Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Basal-like breast cancer stimulates MUC1 to support an epithelial/mesenchymal hybrid state and survive radiotherapy

ABSTRACT: We employed high-throughput sequencing with spatial resolution in the WAP-T mouse model of basal-like breast cancer (BLBC) to investigate the transcriptomic response to radiation therapy (RT). Our analysis revealed a distinct spatial pattern of gene expression (10X visium platform), with irradiated BLBC tumors exhibiting a strong enrichment of epithelial genes and a hybrid epithelial/mesenchymal (E/M) state. Notably, MUC1 expression was upregulated in response to RT, suggesting its role as a key driver of cell survival. These findings provide new insights into the spatial transcriptomic landscape of BLBC under RT and highlight the potential of MUC1 as a therapeutic target or prognostic marker for optimizing patient response to RT.

INSTRUMENT(S): DNBSEQ-G400

ORGANISM(S): Mus musculus

SUBMITTER: Florian Wegwitz

PROVIDER: E-MTAB-15010 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Spatial transcriptomic profiling of primary and recurrent RCAS-derived glioblastoma in a mouse model using 10x Genomics Visium v1

Project description:Two primary and two post-radiotherapy recurrent glioblastoma tumors derived in the RCAS/Nestin-Tv-a mouse model were processed using the 10x Genomics Visium Spatial Gene Expression v1 chemistry.

2026-03-29 | E-MTAB-16421 | 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 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

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 and proteomics of post-transplant HCC recurrence using 10x Visium CytAssist

Project description:Post-transplant hepatocellular carcinoma (HCC) recurrence is a devastating disease with an abysmal prognosis and no established treatment or prevention options. We performed spatial analysis to profile the tumor immune microenvironment in primary HCC at liver transplantation and in recurrent HCC at re-hepatectomy and elucidate the molecular mechanisms that drive recurrence under immunosuppression. This analysis offers potential for developing new therapeutic strategies against post-transplant HCC recurrence. Paired FFPE samples from primary and recurrent sites were collected from patients who underwent re-hepatectomy for HCC recurrence after liver transplantation due to HCC. The Visium CytAssist Spatial Gene and Protein Expression for FFPE, 11 mm (10x Genomics) was utilized to perform Visium experiments on FFPE tissue from the primary tumor and the recurrent tumor (comprising tumor and non-tumor regions).

2026-04-01 | E-MTAB-15756 | biostudies-arrayexpress

spatial transcriptomics (10x Visium) of first and second trimester human reproductive tract

Project description:spatial transcriptomics by means of 10x Visium of first and second trimester human reproductive tract (including female and male internal and external genitalia)

2025-08-06 | E-MTAB-15471 | biostudies-arrayexpress

Spatial transcriptomic profiling of healthy brain and RCAS-derived glioblastoma in a mouse model using 10x Genomics Visium HD

Project description:One healthy mouse brain and one glioblastoma tumor derived in the RCAS/Nestin-Tv-a mouse model were processed using the 10x Genomics Visium HD Spatial Gene Expression chemistry.

2026-03-29 | E-MTAB-16420 | biostudies-arrayexpress

Spatial transcriptomics of the axolotl forebrain

Project description:To investigate spatial heterogeneities in the axolotl forebrain, a coronal section of it was obtained for spatial transcriptomics using Visium V1.

2022-07-20 | E-MTAB-11665 | 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

RNA-seq data of barley embryos of wild-type ‘Sebastian’ and double mutant hvcbp20.ab/hvcbp80.b under control conditions and in the presence of 75 µM ABA

Project description:The spatial transcriptomic analysis of barley embryos in response to 75 µM ABA was investigated using Visium Spatial Transcriptomics (10×Genomics) technology. Embryo sections were collected from wild-type 'Sebastian' and a double mutant hvcbp20.ab/hvcbp80.b impaired in both subunits of the Cap-Binding Complex (CBC): CBP20 and CBP80 at 1 day after imbibition (DAI) under control and 75 µM ABA conditions. Cryosectioned tissues were stained, mounted on Visium slides, and processed for spatial gene expression profiling. Sequencing was performed on an Illumina NovaSeq 6000 platform (paired-end, 151 bp). The data were aligned to the barley reference genome (cv. MorexV3) and used to identify differentially expressed genes (DEGs) across six distinguished embryonic regions: coleoptile, cotyledon, mesocotyl, plumule, scutellum, and radicle. The dataset provides insights into the spatial regulation of ABA-responsive genes in embryos during barley seed germination.

2025-07-31 | E-MTAB-14835 | biostudies-arrayexpress

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