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spatial transcriptome sequencing (st-seq) dataset (Mendeley Ltd)

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Mendeley Ltd spatial transcriptome sequencing (st-seq) dataset

Transcription programs of ccRCC cells in response to cuproptosis. A UMAP showing the 10 subtypes of 26,981 Epithelial cells; B heatmap showing inferred CNV of scRNA-seq dataset; C dot plot of the relative cellular proportions of Epithelial subtypes in each group; D GSEA analysis revealed the activated CRGs enriched in Normal Epithelial cells; E violin plot showing the relative CRGs score in each cancer subtype; F survival plot of HILPDA + ccRCC1 signature high and low group in the KIRC samples; G violin plots of HILPDA expression levels and hypoxia scores in each cancer subtypes; H spatial <t>transcriptome</t> displayed the distribution of CRGs, HILPDA + ccRCC1 signatures, hypoxia scores and HILPDA expression; I the regulon specificity scores of TFs in HILPDA + ccRCC1 subtype. The top 5 TFs ordered by scores were listed; J violin plot showing the expression levels of the top 5 TFs in HILPDA + ccRCC1 subtype across stage I–IV.

Spatial Transcriptome Sequencing (St Seq) Dataset, supplied by Mendeley Ltd, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/spatial+transcriptomics+st+seq/spatial+transcriptomic+data/pmc11266328-46-1-9
Average 90 stars, based on 1 article reviews

spatial transcriptome sequencing (st-seq) dataset - by Bioz Stars, 2026-09

90/100 stars

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1) Product Images from "Characterization of cuproptosis signature in clear cell renal cell carcinoma by single cell and spatial transcriptome analysis"

Article Title: Characterization of cuproptosis signature in clear cell renal cell carcinoma by single cell and spatial transcriptome analysis

Journal: Discover Oncology

doi: 10.1007/s12672-024-01162-2

Figure Legend Snippet: Transcription programs of ccRCC cells in response to cuproptosis. A UMAP showing the 10 subtypes of 26,981 Epithelial cells; B heatmap showing inferred CNV of scRNA-seq dataset; C dot plot of the relative cellular proportions of Epithelial subtypes in each group; D GSEA analysis revealed the activated CRGs enriched in Normal Epithelial cells; E violin plot showing the relative CRGs score in each cancer subtype; F survival plot of HILPDA + ccRCC1 signature high and low group in the KIRC samples; G violin plots of HILPDA expression levels and hypoxia scores in each cancer subtypes; H spatial transcriptome displayed the distribution of CRGs, HILPDA + ccRCC1 signatures, hypoxia scores and HILPDA expression; I the regulon specificity scores of TFs in HILPDA + ccRCC1 subtype. The top 5 TFs ordered by scores were listed; J violin plot showing the expression levels of the top 5 TFs in HILPDA + ccRCC1 subtype across stage I–IV.

Techniques Used: Expressing

Dissection of immunosuppressive cells of cuproptosis-related tumor microenvironment. A UMAP showing the 16 subtypes of 99,210 Immune cells; B violin plot of the relative expression levels of the canocial markers in each subtype; C heatmap showing the enrichment of immune checkpoint and suppressive genes; D spatial transcriptome displayed the distribution of Treg, CD8_Exhausted and TAM signature scores; E heatmap showing the four gene expression patterns deduced by TDEseq analysis; F violin plots showing the relative expression levels of CRG scores in the immunosuppressive cells across different stages; G Chord diagram showing the number of interactions among the four subtypes; H Bubble plot showing the ligand-receptor pairs in the main subtype; I Heatmap showing the relative expression levels of key genes of the four subtypes among the different stages. The paired ligand-receptor shown in H were connected by lines.

Figure Legend Snippet: Dissection of immunosuppressive cells of cuproptosis-related tumor microenvironment. A UMAP showing the 16 subtypes of 99,210 Immune cells; B violin plot of the relative expression levels of the canocial markers in each subtype; C heatmap showing the enrichment of immune checkpoint and suppressive genes; D spatial transcriptome displayed the distribution of Treg, CD8_Exhausted and TAM signature scores; E heatmap showing the four gene expression patterns deduced by TDEseq analysis; F violin plots showing the relative expression levels of CRG scores in the immunosuppressive cells across different stages; G Chord diagram showing the number of interactions among the four subtypes; H Bubble plot showing the ligand-receptor pairs in the main subtype; I Heatmap showing the relative expression levels of key genes of the four subtypes among the different stages. The paired ligand-receptor shown in H were connected by lines.

Techniques Used: Dissection, Expressing, Gene Expression

Over Expression:

Article Title: Effect of Sortilin1 on promoting angiogenesis and systemic metastasis in hepatocellular carcinoma via the Notch signaling pathway and CD133
Article Snippet: .. Additionally, 10X Visium-derived spatial transcriptomic data obtained from Mendeley demonstrated significant SORT1 overexpression in malignant hepatocytes compared to that in non-malignant hepatocytes (Fig. ) [ ]. ..

other:

Article Title: LIANA+ provides an all-in-one framework for cell-cell communication inference.
Article Snippet: Spatially resolved metabolome–transcriptome data26 were obtained from https://data.mendeley.com/datasets/w7nw4km7xd/1, also available under GEO repository accession number GSE232910.

Article Title: LIANA+ provides an all-in-one framework for cell–cell communication inference
Article Snippet: Spatially resolved metabolome–transcriptome data were obtained from https://data.mendeley.com/datasets/w7nw4km7xd/1 , also available under GEO repository accession number GSE232910 .

Biomarker Discovery:

Article Title: Integration of Clinical Trial Spatial Multi-omics Analysis and Virtual Clinical Trials Enables Immunotherapy Response Prediction and Biomarker Discovery
Article Snippet: Spatial transcriptomics preprocessed data from CABO/NIVO trial is available at NCBI GEO GSE238264 ( https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE238264 ). .. Spatial transcriptomic data from Liu et al. ( 26 ) for our model validation is available at ( https://data.mendeley.com/datasets/skrx2fz79n/1 ). ..

Gene Expression:

Article Title: SPathDB: a comprehensive database of spatial pathway activity atlas.
Article Snippet: .. Collection of spatial transcriptome data Spatial transcriptome datasets of human and mouse were collected from the Gene Expression Omnibus (GEO) database ( 15 ), 10 × Genomics ( https://www.10xgenomics. com/), Mendeley Data ( https://data.mendeley.com/) and CROST ( https:// ngdc.cncb.ac.cn/ crost/ ). ..