Review




Structured Review

Mendeley Ltd spatial transcriptome datasets
Overview of data content and functions of SPathDB. The left panel contains the database content, which includes the spatial <t>transcriptome</t> dataset and pathway data content, and construction of spatial pathway activity profiles. The right panel contains the tools of SPathDB to retrieve, analyze and visualize spatial pathway activity.
Spatial Transcriptome Datasets, supplied by Mendeley Ltd, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/spatial+transcriptomic+(st)+dataset/datasets+spatial+transcriptome/pmc11701687-28-0-22
Average 86 stars, based on 1 article reviews
spatial transcriptome datasets - by Bioz Stars, 2026-09
86/100 stars

Images

1) Product Images from "SPathDB: a comprehensive database of spatial pathway activity atlas"

Article Title: SPathDB: a comprehensive database of spatial pathway activity atlas

Journal: Nucleic Acids Research

doi: 10.1093/nar/gkae1041

Overview of data content and functions of SPathDB. The left panel contains the database content, which includes the spatial transcriptome dataset and pathway data content, and construction of spatial pathway activity profiles. The right panel contains the tools of SPathDB to retrieve, analyze and visualize spatial pathway activity.
Figure Legend Snippet: Overview of data content and functions of SPathDB. The left panel contains the database content, which includes the spatial transcriptome dataset and pathway data content, and construction of spatial pathway activity profiles. The right panel contains the tools of SPathDB to retrieve, analyze and visualize spatial pathway activity.

Techniques Used: Activity Assay

Related Articles

Expressing:

Article Title: Targeting SPAK suppresses progression and averts an immune exhaustive microenvironment in hepatocellular carcinoma.
Article Snippet: .. Combined targeting SPAK and PD-1 showed enhanced efficacy in HCC. (a) Representative tissue region maps and expression analysis of SPAK levels from a spatial transcriptome dataset of ICI responders and non-responders (Mendeley Data: skrx2fz79n). (b) Representative abdominal MRI images, representative IHC staining and quantitative IHC analysis of SPAK levels performed on human HCC tissue obtained before and after treatment of ICI responders (n = 7 patients) and non-responders (n = 12 patients) (scale bars, 100 μm). (c) A schematic representation of the treatment strategy in the DEN/CCl4-induced HCC model. (d-e) Gross images of livers (scale bars, 5 mm), representative H&E staining (scale bars, 1000 μm), and tumor burden (n = 5 mice) from the indicated DEN/CCl4-induced HCC model. (f) A schematic representation of the treatment strategy in the AKT/NRasV12-induced HCC model. (g-h) Gross images of livers (scale bars, 5 mm), representative H&E staining (scale bars, 1000 μm), and tumor burden (n = 5 mice) from the indicated AKT/NRasV12-induced HCC model. (i) A schematic representation of the treatment strategy in the Hepa1-6-induced HCC model. (j-k) Gross images of livers (scale bars, 5 mm), representative H&E staining (scale bars, 200 μm), and tumor burden (n = 6 mice) from the indicated Hepa1-6-induced HCC model. (l-m) Total flux curve and bioluminescence images of mice from the indicated Hepa1-6-induced HCC model for the indicated days (n = 6 mice); a, b, e, h, k, m P values were calculated using an unpaired t test (two-tailed). ..

Article Title: Targeting SPAK suppresses progression and averts an immune exhaustive microenvironment in hepatocellular carcinoma
Article Snippet: .. Fig. 8 Combined targeting SPAK and PD-1 showed enhanced efficacy in HCC. a Representative tissue region maps and expression analysis of SPAK levels from a spatial transcriptome dataset of ICI responders and non-responders (Mendeley Data: skrx2fz79n). b Representative abdominal MRI images, representative IHC staining and quantitative IHC analysis of SPAK levels performed on human HCC tissue obtained before and after treatment of ICI responders ( n = 7 patients) and non-responders ( n = 12 patients) (scale bars, 100 μm). c A schematic representation of the treatment strategy in the DEN/CCl4-induced HCC model. d , e Gross images of livers (scale bars, 5 mm), representative H&E staining (scale bars, 1000 μm), and tumor burden ( n = 5 mice) from the indicated DEN/CCl4-induced HCC model. f A schematic representation of the treatment strategy in the AKT/NRasV12 -induced HCC model. g , h Gross images of livers (scale bars, 5 mm), representative H&E staining (scale bars, 1000 μm), and tumor burden ( n = 5 mice) from the indicated AKT/NRasV12-induced HCC model. i A schematic representation of the treatment strategy in the Hepa1-6-induced HCC model. j , k Gross images of livers (scale bars, 5 mm), representative H&E staining (scale bars, 200 μm), and tumor burden ( n = 6 mice) from the indicated Hepa1-6-induced HCC model. l , m Total flux curve and bioluminescence images of mice from the indicated Hepa1-6-induced HCC model for the indicated days ( n = 6 mice); a , b , e , h , k , m P values were calculated using an unpaired t test (two-tailed). ..

Magnetic Resonance Imaging:

Article Title: Targeting SPAK suppresses progression and averts an immune exhaustive microenvironment in hepatocellular carcinoma.
Article Snippet: .. Combined targeting SPAK and PD-1 showed enhanced efficacy in HCC. (a) Representative tissue region maps and expression analysis of SPAK levels from a spatial transcriptome dataset of ICI responders and non-responders (Mendeley Data: skrx2fz79n). (b) Representative abdominal MRI images, representative IHC staining and quantitative IHC analysis of SPAK levels performed on human HCC tissue obtained before and after treatment of ICI responders (n = 7 patients) and non-responders (n = 12 patients) (scale bars, 100 μm). (c) A schematic representation of the treatment strategy in the DEN/CCl4-induced HCC model. (d-e) Gross images of livers (scale bars, 5 mm), representative H&E staining (scale bars, 1000 μm), and tumor burden (n = 5 mice) from the indicated DEN/CCl4-induced HCC model. (f) A schematic representation of the treatment strategy in the AKT/NRasV12-induced HCC model. (g-h) Gross images of livers (scale bars, 5 mm), representative H&E staining (scale bars, 1000 μm), and tumor burden (n = 5 mice) from the indicated AKT/NRasV12-induced HCC model. (i) A schematic representation of the treatment strategy in the Hepa1-6-induced HCC model. (j-k) Gross images of livers (scale bars, 5 mm), representative H&E staining (scale bars, 200 μm), and tumor burden (n = 6 mice) from the indicated Hepa1-6-induced HCC model. (l-m) Total flux curve and bioluminescence images of mice from the indicated Hepa1-6-induced HCC model for the indicated days (n = 6 mice); a, b, e, h, k, m P values were calculated using an unpaired t test (two-tailed). ..

Article Title: Targeting SPAK suppresses progression and averts an immune exhaustive microenvironment in hepatocellular carcinoma
Article Snippet: .. Fig. 8 Combined targeting SPAK and PD-1 showed enhanced efficacy in HCC. a Representative tissue region maps and expression analysis of SPAK levels from a spatial transcriptome dataset of ICI responders and non-responders (Mendeley Data: skrx2fz79n). b Representative abdominal MRI images, representative IHC staining and quantitative IHC analysis of SPAK levels performed on human HCC tissue obtained before and after treatment of ICI responders ( n = 7 patients) and non-responders ( n = 12 patients) (scale bars, 100 μm). c A schematic representation of the treatment strategy in the DEN/CCl4-induced HCC model. d , e Gross images of livers (scale bars, 5 mm), representative H&E staining (scale bars, 1000 μm), and tumor burden ( n = 5 mice) from the indicated DEN/CCl4-induced HCC model. f A schematic representation of the treatment strategy in the AKT/NRasV12 -induced HCC model. g , h Gross images of livers (scale bars, 5 mm), representative H&E staining (scale bars, 1000 μm), and tumor burden ( n = 5 mice) from the indicated AKT/NRasV12-induced HCC model. i A schematic representation of the treatment strategy in the Hepa1-6-induced HCC model. j , k Gross images of livers (scale bars, 5 mm), representative H&E staining (scale bars, 200 μm), and tumor burden ( n = 6 mice) from the indicated Hepa1-6-induced HCC model. l , m Total flux curve and bioluminescence images of mice from the indicated Hepa1-6-induced HCC model for the indicated days ( n = 6 mice); a , b , e , h , k , m P values were calculated using an unpaired t test (two-tailed). ..

Immunohistochemistry:

Article Title: Targeting SPAK suppresses progression and averts an immune exhaustive microenvironment in hepatocellular carcinoma.
Article Snippet: .. Combined targeting SPAK and PD-1 showed enhanced efficacy in HCC. (a) Representative tissue region maps and expression analysis of SPAK levels from a spatial transcriptome dataset of ICI responders and non-responders (Mendeley Data: skrx2fz79n). (b) Representative abdominal MRI images, representative IHC staining and quantitative IHC analysis of SPAK levels performed on human HCC tissue obtained before and after treatment of ICI responders (n = 7 patients) and non-responders (n = 12 patients) (scale bars, 100 μm). (c) A schematic representation of the treatment strategy in the DEN/CCl4-induced HCC model. (d-e) Gross images of livers (scale bars, 5 mm), representative H&E staining (scale bars, 1000 μm), and tumor burden (n = 5 mice) from the indicated DEN/CCl4-induced HCC model. (f) A schematic representation of the treatment strategy in the AKT/NRasV12-induced HCC model. (g-h) Gross images of livers (scale bars, 5 mm), representative H&E staining (scale bars, 1000 μm), and tumor burden (n = 5 mice) from the indicated AKT/NRasV12-induced HCC model. (i) A schematic representation of the treatment strategy in the Hepa1-6-induced HCC model. (j-k) Gross images of livers (scale bars, 5 mm), representative H&E staining (scale bars, 200 μm), and tumor burden (n = 6 mice) from the indicated Hepa1-6-induced HCC model. (l-m) Total flux curve and bioluminescence images of mice from the indicated Hepa1-6-induced HCC model for the indicated days (n = 6 mice); a, b, e, h, k, m P values were calculated using an unpaired t test (two-tailed). ..

Article Title: Targeting SPAK suppresses progression and averts an immune exhaustive microenvironment in hepatocellular carcinoma
Article Snippet: .. Fig. 8 Combined targeting SPAK and PD-1 showed enhanced efficacy in HCC. a Representative tissue region maps and expression analysis of SPAK levels from a spatial transcriptome dataset of ICI responders and non-responders (Mendeley Data: skrx2fz79n). b Representative abdominal MRI images, representative IHC staining and quantitative IHC analysis of SPAK levels performed on human HCC tissue obtained before and after treatment of ICI responders ( n = 7 patients) and non-responders ( n = 12 patients) (scale bars, 100 μm). c A schematic representation of the treatment strategy in the DEN/CCl4-induced HCC model. d , e Gross images of livers (scale bars, 5 mm), representative H&E staining (scale bars, 1000 μm), and tumor burden ( n = 5 mice) from the indicated DEN/CCl4-induced HCC model. f A schematic representation of the treatment strategy in the AKT/NRasV12 -induced HCC model. g , h Gross images of livers (scale bars, 5 mm), representative H&E staining (scale bars, 1000 μm), and tumor burden ( n = 5 mice) from the indicated AKT/NRasV12-induced HCC model. i A schematic representation of the treatment strategy in the Hepa1-6-induced HCC model. j , k Gross images of livers (scale bars, 5 mm), representative H&E staining (scale bars, 200 μm), and tumor burden ( n = 6 mice) from the indicated Hepa1-6-induced HCC model. l , m Total flux curve and bioluminescence images of mice from the indicated Hepa1-6-induced HCC model for the indicated days ( n = 6 mice); a , b , e , h , k , m P values were calculated using an unpaired t test (two-tailed). ..

Staining:

Article Title: Targeting SPAK suppresses progression and averts an immune exhaustive microenvironment in hepatocellular carcinoma.
Article Snippet: .. Combined targeting SPAK and PD-1 showed enhanced efficacy in HCC. (a) Representative tissue region maps and expression analysis of SPAK levels from a spatial transcriptome dataset of ICI responders and non-responders (Mendeley Data: skrx2fz79n). (b) Representative abdominal MRI images, representative IHC staining and quantitative IHC analysis of SPAK levels performed on human HCC tissue obtained before and after treatment of ICI responders (n = 7 patients) and non-responders (n = 12 patients) (scale bars, 100 μm). (c) A schematic representation of the treatment strategy in the DEN/CCl4-induced HCC model. (d-e) Gross images of livers (scale bars, 5 mm), representative H&E staining (scale bars, 1000 μm), and tumor burden (n = 5 mice) from the indicated DEN/CCl4-induced HCC model. (f) A schematic representation of the treatment strategy in the AKT/NRasV12-induced HCC model. (g-h) Gross images of livers (scale bars, 5 mm), representative H&E staining (scale bars, 1000 μm), and tumor burden (n = 5 mice) from the indicated AKT/NRasV12-induced HCC model. (i) A schematic representation of the treatment strategy in the Hepa1-6-induced HCC model. (j-k) Gross images of livers (scale bars, 5 mm), representative H&E staining (scale bars, 200 μm), and tumor burden (n = 6 mice) from the indicated Hepa1-6-induced HCC model. (l-m) Total flux curve and bioluminescence images of mice from the indicated Hepa1-6-induced HCC model for the indicated days (n = 6 mice); a, b, e, h, k, m P values were calculated using an unpaired t test (two-tailed). ..

Article Title: Targeting SPAK suppresses progression and averts an immune exhaustive microenvironment in hepatocellular carcinoma
Article Snippet: .. Fig. 8 Combined targeting SPAK and PD-1 showed enhanced efficacy in HCC. a Representative tissue region maps and expression analysis of SPAK levels from a spatial transcriptome dataset of ICI responders and non-responders (Mendeley Data: skrx2fz79n). b Representative abdominal MRI images, representative IHC staining and quantitative IHC analysis of SPAK levels performed on human HCC tissue obtained before and after treatment of ICI responders ( n = 7 patients) and non-responders ( n = 12 patients) (scale bars, 100 μm). c A schematic representation of the treatment strategy in the DEN/CCl4-induced HCC model. d , e Gross images of livers (scale bars, 5 mm), representative H&E staining (scale bars, 1000 μm), and tumor burden ( n = 5 mice) from the indicated DEN/CCl4-induced HCC model. f A schematic representation of the treatment strategy in the AKT/NRasV12 -induced HCC model. g , h Gross images of livers (scale bars, 5 mm), representative H&E staining (scale bars, 1000 μm), and tumor burden ( n = 5 mice) from the indicated AKT/NRasV12-induced HCC model. i A schematic representation of the treatment strategy in the Hepa1-6-induced HCC model. j , k Gross images of livers (scale bars, 5 mm), representative H&E staining (scale bars, 200 μm), and tumor burden ( n = 6 mice) from the indicated Hepa1-6-induced HCC model. l , m Total flux curve and bioluminescence images of mice from the indicated Hepa1-6-induced HCC model for the indicated days ( n = 6 mice); a , b , e , h , k , m P values were calculated using an unpaired t test (two-tailed). ..

Gene Expression:

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



Similar Products

90
Biotechnology Information spatial transcriptomic (st) dataset
Spatial Transcriptomic (St) Dataset, supplied by Biotechnology Information, 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+transcriptomic+(st)+dataset/spatial+transcriptomic++st++dataset/pmc11847939-580-3-15
Average 90 stars, based on 1 article reviews
spatial transcriptomic (st) dataset - by Bioz Stars, 2026-09
90/100 stars
  Buy from Supplier

90
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+transcriptomic+(st)+dataset/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
  Buy from Supplier

90
Spatial Transcriptomics Inc spatial transcriptomics (st) 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 Transcriptomics (St) Dataset, supplied by Spatial Transcriptomics Inc, 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+transcriptomic+(st)+dataset/spatial+transcriptomics++st+/pmc11169532-351-66-72
Average 90 stars, based on 1 article reviews
spatial transcriptomics (st) dataset - by Bioz Stars, 2026-09
90/100 stars
  Buy from Supplier

Image Search Results


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.

Journal: Discover Oncology

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

doi: 10.1007/s12672-024-01162-2

Figure Lengend 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.

Article Snippet: The spatial transcriptome sequencing (ST-seq) dataset was obtained from Mendeley Data platform ( https://data.mendeley.com/datasets/g67bkbnhhg/1 ) and input to python environment.

Techniques: 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.

Journal: Discover Oncology

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

doi: 10.1007/s12672-024-01162-2

Figure Lengend 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.

Article Snippet: The spatial transcriptome sequencing (ST-seq) dataset was obtained from Mendeley Data platform ( https://data.mendeley.com/datasets/g67bkbnhhg/1 ) and input to python environment.

Techniques: Dissection, Expressing, Gene Expression