Review




Structured Review

KU Leuven single-cell rna sequencing profiles
scCMS of individual cells. ( a ) Heatmap plot of normalized enrichment scores of the 27 marker gene-sets across all single tumor cells of 10 CRC samples from Lee et al. cohort. ( b ) UMAP plot of different tumor-tissue cell lineages. ( c ) UMAP plot of the four scCMS distributions and mixed transcriptomic states of the single tumor cells. ( d ) Proportions of scCMS groups in different cell lineages from Lee et al. <t>scRNASeq</t> dataset. ( e ) The UMAP plot of the epithelial-cell subtypes. ( f ) scCMS distributions within the epithelial-cell cluster. ( g ) Proportions of scCMSs in the populations of enterocytes and goblet- and transit-amplifying (TA) cells.
Single Cell Rna Sequencing Profiles, supplied by KU Leuven, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Images

1) Product Images from "Implications of Intratumor Heterogeneity on Consensus Molecular Subtype (CMS) in Colorectal Cancer"

Article Title: Implications of Intratumor Heterogeneity on Consensus Molecular Subtype (CMS) in Colorectal Cancer

Journal: Cancers

doi: 10.3390/cancers13194923

scCMS of individual cells. ( a ) Heatmap plot of normalized enrichment scores of the 27 marker gene-sets across all single tumor cells of 10 CRC samples from Lee et al. cohort. ( b ) UMAP plot of different tumor-tissue cell lineages. ( c ) UMAP plot of the four scCMS distributions and mixed transcriptomic states of the single tumor cells. ( d ) Proportions of scCMS groups in different cell lineages from Lee et al. scRNASeq dataset. ( e ) The UMAP plot of the epithelial-cell subtypes. ( f ) scCMS distributions within the epithelial-cell cluster. ( g ) Proportions of scCMSs in the populations of enterocytes and goblet- and transit-amplifying (TA) cells.
Figure Legend Snippet: scCMS of individual cells. ( a ) Heatmap plot of normalized enrichment scores of the 27 marker gene-sets across all single tumor cells of 10 CRC samples from Lee et al. cohort. ( b ) UMAP plot of different tumor-tissue cell lineages. ( c ) UMAP plot of the four scCMS distributions and mixed transcriptomic states of the single tumor cells. ( d ) Proportions of scCMS groups in different cell lineages from Lee et al. scRNASeq dataset. ( e ) The UMAP plot of the epithelial-cell subtypes. ( f ) scCMS distributions within the epithelial-cell cluster. ( g ) Proportions of scCMSs in the populations of enterocytes and goblet- and transit-amplifying (TA) cells.

Techniques Used: Marker

scCMSs from two CRC with mixed subtype from bulk transcriptome. UMAP plots of different single-cell types and scCMS predictions in ( a , b ) Patient #1 and ( c , d ) Patient #2 scRNAseq profiles, respectively. UMAP plots of single tumor cells were plotted using the normalized enrichment scores of the 27 marker gene sets obtained from ssGSEA. ( e ) Distributions of scCMSs in immune-, epithelial-, and stromal cell populations in patient #1 and patient #2.
Figure Legend Snippet: scCMSs from two CRC with mixed subtype from bulk transcriptome. UMAP plots of different single-cell types and scCMS predictions in ( a , b ) Patient #1 and ( c , d ) Patient #2 scRNAseq profiles, respectively. UMAP plots of single tumor cells were plotted using the normalized enrichment scores of the 27 marker gene sets obtained from ssGSEA. ( e ) Distributions of scCMSs in immune-, epithelial-, and stromal cell populations in patient #1 and patient #2.

Techniques Used: Marker

Related Articles

other:

Article Title: MGP + and IDO1 + tumor-associated macrophages facilitate immunoresistance in breast cancer revealed by single-cell RNA sequencing.
Article Snippet: Immunotherapy is widely applied for the treatment of breast cancer, but to which some patients respond poorly or develop resistance.. Therefore, the mechanism needs to be further studied.. Transcriptomic data of 31 breast cancer patients treated with anti-programmed death receptor 1 (PD-1) was downloaded from the VIB-KULeuven Center for Cancer Biology to analyze the changes in myeloid cells in tumor tissues before and after immunotherapy.

Article Title: Local glycolysis supports injury-induced axonal regeneration.
Article Snippet: Leveraging a previously published large single-cell RNA sequencing (scRNAseq) dataset of wild-type (WT) and genetically modified retinal ganglion cells (RGCs), in this study, we uncovered that RGCs co-deleted for Pten and Socs3 promptly ............................................................................................................................................................................. 1Department of Biology, Animal Physiology and Neurobiology Section, KU Leuven, Leuven Brain Institute, Leuven, Belgium; 2Neuro-Electronics Research Flanders, Vlaams Instituut voor Biotechnologie, Leuven, Belgium; 3imec, Leuven, Belgium.

Article Title: A subpopulation of luminal progenitors secretes pleiotrophin to promote angiogenesis and metastasis in inflammatory breast cancer.
Article Snippet: 8 scRNA-seq, single-cell RNA sequencing; WES, whole-exome sequencing; 9 KULEUVEN, KU Leuven; TKCC, the Kinghorn Cancer Centre; WEHI, the Walter 10 and Eliza Hall Institute; TCGA, The Cancer Genome Atlas; MDA, MD Anderson 11 Cancer Center.

Article Title: Pan-cancer Analysis Reveals Cancer-dependent Expression of SOX17 and Associated Clinical Outcomes.
Article Snippet: The drug response data were obtained from Genomics of Drug Sensitivity in Cancer (https://www.cancerrxgene.org/), and single-cell RNA sequencing data were obtained from VIB-KU LEUVEN CENTER FOR CANCER BIOLOGY (http://blueprint.lambrechtslab.org).

Article Title: Uncovering minimal pathways in melanoma initiation.
Article Snippet: Generation of Braf CA/+ PtenΔ/+ Sox2-deficient mice Sox2-floxed mice were purchased from Jackson laboratories (STOCK Sox2tm1.1Lan/J strain#:013093, Table 1) and crossed toBraf CA-fl/+ Ptenfl/+ mice.

Article Title: Cancer immunotherapies transition endothelial cells into HEVs that generate TCF1 + T lymphocyte niches through a feed-forward loop.
Article Snippet: At VIB- KU Leuven, we thank K. Feyen and N. Dupont for their technical assistance, P. Zhao and Dr. J. Po zniak for assistance with the scRNA-seq analysis, the VIB histology core for histology assistance, the VIB Bio Imaging Core for microscopy assistance, S. Vlayen for administrative and logistical support, and the KU Leuven FACS core and Dr. O. Burton (University of Cambridge) for assistance with flow cytometry.

Single Cell:

Article Title: Stromal lipid species dictate melanoma metastasis and tropism.
Article Snippet: .. Single cell RNA sequencing (Pozniak et al., 2024)43 data was downloaded from KU Leuven Research Data Repository. ..

Article Title: Traumatic brain injury promotes neurogenesis at the cost of astrogliogenesis in the adult hippocampus of male mice
Article Snippet: .. M.G.H. provided funding, access to the single-cell sequencing facility at VIB-KU Leuven and arranged early access to the Molecular Cartography platform. ..

RNA Sequencing:

Article Title: Stromal lipid species dictate melanoma metastasis and tropism.
Article Snippet: .. Single cell RNA sequencing (Pozniak et al., 2024)43 data was downloaded from KU Leuven Research Data Repository. ..

Sequencing:

Article Title: Traumatic brain injury promotes neurogenesis at the cost of astrogliogenesis in the adult hippocampus of male mice
Article Snippet: .. M.G.H. provided funding, access to the single-cell sequencing facility at VIB-KU Leuven and arranged early access to the Molecular Cartography platform. ..



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Image Search Results


Chodl mRNA is highly expressed in quiescent SCs (A) Chodl gene expression in various cell types in the mouse. Data were explored through the Tabula Muris data portal. (B) Relative expression of the Chodl gene in SCs, bladder cells, and a non-annotated cell population in (A). (C) UMAP-embedding of the scRNA-seq data on SCs isolated from non-injured muscles and injured muscles at 5 dpi in 2-month-old mice. (D) Violin plots show subcluster-specific gene expression ( Pax7 , Myog , Mki67 ) and enrichment of Chodl in the QSCs and ASCs. Colored by cluster identity. Abbreviations: QSC, quiescent SCs; SSC, self-renewal SCs; ASC, activated SCs; PSC, proliferating SCs; CSC, committed SCs; DSC, differentiating SCs. (E) qRT-PCR analysis of Chodl expression level in mouse QSC, ASC, and myoblast. n = 3 mice. (F) Immunoblot analysis showing CHODL expression in mouse myoblasts during myogenic differentiation. Relative band densitometry was calculated using ImageJ. (G) qRT-PCR analysis of Chodl in TA muscles post CTX injury in the mouse. n = 4 mice. Data are represented as mean ± SEM. The p values in E and G were analyzed using one-way ANOVA and Tukey post hoc test; ∗ p < 0.05, ∗∗ p < 0.01, and ∗∗∗ p < 0.001.

Journal: iScience

Article Title: Chondrolectin regulates the sublaminar localization and regenerative function of muscle satellite cells in mice

doi: 10.1016/j.isci.2026.115703

Figure Lengend Snippet: Chodl mRNA is highly expressed in quiescent SCs (A) Chodl gene expression in various cell types in the mouse. Data were explored through the Tabula Muris data portal. (B) Relative expression of the Chodl gene in SCs, bladder cells, and a non-annotated cell population in (A). (C) UMAP-embedding of the scRNA-seq data on SCs isolated from non-injured muscles and injured muscles at 5 dpi in 2-month-old mice. (D) Violin plots show subcluster-specific gene expression ( Pax7 , Myog , Mki67 ) and enrichment of Chodl in the QSCs and ASCs. Colored by cluster identity. Abbreviations: QSC, quiescent SCs; SSC, self-renewal SCs; ASC, activated SCs; PSC, proliferating SCs; CSC, committed SCs; DSC, differentiating SCs. (E) qRT-PCR analysis of Chodl expression level in mouse QSC, ASC, and myoblast. n = 3 mice. (F) Immunoblot analysis showing CHODL expression in mouse myoblasts during myogenic differentiation. Relative band densitometry was calculated using ImageJ. (G) qRT-PCR analysis of Chodl in TA muscles post CTX injury in the mouse. n = 4 mice. Data are represented as mean ± SEM. The p values in E and G were analyzed using one-way ANOVA and Tukey post hoc test; ∗ p < 0.05, ∗∗ p < 0.01, and ∗∗∗ p < 0.001.

Article Snippet: To gain insight into the expression pattern of Chodl across various tissues, we conducted a comprehensive analysis using the scRNA-seq data publicly available from Tabula Muris , Our analysis revealed that Chodl mRNA was mainly enriched in SCs, bladder cells, and a non-annotated cell population, while not detected in other cell types, including fibro-adipogenic progenitors (FAPs) ( A and 1B).

Techniques: Gene Expression, Expressing, Isolation, Muscles, Quantitative RT-PCR, Western Blot, Cell Characterization