Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Differences in mitotic chromosome organization between cell types and species [Hi-C]

ABSTRACT: Differences in mitotic chromosome organization between cell types and species [Hi-C]

PROVIDER: PRJNA1048530 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR27050995_1.fastq.gz	Fastqsanger.gz
	SRR27050995_2.fastq.gz	Fastqsanger.gz
	SRR27050996_1.fastq.gz	Fastqsanger.gz
	SRR27050996_2.fastq.gz	Fastqsanger.gz
	SRR27050997_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 46

Similar Datasets

Differences in mitotic chromosome organization between cell types and species [Hi-C]

Project description:We performed Hi-C analysis of different mouse and human cell types to observe chromosome organization in mitosis with and without retained CTCF binding

2025-05-13 | GSE249328 | GEO

Differences in mitotic chromosome organization between cell types and species

Project description:Differences in mitotic chromosome organization between cell types and species

| PRJNA1048527 | ENA

Differences in mitotic chromosome organization between cell types and species [ATAC-Seq]

Project description:Differences in mitotic chromosome organization between cell types and species [ATAC-Seq]

| PRJNA1048532 | ENA

Metaphase-Chromosome-Organization

Project description:Mitotic chromosomes are among the most recognizable structures in the cell, yet for over a century their internal organization remains largely unsolved. We applied chromosome conformation capture methods, 5C and Hi-C, across the cell cycle and revealed two alternative three-dimensional folding states of the human genome. We show that the highly compartmentalized and cell-type-specific organization described previously for non-synchronous cells is restricted to interphase. In metaphase, we identify a homogenous folding state, which is locus-independent, common to all chromosomes, and consistent among cell types, suggesting a general principle of metaphase chromosome organization. Using polymer simulations, we find that metaphase Hi-C data is inconsistent with classic hierarchical models, and is instead best described by a linearly-organized longitudinally compressed array of consecutive chromatin loops.

2013-11-05 | E-MTAB-1948 | biostudies-arrayexpress

Differences in mitotic chromosome organization between cell types and species

Project description:This SuperSeries is composed of the SubSeries listed below.

2025-05-13 | GSE249331 | GEO

Rules of engagement for cohesin and condensin complexes during mitotic chromosome formation

Project description:During mitosis interphase chromatin is rapidly converted into rod-shaped mitotic chromosomes. Using Hi-C, imaging, proteomics, and polymer modeling we determine how the interplay between loop-extruding SMC motors accomplishes this dramatic transition. We find that condensin disassembles interphase chromatin loop organization by evicting or displacing extrusive cohesin. In contrast, condensins bypass cohesive cohesins, thereby maintaining sister chromatid cohesion while separating the sisters. We also estimate a speed of loop extrusion in vivo ~1-3 kb/sec. Our new models of mitotic chromosome conformation reveal that the loop organization by a discontinuous helical condensin II scaffold can vary greatly between chromosomes. We define a small set of rules of engagement for SMC complexes that together explain how cells refold interphase chromatin into mitotic chromosomes.

2025-01-25 | GSE262525 | GEO

Differences in mitotic chromosome organization between cell types and species [ATAC-Seq]

Project description:We performed ATAC-seq on mouse myoblast cells C2C12 in interphase and mitosis to observe footprinting on CTCF sites

2025-05-13 | GSE249329 | GEO

Hi-C during mitotic release and G1 entry

Project description:Hi-C during mitotic release and G1 entry

| PRJNA551502 | ENA

Selective compartmentalization in condensin-depleted mitotic chromosomes [Hi-C]

Project description:Selective compartmentalization in condensin-depleted mitotic chromosomes [Hi-C]

| PRJNA953365 | ENA

Allele-specific control of replication timing and genome organization during development [Promoter Capture Hi-C]

Project description:DNA replication occurs in a defined temporal order known as the replication-timing (RT) program. RT is regulated during development in discrete chromosomal units, coordinated with transcriptional activity and 3D genome organization. Here, we derived distinct cell types from F1 hybrid musculus X castaneus mouse crosses and exploited the high single nucleotide polymorphism (SNP) density to characterize allelic differences in RT (Repli-seq), genome organization (Hi-C and promoter-capture Hi-C), gene expression (total nuclear RNA-seq) and chromatin accessibility (ATAC-seq). We also present HARP: a new computational tool for sorting SNPs in phased genomes to efficiently measure allele-specific genome-wide data. Analysis of six different hybrid mESC clones with different genomes (C57BL/6, 129/sv and CAST/Ei), parental configurations and gender revealed significant RT asynchrony between alleles across ~12% of the autosomal genome linked to sub-species genomes but not to parental origin, growth conditions or gender. RT asynchrony in mESCs strongly correlated with changes in Hi-C compartments between alleles but not SNP density, gene expression, imprinting or chromatin accessibility. We then tracked mESC RT asynchronous regions during development by analyzing differentiated cell types including extraembryonic endoderm stem (XEN) cells, 4 male and female primary mouse embryonic fibroblasts (MEFs) and neural precursor cells (NPCs) differentiated in vitro from mESCs with opposite parental configurations. We found that RT asynchrony and allelic discordance in Hi-C compartments seen in mESCs was largely lost in all differentiated cell types, coordinated with a more uniform Hi-C compartment arrangement, suggesting that genome organization of homologues converges to similar folding patterns during cell fate commitment.

2018-05-22 | GSE114746 | 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