Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Spatial Transcriptome

ABSTRACT: 10x Genomics Visium

TISSUE(S): ['liver']

SUBMITTER: Hong Li

PROVIDER: OEX00021154 | NODE | 2024-06-26

REPOSITORIES: NODE

ACCESS DATA

Json Xml

Similar Datasets

Spatial transcriptome analysis of brain region in grass puffer (Takifugu alboplumbeus)

Project description:We have applied spatial transcriptomics on puffer brain using Visium Spatial Gene Expression platform (10X Genomics) to examine each genes expression level and site in the brain.

2022-09-27 | GSE186818 | GEO

Visium Analysis of head and neck squamous carcinoma (HNSCC) spatial transcriptome evolution

Project description:We collected HNSCC primary tumor sections from head and neck squamous cell carcinoma patients at the Taipei Veterans General Hospital (TVGH) for 10x Genomics Visium analysis.

2022-08-29 | GSE181300 | GEO

Spatial transcriptomics reveals ovarian cancer subclones with different microenvironments

Project description:8 spatial RNA-seq experiments (10x Genomics Visium) and 5 single-cell RNA-seq experiments (10x Genomics Chromium) using high-grade serous ovarian carcinoma (HGSOC) samples obtained from the ovaries during the interval debulking surgery

2022-08-29 | GSE211956 | GEO

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).

2024-07-23 | E-MTAB-12105 | biostudies-arrayexpress

Spatial transcriptomics of seven hepatocellular carcinoma cases

Project description:10x Genomics Visium v2 spatial transcriptomic analysis of seven hepatocellular carcinoma (HCC) cases. The patients’ underlying liver diseases were metabolic-associated steatohepatitis (MASH, n = 2), hepatitis C (n = 2), hepatitis B (n = 1), and alcoholic liver disease (n = 1).

2025-12-31 | E-MTAB-15226 | biostudies-arrayexpress

Spatial transcriptomics of human colorectal cancer liver metastatic samples

Project description:These samples are part of a study investigating cancer cell plasticity in colorectal cancer metastasis. Spatial transcriptomics was performed using 10x Genomics Visium on colorectal cancer liver metastatic patient samples.

2025-04-22 | E-MTAB-13655 | biostudies-arrayexpress

Spatial RNA sequencing of mouses brain slices following spatial object recognition training

Project description:We report a spatial transcriptomics dataset of mouse brain tissue generated with the 10x Genomics Visium platform to identify gene expression profiles of spatial object recognition training.

2022-11-01 | GSE201610 | GEO

Spatial transcriptomics of colorectal cancer tissues

Project description:We study and report the whole transcriptome spatial profiling insights in colorectal cancer using the Visium spatial technique (Visium CytAssist, 10x genomics).

2024-05-17 | GSE267401 | GEO

Spatial transcriptomics on human lumbar spinal cord

Project description:This study includes spatial transcriptomics on the human lumbar spinal cord using the 10x Genomics Visium platform. Frozen sections of spinal cord were placed on Visium slide arrays and processed using the 10x Genomics workflow, followed by alignment and quantification using the spaceranger package. Update on 5/25/2026: The patient ID mapping file (GSE222322_donor_to_patient_ids.csv.gz) contains an error: the last line should map Visium_ID Donor45 to Patient_ID 15 (with Patient_IDs corresponding to the Donor column in Supplemental Table 1 of the manuscript).

2023-01-31 | GSE222322 | GEO

Spatial RNA sequencing of regenerating mouse hindlimb muscle

Project description:We report a series of spatial transcriptomics datasets of regenerating mouse muscle tissue generated with the 10x Genomics Visium platform.

2020-12-02 | GSE161318 | 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