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 [ST]

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

PROVIDER: PRJNA910304 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR22580422_1.fastq.gz	Fastqsanger.gz
	SRR22580422_2.fastq.gz	Fastqsanger.gz
	SRR22580423_1.fastq.gz	Fastqsanger.gz
	SRR22580423_2.fastq.gz	Fastqsanger.gz

Items per page:

1 - 4 of 4

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 [scRNA-seq]

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

| PRJNA910305 | ENA

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

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 | GSE220572 | GEO

Open-ST: High-resolution spatial transcriptomics in 3D

Project description:Spatial transcriptomics (ST) methods unlock molecular mechanisms underlying tissue development, homeostasis, or disease. However, there is a need for easy-to-use, high-resolution, cost-efficient, and 3D-scalable methods. Here, we report Open-ST, a sequencing-based, open-source experimental and computational resource to address these challenges and to study the molecular organization of tissues in 2D and 3D. In mouse brain, Open-ST captured transcripts at subcellular resolution and reconstructed cell types. In primary head-and-neck tumors and patient-matched healthy/metastatic lymph nodes, Open-ST captured the diversity of immune, stromal, and tumor populations in space, validated by imaging-based ST. Distinct cell states were organized around cell-cell communication hotspots in the tumor but not the metastasis. Strikingly, the 3D reconstruction and multimodal analysis of the metastatic lymph node revealed spatially contiguous structures not visible in 2D and potential biomarkers precisely at the 3D tumor/lymph node boundary. All protocols and software are available at https://rajewsky-lab.github.io/openst.

2024-06-23 | GSE251926 | GEO

Open-ST: High-resolution spatial transcriptomics in 3D [xenium]

2024-06-23 | GSE263498 | GEO

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

2023-08-08 | GSE220571 | GEO

Open-ST: High-resolution spatial transcriptomics in 3D

Project description:Open-ST: High-resolution spatial transcriptomics in 3D

| PRJNA1055947 | ENA

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

Open-ST: High-resolution spatial transcriptomics in 3D [xenium]

Project description:Open-ST: High-resolution spatial transcriptomics in 3D [xenium]

| PRJNA1097649 | ENA