intra- versus inter-chromosomal interactions. Furthermore, we observe a linear relationship between Hi-C signal intensity and contact frequency. These findings illuminate the intrinsic properties of the Hi-C assay and provide a robust framework for its calibration.

2024-12-11 | GSE283767 | GEO

Chromosome Conformation of Human Fibroblasts Grown in 3-Dimensional Spheroids

Project description:In the study of interphase chromosome organization, genome-wide chromosome conformation capture (Hi-C) maps are often generated using 2-dimensional (2D) monolayer cultures. These 2D cells have morphological deviations from cells that exist in 3-dimensional (3D) tissues in vivo, and may not maintain the same chromosome conformation. We used Hi-C maps to test the extent of differences in chromosome conformation between human fibroblasts grown in 2D cultures and those grown in 3D spheroids. Significant differences in chromosome conformation were found between 2D cells and those grown in spheroids. Intra-chromosomal interactions were generally increased in spheroid cells, with a few exceptions, while inter-chromosomal interactions were generally decreased. Overall, chromosomes located closer to the nuclear periphery had increased intra-chromosomal contacts in spheroid cells, while those located more centrally had decreased interactions. This study highlights the necessity to conduct studies on the topography of the interphase nucleus under conditions that mimic an in vivo environment.

2016-01-26 | GSE77237 | GEO

Detecting chromatin interactions along and between sister chromatids with SisterC

Project description:Novel chromosome conformation technique captures inter- and intra-sister interactions in mitotic yeast chromosomes

2020-06-17 | GSE145695 | GEO

DNA Methylation-Based High-Resolution Mapping of Long-Distance Chromosomal Interactions in Nucleosome-Depleted Regions (RNA)

Project description:Here, we present Methyltransferase Targeting-based chromosome Architecture Capture (MTAC), a method that maps the contacts between a target site (viewpoint) and the rest of the genome with high resolution and sensitivity. By targeting M.CviPI DNA methyltransferase to the viewpoint and by detecting differentially methylated regions, MTAC detects hundreds of intra- and inter-chromosomal interactions in the budding yeast genome that cannot be captured by 4C, Hi-C, or Micro-C.

2023-09-05 | GSE242399 | GEO

DNA Methylation-Based High-Resolution Mapping of Long-Distance Chromosomal Interactions in Nucleosome-Depleted Regions (MeDIP)

2023-09-05 | GSE242398 | GEO

DNA Methylation-Based High-Resolution Mapping of Long-Distance Chromosomal Interactions in Nucleosome-Depleted Regions (HiC)

2023-09-05 | GSE242396 | GEO

DNA Methylation-Based High-Resolution Mapping of Long-Distance Chromosomal Interactions in Nucleosome-Depleted Regions (ChIP)

2023-09-05 | GSE242395 | GEO

DNA Methylation-Based High-Resolution Mapping of Long-Distance Chromosomal Interactions in Nucleosome-Depleted Regions (4C)

2023-09-05 | GSE242394 | GEO

Three-dimensional folding and functional organization principles of the Drosophila genome

Project description:Chromosomes are the physical realization of genetic information and thus form the basis for its reading, hindering and propagation. Here we present a high-resolution chromosomal contact map derived from a new genome-wide chromosome conformation capture approach (a simplified version of the Hi-C method) applied to Drosophila embryonic nuclei. The data show that the entire genome is linearly partitioned into well-demarcated physical domains that overlap extensively with active and repressive epigenetic marks. Chromosomal contacts are hierarchically organized between domains. Global modeling of compaction and clustering of domains show that inactive domains are condensed and confined to their chromosomal territories, while active domains reach out of the territory to form remote intra- and inter-chromosomal contacts.

2012-01-20 | GSE34453 | GEO

Illumina HiSeq next -generation sequencing of telomere fusion amplicons purified from crisis-stage MCR5HPVE6E7 and TALEN-transfected HCT116 cell lines at 48 and 120 hours post-transfection.

Project description:We sequenced and characterised inter-chromosomal and intra-chromosomal telomere fusions amplified from crisis-stage MCR5HPVE6E7 fibroblasts and DNA repair-compromised HCT116 cell lines nucleofected with plasmids encoding TALEN pairs to induce targeted cleavage at the 17p telomere.

2016-02-24 | E-MTAB-3811 | biostudies-arrayexpress

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