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rna-seq data from spatial transcriptomics analyses  (Spatial Transcriptomics Inc)

 
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    Spatial Transcriptomics Inc rna-seq data from spatial transcriptomics analyses
    Rna Seq Data From Spatial Transcriptomics Analyses, 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/rna+seq+data+analyses/spatial+transcriptomics+sequencing/pm39187136-159-14-13
    Average 90 stars, based on 1 article reviews
    rna-seq data from spatial transcriptomics analyses - by Bioz Stars, 2026-09
    90/100 stars

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    Related Articles

    Spatial Transcriptomics:

    Article Title: Spatialsmooth: a spatially-aware convolutional autoencoder framework for enhanced deconvolution of spatial transcriptomics data.
    Article Snippet: .. Spatial transcriptomics was constructed using single-cell RNA sequencing (scRNA-seq) data from human pancreatic ductal adenocarcinoma, comprising 1,926 single cells and 20 cell types, to obtain the composition of cell types as ground truth. ..

    Article Title: NONO links circadian rhythm disruption and enhanced tumor-fibroblast crosstalk in right-sided colorectal cancer.
    Article Snippet: .. Spatial transcriptomics RNA sequencing (stRNA-seq) data for primary colorectal cancer were sourced from the single-cell colorectal cancer liver metastasis (CRLM) atlas portal ( h t t p : / / w w w . c a n c e r d i v e r s i t y . a s i a / s c C R L M). ..

    Article Title: NONO links circadian rhythm disruption and enhanced tumor-fibroblast crosstalk in right-sided colorectal cancer
    Article Snippet: .. Spatial transcriptomics RNA sequencing (stRNA-seq) data for primary colorectal cancer were sourced from the single-cell colorectal cancer liver metastasis (CRLM) atlas portal ( http://www.cancerdiversity.asia/scCRLM ). ..

    Construct:

    Article Title: Spatialsmooth: a spatially-aware convolutional autoencoder framework for enhanced deconvolution of spatial transcriptomics data.
    Article Snippet: .. Spatial transcriptomics was constructed using single-cell RNA sequencing (scRNA-seq) data from human pancreatic ductal adenocarcinoma, comprising 1,926 single cells and 20 cell types, to obtain the composition of cell types as ground truth. ..

    Article Title: Spatialsmooth: a spatially-aware convolutional autoencoder framework for enhanced deconvolution of spatial transcriptomics data
    Article Snippet: Spatial transcriptomics was constructed using single-cell RNA sequencing (scRNA-seq) data from human pancreatic ductal adenocarcinoma, comprising 1,926 single cells and 20 cell types, to obtain the composition of cell types as ground truth. .. Spatial transcriptomics was constructed using single-cell RNA sequencing (scRNA-seq) data from human pancreatic ductal adenocarcinoma, comprising 1,926 single cells and 20 cell types, to obtain the composition of cell types as ground truth. ..

    Single Cell:

    Article Title: Spatialsmooth: a spatially-aware convolutional autoencoder framework for enhanced deconvolution of spatial transcriptomics data.
    Article Snippet: .. Spatial transcriptomics was constructed using single-cell RNA sequencing (scRNA-seq) data from human pancreatic ductal adenocarcinoma, comprising 1,926 single cells and 20 cell types, to obtain the composition of cell types as ground truth. ..

    Article Title: NONO links circadian rhythm disruption and enhanced tumor-fibroblast crosstalk in right-sided colorectal cancer.
    Article Snippet: .. Spatial transcriptomics RNA sequencing (stRNA-seq) data for primary colorectal cancer were sourced from the single-cell colorectal cancer liver metastasis (CRLM) atlas portal ( h t t p : / / w w w . c a n c e r d i v e r s i t y . a s i a / s c C R L M). ..

    Article Title: NONO links circadian rhythm disruption and enhanced tumor-fibroblast crosstalk in right-sided colorectal cancer
    Article Snippet: .. Spatial transcriptomics RNA sequencing (stRNA-seq) data for primary colorectal cancer were sourced from the single-cell colorectal cancer liver metastasis (CRLM) atlas portal ( http://www.cancerdiversity.asia/scCRLM ). ..

    RNA Sequencing:

    Article Title: Spatialsmooth: a spatially-aware convolutional autoencoder framework for enhanced deconvolution of spatial transcriptomics data.
    Article Snippet: .. Spatial transcriptomics was constructed using single-cell RNA sequencing (scRNA-seq) data from human pancreatic ductal adenocarcinoma, comprising 1,926 single cells and 20 cell types, to obtain the composition of cell types as ground truth. ..

    Article Title: Spatialsmooth: a spatially-aware convolutional autoencoder framework for enhanced deconvolution of spatial transcriptomics data
    Article Snippet: Spatial transcriptomics was constructed using single-cell RNA sequencing (scRNA-seq) data from human pancreatic ductal adenocarcinoma, comprising 1,926 single cells and 20 cell types, to obtain the composition of cell types as ground truth. .. Spatial transcriptomics was constructed using single-cell RNA sequencing (scRNA-seq) data from human pancreatic ductal adenocarcinoma, comprising 1,926 single cells and 20 cell types, to obtain the composition of cell types as ground truth. ..

    Article Title: NONO links circadian rhythm disruption and enhanced tumor-fibroblast crosstalk in right-sided colorectal cancer.
    Article Snippet: .. Spatial transcriptomics RNA sequencing (stRNA-seq) data for primary colorectal cancer were sourced from the single-cell colorectal cancer liver metastasis (CRLM) atlas portal ( h t t p : / / w w w . c a n c e r d i v e r s i t y . a s i a / s c C R L M). ..

    Article Title: NONO links circadian rhythm disruption and enhanced tumor-fibroblast crosstalk in right-sided colorectal cancer
    Article Snippet: .. Spatial transcriptomics RNA sequencing (stRNA-seq) data for primary colorectal cancer were sourced from the single-cell colorectal cancer liver metastasis (CRLM) atlas portal ( http://www.cancerdiversity.asia/scCRLM ). ..

    other:

    Article Title: Sequencing of a Chinese tetralogy of Fallot cohort reveals clustering mutations in myogenic heart progenitors
    Article Snippet: Two of these were data from a spatial transcriptomics study: 1 data set derived from a single-cell RNA-Seq analysis of a 6.5 to 7 weeks postconception (PCW) human heart, and a second data set derived from a spatial transcriptomics single-cell RNA-Seq analysis of a 6.5–7 PCW human heart.

    Article Title: Histone lactylation-related genes correlate with the molecular patterns and functions of cancer-associated fibroblasts and have significant clinical implications in clear cell renal cell carcinoma
    Article Snippet: The single-cell RNA sequencing (scRNA-seq) data, single-cell Assay for Transposase-Accessible Chromatin using sequencing (scATAC-seq) data and Spatial Transcriptomics (ST) data can be accessed in GSE207493 [ ], GSE210042 [ ] and GSE175540 [ ].



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    Generating a humanized stroma PDX (HS-PDX). A Tumor growth curves (i–iii) and (iv) summary of relative final tumor volumes of HS-PDXs with the indicate EC (combination iHUVEC/iHDMEC or EPC sources. TC + CA-MSC in the absence or presence of human EC (TC + CA-MSC; n = 6) (iHDMEC + iHUVEC) and Pt. EC/EPC (TC + CA-MSC + EC/EPC; n = 7). Tumor volumes in A (iv) are normalized TC + CA-MSC alone at 100%. B Representative IF evaluation of human tumor vascular antigen CD31 (red) in PDXs with the indicated EC/EPC sources. 4′,6-diamidino-2-phenylindole (DAPI; blue) was used to label cell nuclei. C IF evaluation of a tumor-specific vascular marker EGFL6 (red). Cell nuclei were counterstained with DAPI (blue). D <t>RNA-Seq-based</t> relative mRNA expression for two patient PDXs without and with the addition of human endothelial cells. E Growth curves for standard PDX and HS-PDX, derived from a patient with platinum refractory ovarian cancer, treated with carboplatin (blue arrows indicate timing of carboplatin administration ( n = 4–7/treatment group). Tumor volumes are internally normalized to the initial measurement for each tumor (~ 100 mm 3 ). Abbreviations : CA-MSC, cancer-associated mesenchymal stem cells; EC, endothelial cells; EPC, endothelial progenitor cells; iHDMEC, immortalized human dermal microvascular endothelial cells; iHUVEC, immortalized human umbilical vein endothelial cells; PDX, patient-derived xenograft; P0 and P1, passage 0 and passage 1. The first generation of PDX is denoted P0, and P0 is subsequently passaged to second generation (P1); Pt., patient; TC, tumor cells. * p < 0.05, ** p < 0.01, *** p < 0.001. Scale bars in B and C are 20 µm
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    Generating a humanized stroma PDX (HS-PDX). A Tumor growth curves (i–iii) and (iv) summary of relative final tumor volumes of HS-PDXs with the indicate EC (combination iHUVEC/iHDMEC or EPC sources. TC + CA-MSC in the absence or presence of human EC (TC + CA-MSC; n = 6) (iHDMEC + iHUVEC) and Pt. EC/EPC (TC + CA-MSC + EC/EPC; n = 7). Tumor volumes in A (iv) are normalized TC + CA-MSC alone at 100%. B Representative IF evaluation of human tumor vascular antigen CD31 (red) in PDXs with the indicated EC/EPC sources. 4′,6-diamidino-2-phenylindole (DAPI; blue) was used to label cell nuclei. C IF evaluation of a tumor-specific vascular marker EGFL6 (red). Cell nuclei were counterstained with DAPI (blue). D <t>RNA-Seq-based</t> relative mRNA expression for two patient PDXs without and with the addition of human endothelial cells. E Growth curves for standard PDX and HS-PDX, derived from a patient with platinum refractory ovarian cancer, treated with carboplatin (blue arrows indicate timing of carboplatin administration ( n = 4–7/treatment group). Tumor volumes are internally normalized to the initial measurement for each tumor (~ 100 mm 3 ). Abbreviations : CA-MSC, cancer-associated mesenchymal stem cells; EC, endothelial cells; EPC, endothelial progenitor cells; iHDMEC, immortalized human dermal microvascular endothelial cells; iHUVEC, immortalized human umbilical vein endothelial cells; PDX, patient-derived xenograft; P0 and P1, passage 0 and passage 1. The first generation of PDX is denoted P0, and P0 is subsequently passaged to second generation (P1); Pt., patient; TC, tumor cells. * p < 0.05, ** p < 0.01, *** p < 0.001. Scale bars in B and C are 20 µm
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    Image Search Results


    Generating a humanized stroma PDX (HS-PDX). A Tumor growth curves (i–iii) and (iv) summary of relative final tumor volumes of HS-PDXs with the indicate EC (combination iHUVEC/iHDMEC or EPC sources. TC + CA-MSC in the absence or presence of human EC (TC + CA-MSC; n = 6) (iHDMEC + iHUVEC) and Pt. EC/EPC (TC + CA-MSC + EC/EPC; n = 7). Tumor volumes in A (iv) are normalized TC + CA-MSC alone at 100%. B Representative IF evaluation of human tumor vascular antigen CD31 (red) in PDXs with the indicated EC/EPC sources. 4′,6-diamidino-2-phenylindole (DAPI; blue) was used to label cell nuclei. C IF evaluation of a tumor-specific vascular marker EGFL6 (red). Cell nuclei were counterstained with DAPI (blue). D RNA-Seq-based relative mRNA expression for two patient PDXs without and with the addition of human endothelial cells. E Growth curves for standard PDX and HS-PDX, derived from a patient with platinum refractory ovarian cancer, treated with carboplatin (blue arrows indicate timing of carboplatin administration ( n = 4–7/treatment group). Tumor volumes are internally normalized to the initial measurement for each tumor (~ 100 mm 3 ). Abbreviations : CA-MSC, cancer-associated mesenchymal stem cells; EC, endothelial cells; EPC, endothelial progenitor cells; iHDMEC, immortalized human dermal microvascular endothelial cells; iHUVEC, immortalized human umbilical vein endothelial cells; PDX, patient-derived xenograft; P0 and P1, passage 0 and passage 1. The first generation of PDX is denoted P0, and P0 is subsequently passaged to second generation (P1); Pt., patient; TC, tumor cells. * p < 0.05, ** p < 0.01, *** p < 0.001. Scale bars in B and C are 20 µm

    Journal: Cancer Immunology, Immunotherapy : CII

    Article Title: A novel humanized immune stroma PDX cancer model for therapeutic studies

    doi: 10.1007/s00262-026-04349-4

    Figure Lengend Snippet: Generating a humanized stroma PDX (HS-PDX). A Tumor growth curves (i–iii) and (iv) summary of relative final tumor volumes of HS-PDXs with the indicate EC (combination iHUVEC/iHDMEC or EPC sources. TC + CA-MSC in the absence or presence of human EC (TC + CA-MSC; n = 6) (iHDMEC + iHUVEC) and Pt. EC/EPC (TC + CA-MSC + EC/EPC; n = 7). Tumor volumes in A (iv) are normalized TC + CA-MSC alone at 100%. B Representative IF evaluation of human tumor vascular antigen CD31 (red) in PDXs with the indicated EC/EPC sources. 4′,6-diamidino-2-phenylindole (DAPI; blue) was used to label cell nuclei. C IF evaluation of a tumor-specific vascular marker EGFL6 (red). Cell nuclei were counterstained with DAPI (blue). D RNA-Seq-based relative mRNA expression for two patient PDXs without and with the addition of human endothelial cells. E Growth curves for standard PDX and HS-PDX, derived from a patient with platinum refractory ovarian cancer, treated with carboplatin (blue arrows indicate timing of carboplatin administration ( n = 4–7/treatment group). Tumor volumes are internally normalized to the initial measurement for each tumor (~ 100 mm 3 ). Abbreviations : CA-MSC, cancer-associated mesenchymal stem cells; EC, endothelial cells; EPC, endothelial progenitor cells; iHDMEC, immortalized human dermal microvascular endothelial cells; iHUVEC, immortalized human umbilical vein endothelial cells; PDX, patient-derived xenograft; P0 and P1, passage 0 and passage 1. The first generation of PDX is denoted P0, and P0 is subsequently passaged to second generation (P1); Pt., patient; TC, tumor cells. * p < 0.05, ** p < 0.01, *** p < 0.001. Scale bars in B and C are 20 µm

    Article Snippet: RNA-seq data analyses were performed by Novogene and Dr. Hui Shen’s research group.

    Techniques: Marker, RNA Sequencing, Expressing, Derivative Assay

    Identifying the optimal humanized bone marrow mouse type for the humanized immune stroma PDX (HIS-PDX). PDX models established in immunodeficient NSG, humanized HuNSG-SGM3 and humanized BLT mice were named as NSG-PDX, HuSGM3-PDX and BLT-PDX models, respectively. A-C RNA-seq-based mRNA analysis of the indicated lymphocyte ( A ), myeloid cell ( B ) and NK cell ( C ) markers genes in NSG-PDX, HuSGM3-PDX and BLT-PDX tumors. Expression is normalized using the expression in matched primary patient-derived tumor. D IF for human CD3, CD8, CD14 and CD163 evaluating tumor immune infiltrates in the indicated PDX tumor models. Cell nuclei were counterstained with DAPI (blue). Scale bars, 20 µm

    Journal: Cancer Immunology, Immunotherapy : CII

    Article Title: A novel humanized immune stroma PDX cancer model for therapeutic studies

    doi: 10.1007/s00262-026-04349-4

    Figure Lengend Snippet: Identifying the optimal humanized bone marrow mouse type for the humanized immune stroma PDX (HIS-PDX). PDX models established in immunodeficient NSG, humanized HuNSG-SGM3 and humanized BLT mice were named as NSG-PDX, HuSGM3-PDX and BLT-PDX models, respectively. A-C RNA-seq-based mRNA analysis of the indicated lymphocyte ( A ), myeloid cell ( B ) and NK cell ( C ) markers genes in NSG-PDX, HuSGM3-PDX and BLT-PDX tumors. Expression is normalized using the expression in matched primary patient-derived tumor. D IF for human CD3, CD8, CD14 and CD163 evaluating tumor immune infiltrates in the indicated PDX tumor models. Cell nuclei were counterstained with DAPI (blue). Scale bars, 20 µm

    Article Snippet: RNA-seq data analyses were performed by Novogene and Dr. Hui Shen’s research group.

    Techniques: RNA Sequencing, Expressing, Derivative Assay

    Analysis of complete humanized immune stroma PDX (HIS-PDX). HIS-PDX were created by co-engraftment of PDX TC, CA-MSC and EC (iHUVEC + iHDMEC). A IF for alpha smooth muscle actin (αSMA; red), and human-specific mitochondrial antigen (hMitoc; green) or pan-cytokeratin (PanCK; green) to label tumor cells in standard and HIS-PDX. Cell nuclei were counterstained with DAPI (blue) ( n = 3). B Hematoxylin and eosin (H&E) staining for a cell line-derived xenograft, standard PDX, humanized immune stroma PDX (HIS-PDX) and matched patient’s primary tumor ( n = 3). C RNA-seq derived heat map for stromal and immune gene expression in solid tumor-derived standard PDXs (StndPDX), HIS-PDX and patient primary tumor ( n = 3). D Total gene expression correlation between primary human tumor and primary tumor-derived HIS-PDX for patient 1 and patient 4. Scale bars in ( A ), 40 µm; scale bars in ( B ), 100 µm

    Journal: Cancer Immunology, Immunotherapy : CII

    Article Title: A novel humanized immune stroma PDX cancer model for therapeutic studies

    doi: 10.1007/s00262-026-04349-4

    Figure Lengend Snippet: Analysis of complete humanized immune stroma PDX (HIS-PDX). HIS-PDX were created by co-engraftment of PDX TC, CA-MSC and EC (iHUVEC + iHDMEC). A IF for alpha smooth muscle actin (αSMA; red), and human-specific mitochondrial antigen (hMitoc; green) or pan-cytokeratin (PanCK; green) to label tumor cells in standard and HIS-PDX. Cell nuclei were counterstained with DAPI (blue) ( n = 3). B Hematoxylin and eosin (H&E) staining for a cell line-derived xenograft, standard PDX, humanized immune stroma PDX (HIS-PDX) and matched patient’s primary tumor ( n = 3). C RNA-seq derived heat map for stromal and immune gene expression in solid tumor-derived standard PDXs (StndPDX), HIS-PDX and patient primary tumor ( n = 3). D Total gene expression correlation between primary human tumor and primary tumor-derived HIS-PDX for patient 1 and patient 4. Scale bars in ( A ), 40 µm; scale bars in ( B ), 100 µm

    Article Snippet: RNA-seq data analyses were performed by Novogene and Dr. Hui Shen’s research group.

    Techniques: Staining, Derivative Assay, RNA Sequencing, Gene Expression