Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Cell type mapping reveals tissue niches and interactions in subcortical multiple sclerosis lesions [snRNA-seq]

ABSTRACT: We generated a paired snRNA-seq (n= 15) and spatial transcriptomics (n=19) dataset from subcortical chronic active and chronic inactive MS lesions, identifying spatial niches and key cell interactions driving inflammation and disease progression at the lesion rim. This repository offers access to all the trancriptomics data that was used in the paper. It includes, all FASTQ files for both transcriptomics, along with the necessary files for running spatial transcriptomic samples (H&E images and JSON files), as well as the curated atlas, all derived cell subtype atlases from the main atlas and all curated ST slides.

ORGANISM(S): Homo sapiens

PROVIDER: GSE279180 | GEO | 2024/10/21

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Cell type mapping reveals tissue niches and interactions in subcortical multiple sclerosis lesions [spatial transcriptomics]

Project description:We generated a paired snRNA-seq (n= 15) and spatial transcriptomics (n=19) dataset from subcortical chronic active and chronic inactive MS lesions, identifying spatial niches and key cell interactions driving inflammation and disease progression at the lesion rim. This repository offers access to all the trancriptomics data that was used in the paper. It includes, all FASTQ files for both transcriptomics, along with the necessary files for running spatial transcriptomic samples (H&E images and JSON files), as well as the curated atlas, all derived cell subtype atlases from the main atlas and all curated ST slides.

2024-10-21 | GSE279181 | GEO

Cell type mapping reveals tissue niches and interactions in subcortical multiple sclerosis lesions [spatial transcriptomics]

Project description:Cell type mapping reveals tissue niches and interactions in subcortical multiple sclerosis lesions [spatial transcriptomics]

| PRJNA1171322 | ENA

SARS-CoV-2 Niches in Human Placenta Revealed by Spatial Transcriptomics

Project description:Diverse placental functions are compartmentalized to separate maternal-fetal antigens and restrict vertical transmission of pathogens. We hypothesized a high-resolution map, with single-cell and spatial resolution, would identify previously undetectable microbe immune microenvironments. To test this hypothesis, we utilized Visium Spatial Transcriptomics paired with H&E staining to generate 17,927 spatial transcriptomes and integrated these data with 273,944 published placenta single-cell and single-nuclei transcriptomes to generate a term placenta atlas of the maternal decidua, fetal chorionic villi, and chorioamniotic membranes. Comparisons of healthy control placentae (n=4), SARS-CoV-2 asymptomatic (n=4; no COVID-19 symptoms), and symptomatic (n=5; pneumonia, respiratory failure) placentae identified distinct thresholds of SARS-CoV-2 detection including (i) no detectable virus, (ii) sparse virus (limit of detection determined to be 1/7,000 cells), and (iii) highly positive SARS-CoV-2 in syncytiotrophoblasts, rigorously cross-validated by RT-qPCR, RNAscope, and immunohistochemistry. High levels of SARS-CoV-2 in placentae were associated with histiocytic intervillositis and perivillous fibrin deposition. Spatial transcriptomics revealed that this led to a significant shift from anti-inflammatory M2 macrophage populations toward intermediate pro-inflammatory M1 macrophages. In conclusion, we identified immune microenvironments representing host-pathogen battlegrounds where SARS-CoV-2 detection in the placenta was not dependent on maternal symptoms. Additional studies utilizing this approach are warranted, especially in the placenta.

2023-07-05 | GSE222987 | GEO

Characteristic of the transcriptomics in the early subcortical vascular cognitive impairment

Project description:Characteristic of the transcriptomics in the early subcortical vascular cognitive impairment

| PRJNA831854 | ENA

An atlas of healthy and injured cell states and niches in the human kidney [snCv3]

Project description:Understanding kidney disease relies upon defining the complexity of cell types and states, their associated molecular profiles, and interactions within tissue neighborhoods. We applied multiple single-cell or -nucleus assays (>400,000 nuclei/cells) and spatial imaging technologies to a broad spectrum of healthy reference (45 donors) and diseased (48 patients) kidneys. This has provided a high resolution cellular atlas of 51 main cell types that include rare and novel cell populations. The multi-omic approach provides detailed transcriptomic profiles, epigenomic regulatory factors, and spatial localizations spanning the entire kidney. We further define 28 cellular states across nephron segments and interstitium that were altered in kidney injury, encompassing cycling, adaptive or maladaptive repair, transitioning and degenerative states. Molecular signatures permitted localization of these states within injury neighborhoods using spatial transcriptomics, while large-scale 3D imaging analysis (~1.2 million neighborhoods) provided corresponding linkages to active immune responses. These analyses defined biological pathways relevant to injury time-course and niches, including signatures underlying epithelial repair that predicted maladaptive states associated with a decline in kidney function. This integrated multimodal spatial cell atlas of healthy and diseased human kidneys represents the most comprehensive benchmark of cellular states, neighborhoods, outcome-associated signatures, and publicly available interactive visualizations.

2022-10-10 | GSE183277 | GEO

An atlas of healthy and injured cell states and niches in the human kidney [scCv3]

2022-10-10 | GSE183276 | GEO

subcortical tissue of decaying Pinus arizonica

Project description:subcortical tissue of decaying Pinus arizonica Metagenome

| PRJNA472996 | ENA

An atlas of healthy and injured cell states and niches in the human kidney [Slide-seq2]

2022-10-10 | GSE183274 | GEO

An atlas of healthy and injured cell states and niches in the human kidney [SNARE-Seq2]

2022-10-10 | GSE183273 | GEO

An atlas of healthy and injured cell states and niches in the human kidney [scRNA-Seq]

2022-10-10 | GSE199711 | GEO