Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Reconstruction of 3-dimensional tissue organization at the single-cell resolution [scRNA-seq]

ABSTRACT: Reconstruction of 3-dimensional tissue organization at the single-cell resolution [scRNA-seq]

PROVIDER: PRJNA910305 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR22580823_1.fastq.gz	Fastqsanger.gz
	SRR22580823_2.fastq.gz	Fastqsanger.gz

Items per page:

1 - 2 of 2

Similar Datasets

Reconstruction of 3-dimensional tissue organization at the single-cell resolution

Project description:Reconstruction of 3-dimensional tissue organization at the single-cell resolution

| PRJNA910215 | ENA

Reconstruction of 3-dimensional tissue organization at the single-cell resolution [ST]

Project description:Reconstruction of 3-dimensional tissue organization at the single-cell resolution [ST]

| PRJNA910304 | ENA

Reconstruction of 3-dimensional tissue organization at the single-cell resolution [scRNA-seq]

Project description:We designed a neural network-based computational method that learns transcriptome-to-space mapping and reconstructs 3D tissue organization by learning from scRNA-seq and spatial transcriptomic data.

2023-08-08 | GSE220571 | GEO

Reconstruction of 3-dimensional tissue organization at the single-cell resolution [ST]

2023-08-08 | GSE220572 | GEO

Reconstruction of 3-dimensional tissue organization at the single-cell resolution

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

2023-08-08 | GSE220573 | GEO

Hi-C map of the three-dimensional genome organization

Project description:The spatial arrangement of interphase chromosomes in the nucleus is important for gene expression and genome function in animals and in plants. The recently developed Hi-C technology is an efficacious method to investigate genome packing. Here we present a detailed Hi-C map of the three-dimensional genome organization of the plant Arabidopsis thaliana. We find that local chromatin packing differs from the patterns seen in animals, with kilobasepair-sized segments that have much higher intra-chromosome interaction rates than neighboring regions and which represent a dominant local structural feature of genome conformation in A. thaliana. These regions appear as positive strips on two-dimensional representations of chromatin interaction and they are enriched in epigenetic marks H3K27me3, H3.1 and H3.3. We also identify over 400 insulator-like regions. Furthermore, although topologically associating domains (TADs), which are prominent in animals, are not the dominant feature of A. thaliana genome packing, we found over 1,000 regions that have properties of TAD boundaries, and a similar number of regions similar to the interior of TADs. These insulator-like, TAD-boundary-like, and TAD-interior-like regions show strong enrichment for distinct epigenetic marks, and correlate with gene transcription levels. We conclude that epigenetic modifications, gene density, and transcriptional activity all contribute to shaping the local structure of the A. thaliana nuclear genome.

2014-09-24 | E-MTAB-4438 | biostudies-arrayexpress

Three-dimensional chromatin re-organization during muscle stem cell aging

Project description:Three-dimensional chromatin re-organization during muscle stem cell aging

| PRJNA883688 | ENA

The dynamic three-dimensional organization of the diploid yeast genome

Project description:The dynamic three-dimensional organization of the diploid yeast genome

| PRJNA349185 | ENA

Transgenerational self-reconstruction of disrupted chromatin organization after exposure to an environmental stressor in mice

Project description:Exposure to environmental stressors is known to increase disease susceptibility in unexposed descendants in the absence of detectable genetic mutations. The mechanisms mediating environmentally-induced transgenerational disease susceptibility are poorly understood. We showed that great-great-grandsons of female mice exposed to tributyltin (TBT) throughout pregnancy and lactation were predisposed to obesity due to altered chromatin organization that subsequently biased DNA methylation and gene expression. Here we analyzed DNA methylomes and transcriptomes from tissues of animals ancestrally exposed to TBT spanning generations, sexes, ontogeny, and cell differentiation state. We found that TBT elicited concerted alterations in the expression of “chromatin organization” genes and inferred that TBT-disrupted chromatin organization might be able to self-reconstruct transgenerationally. We also found that the location of “chromatin organization” and “metabolic” genes is biased similarly in mouse and human genomes, suggesting that exposure to environmental stressors in different species could elicit similar phenotypic effects via self-reconstruction of disrupted chromatin organization.

2019-08-28 | GSE136377 | GEO

Three-dimensional chromatin re-organization during muscle stem cell aging [scATAC-seq]

Project description:Three-dimensional chromatin re-organization during muscle stem cell aging [scATAC-seq]

| PRJNA883691 | ENA