Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

49 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Spatial transcriptomics of skin biopsies from patients with cutaneous T cell lymphoma (CTCL)

ABSTRACT: CTCLs are a group of non-Hodgkin lymphomas, with non-aggressive forms (Mycosis fungoides (MF)) initially presenting with features of cutaneous eczema or psoriasis, posing a challenge for clinical and histological diagnosis. Using spatial transcriptomics, we hope to delineate the molecular signatures of CTCL to provide novel avenues for diagnostics and therapies.

INSTRUMENT(S): Illumina NovaSeq 6000, 10x Genomics CytAssist

ORGANISM(S): Homo sapiens

SUBMITTER: Emily Stephenson

PROVIDER: E-MTAB-13614 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Single cell RNA-seq of skin biopsies from patients with cutaneous T cell lymphoma (CTCL)

Project description:CTCLs are a group of non-Hodgkin lymphomas, with non-aggressive forms (Mycosis fungoides (MF)) initially presenting with features of cutaneous eczema or psoriasis, posing a challenge for clinical and histological diagnosis. Using scRNA-seq, we hope to delineate the molecular signatures of CTCL to provide novel avenues for diagnostics and therapies.

2024-11-11 | E-MTAB-12303 | 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

Oncogenic role of TOX in CTCL

Project description:TOX is a nuclear factor essential for the development of CD4+ T cells in the thymus. TOX is found to be aberrantly up-regulated in the skin biopsies and in the blood CD4+ T cells of cutaneous T cell lymphoma. The goal of this study is to identify potential transcriptional targets of TOX in CTCL by comparison between TOX shRNA transfected CTCL cells (Hut78 and HH) and control CTCL cells. Two color experiment. Lentivirus transduced control vector vs. TOX shRNA vectors on Hut78 and HH cell lines. Biological replicates: 3 control replicates, 3 shRNA tansduced replicates for each cell line.

2014-04-29 | E-GEOD-57122 | 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

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

Project description: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.

2023-01-05 | E-MTAB-12043 | biostudies-arrayexpress

Trem2-expressing multinucleated giant macrophages are a biomarker of good prognosis in head and neck squamous cell carcinoma

Project description:These are the Visium spatial transcriptomic data (10x Genomics) from 9 patients with Head and Neck Squamous Cell Carcinoma (oral cavity) treated in Gustave Roussy. Patients are stratified by their tumoral density of multinucleated giant cells (MGC) : 6 patients have high MGC density (patients 1, 2, 3, 4, 5, 8) and 3 have low MGC density (patients 6, 7, 9). There is one data file for each patient, except for one patient that has 3 data files (patient 1). Accordingly, there are 9 patients but 11 samples. The source code of the is available on GitHub (https://github.com/AhmedAmineAnzali/MGC_Paper_Analysis). The results are published in the paper untitled : Trem2-expressing multinucleated giant macrophages are a biomarker of good prognosis in head and neck squamous cell carcinoma (Gessain et al., 2024, Cancer Discovery). Please contact the corresponding author for more information.

2024-09-20 | E-MTAB-14409 | 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

Gene expression in cutaneous T cell lymphoma (CTCL), dermatitis (D), and healthy subjects (HS)

Project description:FFPE skin biopsy samples from patients with CTCL, dermatitis, or healthy controls were profiled by NanoString gene expression analysis A classifier was constructed that was able to identify mycosis fungoides (MF) samples from dermatitis and healthy controls.

2020-06-16 | GSE143382 | GEO

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

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