Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

49 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA Spatial Sequencing of Colorectal Liver Metastases regarding their Histopathological Growth Patterns

ABSTRACT: Molecular characterization of tissue areas in Colorectal Cancer Liver Metastases (CRCLM) and adjacent healthy liver tissue focusing on the comparison between the two main histopathological growth patterns (HGPs): desmoplastic HGP and replacement HGP with the intent to identify possible biomarkers or treatment targets especially for the more aggressive replacement HGP.

INSTRUMENT(S): DNBSEQ-G400

ORGANISM(S): Homo sapiens

SUBMITTER:

PROVIDER: E-MTAB-12043 | biostudies-arrayexpress |

SECONDARY ACCESSION(S): E-MTAB-12022

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

RNA Single Cell Sequencing of Colorectal Liver Metastasis regarding their Histopathological Growth Pattern

Project description:Molecular characterization of single cells in Colorectal Cancer Liver Metastases (CRCLM) and corresponding healthy liver tissue focusing on the comparison between the two main histopathological growth patterns (HGPs): desmoplastic HGP (dHGP) and replacement HGP (rHGP) with the intent to identify possible biomarkers or treatment targets especially for the more aggressive replacement HGP.

2023-01-05 | E-MTAB-12022 | biostudies-arrayexpress

Spatially resolved multiomics of human cardiac niches - Visium

Project description:Using Multiome and previously published sc/snRNA-seq data, we studied eight anatomical regions of the human heart including left and right ventricular free walls (LV and RV), left and right atria (LA and RA), left ventricular apex (AX), interventricular septum (SP), sino-atrial node (SAN) and atrioventricular node (AVN). For the first time, we profile the cells of the human cardiac conduction system, revealing their distinctive repertoire of ion channels, G-protein coupled receptors and cell-cell interactions. We map the identified cells to spatial transcriptomic data to discover cellular niches within the eight regions of the heart.

2023-06-01 | E-MTAB-12975 | biostudies-arrayexpress

Steroids-producing adrenocortical nodules (spatial transcriptomics)

Project description:This data was used in the analysis of the article titled: Steroids-producing adrenocortical nodules: a novel two-layered structure as a precursor lesion of cortisol-producing adenoma

2023-06-30 | E-MTAB-13127 | biostudies-arrayexpress

Single-Cell and Spatial Transcriptomics Analysis of Human Adrenal Aging (spatial transcriptomics)

Project description:These data were used in the spatial transcriptomics analysis of the article titled \\"Single-Cell and Spatial Transcriptomics Analysis of Human Adrenal Aging\\".

2024-04-22 | E-MTAB-13991 | biostudies-arrayexpress

A robust experimental and computational framework analysis at multiple resolutions, modalities and coverages

Project description:We assessed the utilities of integrating four advanced sequencing and multiplex imaging technologies to study cancer-immune cell interactions. These four technologies include single-cell RNA sequencing and Spatial Transcriptomic (both measuring over >20,000 genes), RNA In Situ Hybridization (multiplex 4-12 genes) and Opal multiplex protein staining (4-9 proteins). We evaluated the approach to discover and validate cell-cell interaction in situ through in-depth analysis of two types of cancer, basal cell carcinoma (BCC) and squamous cell carcinoma (SCC), which account for over 70% of skin cancer cases.

2022-07-26 | E-MTAB-11932 | biostudies-arrayexpress

Spatial Transcriptomics of the human musculotendinous unit, the myotendinous junction

Project description:Identification of cell types in the interphase between muscle and tendon by Visium Spatial Transcriptomics of four human semitendinous muscle-tendon biopsies. Cell types identified by single nuclei RNA seq on similar tissue were localized in situ with the use of Spatial Transcriptomics.

2023-03-02 | E-MTAB-12530 | biostudies-arrayexpress

Multiscale spatial mapping of cell populations across anatomical sites in healthy human skin and basal cell carcinoma - Spatial Transcriptomics - 10X Visium

Project description:Our understanding of how human skin cells differ according to body site and tumour formation is limited. To address this we have created a multi-scale spatial atlas of healthy skin and basal cell carcinoma (BCC), incorporating in vivo optical coherence tomography, single cell RNA sequencing, spatial global transcriptional profiling and in situ sequencing. Computational spatial deconvolution and projection revealed the localisation of distinct cell populations to specific tissue contexts. Although cell populations were conserved between healthy anatomical sites and in BCC, mesenchymal cell populations including fibroblasts and pericytes retain signatures of developmental origin. Spatial profiling and in silico lineage tracing support a hair follicle origin for BCC and demonstrate that cancer-associated fibroblasts are an expansion of a POSTN+ subpopulation associated with hair follicles in healthy skin. RGS5+ pericytes are also expanded in BCC suggesting a role in vascular remodelling during cancer neovascularization. Our findings suggest that the identity of mesenchymal cell populations is regulated by signals emanating from adjacent structures and that these signals are repurposed to promote the expansion of skin cancer stroma. The resource we have created is publicly available in an interactive format for the research community.

2023-12-22 | E-MTAB-13084 | biostudies-arrayexpress

Spatial transcriptomics of 3-month-old and 18-month-old mouse ovarian and uterine tissues

Project description:We used Visium technology (10X Genomics) to infer cell-to-cell communication in ovarian and uterine tissue based on spatial proximity. Organs from 3-month mice in diestrus and 18-month old mice were collected and frozen in OCT. 10 µm thick tissue slices were placed on Visium Spatial Gene Expression Slides (10X Genomics) and stained with Hematoxylin and Eosin (H&E). Libraries were prepared by manufacturer’s recommendations and sequenced on NovaSeq6000. For samples that were sequenced in two runs, both sequencing runs were merged when running spaceranger (10X Genomics). Original nd2 microscopy images and results of scRNA-seq (linked datasets) and spatial transcriptomics analysis are available at Biostudies (S-BIAD482 and S-BSST852).

2024-01-30 | E-MTAB-12105 | biostudies-arrayexpress

Mapping immune development across tissues in the human fetus - 10X spatial transcriptomics

Project description:To study the spatial localisations of the cell populations in an early haematopoietic tissue and lymphoid organs critical for T and B cell development, we profiled fetal liver, thymus and spleen from 3 donors at 18 PCW with sequencing-based spatial transcriptomics (10x Genomics Visium).

2022-05-12 | E-MTAB-11341 | biostudies-arrayexpress

Spatial transcriptomics from murine inguinal and mesenteric lymph nodes

Project description:B cell-interacting reticular cells (BRC) form transcriptionally and topologically stable immune-interacting microenvironments that direct efficient humoral immunity. While several immune niche factors have been elucidated, the cues sustaining BRC function and topology across activation states remain unclear. Here, we employed spatial transcriptome analysis of murine ingunal and mesenteric lymph nodes to examine co-localization of distinct BRC subsets and immune cells complementing BRC-immune cell interaction analysis. Spatial analysis supported predicted feedforward BRC-immune cell circuits that sustain topologically-organized, functional niches across inflammatory states, lymphoid organs and species.

2023-03-29 | E-MTAB-12468 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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