Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

D62c7def-217d-42b0-bf99-f8327a621159 - samples

ABSTRACT: This dataset contains the raw sequencing data (Runs) from all of the 10x Genomics single-cell Visium Experiments, as well as the corresponding imaging data (Analyses).

PROVIDER: EGAD00001009821 | EGA |

REPOSITORIES: EGA

ACCESS DATA

Json Xml

Similar Datasets

Spatial

Project description:This dataset contains the raw sequencing data (Runs) from all of the 10x Genomics single-cell Visium Experiments, as well as the corresponding imaging data (Analyses).

| EGAD00010002379 | EGA

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

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

Histopathological-based analysis of human kidney spatial transcriptomics data: toward precision pathology

Project description:In this study, we conducted a histopathological-based analysis of 10x Genomics Visium spatial transcriptomics data on a human kidney sample corresponding as closely as possible to the reality of the interpretation of a kidney biopsy in a healthcare or research context.

2024-06-27 | GSE261545 | 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.

2023-01-31 | GSE222322 | 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

Nextflow Pipeline for Visium and H&E Data from Patient-Derived Xenograft Samples

Project description:We designed a Nextflow DSL2-based pipeline, Spatial Transcriptomics Quantification (STQ), for simultaneous processing of 10x Genomics Visium spatial transcriptomics data and a matched hematoxylin and eosin (H&E)-stained whole slide image (WSI), optimized for Patient-Derived Xenograft (PDX) cancer specimens. Our pipeline enables the classification of sequenced transcripts for deconvolving the mouse and human species and mapping the transcripts to reference transcriptomes. We align the H&E WSI with the spatial layout of the Visium slide and generate imaging and quantitative morphology features for each Visium spot. The pipeline design enables multiple analysis workflows, including single or dual reference genomes input and stand-alone image analysis. We show the utility of our pipeline on a dataset from Visium profiling of four melanoma PDX samples. The clustering of Visium spots and clustering of H&E imaging features reveal similar patterns arising from the two data modalities.

2024-05-21 | GSE238004 | GEO

Spatial transcriptomics of post-mortem lung tissue from COVID-19 donors

Project description:Visualization of gene expression in lung tissue was performed using Visium spatial gene expression kits (10x Genomics) following the manufacturer`s protocol. The four capture areas in a 10x Genomics Visium Gene Expression slide consist of 5000 spots with DNA oligos for mRNA capture that have a unique spatial barcode and a unique Molecular Identifier (UMI). Each spot has 55 µm diameter and can therefore capture mRNA from 1 to 10 cells. We report the spatially resolved transcriptome of 3 control lung samples from non-COVID-19-related pneumonia donors and 9 COVID-19 lung samples analyzed with the 10x Visium platform.

2022-12-21 | GSE190732 | GEO

5eec21b6-a801-418c-83bc-21249ef99526 - samples

Project description:This dataset contains the raw sequencing data (Runs) for all 10x Genomics single-cell RNA-seq Experiments.

| EGAD00001009823 | EGA

c5639dd3-e2b9-4f16-909e-8f7d6970e16b - samples

Project description:This dataset contains the raw sequencing data (Runs) from all of the 10x Genomics single-cell Multiome Experiments

| EGAD00001009824 | EGA