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10X Genomics
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Image Search Results
Journal: Cell reports. Medicine
Article Title: Cell states and neighborhoods in distinct clinical stages of primary and metastatic esophageal adenocarcinoma.
doi: 10.1016/j.xcrm.2025.102188
Figure Lengend Snippet: Figure 1. EAC primary and metastatic samples show a diverse landscape of TME and malignant cells in transcriptomic and epigenetic data (A) Schematic representation of the study workflow. Biopsies from 10 patients in our discovery cohort, including normal adjacent tissue (NAT), primary tissue, and metastatic samples, were subjected to single-nuclei RNA and ATAC sequencing using 10X Chromium technology. For a subset of these patients as well as three additional patients, matched primary and metastatic samples were profiled with 10X Visium and 10X Xenium spatial transcriptomics (ST) technologies. For single- nuclei data, cells were annotated by cell type and categorized into malignant and TME components. TME subtypes were linked to metastasis, with validation against an external pan-cancer fibroblast atlas. 16 The malignant cell components underwent analysis using consensus non-negative matrix factorization (cNMF) to uncover malignant programs, which were further characterized for transcriptional and epigenetic heterogeneity at a single-cell and spatial level and candidate master transcription factors. External validation was performed in two single-cell validation cohorts, 9,10 and associations with clinical and molecular charac- teristics, as well as survival, were assessed in three bulk validation cohorts. 7,10,17
Article Snippet: *_ga_B3E4QL2TPR* MTcxMDc3MDI1My4yMS4wLjE3MTA3Nz AzNTcuMC4wLjAhttps://tcga-pancanatlas-hub.s3.us-east-1.amazonaws.com/ download/Survival_SupplementalTable_ S1_20171025_xena_sp Fibroblast atlas single-cell data, Luo et al. https://www.nature.com/ articles/s41467-022-34395-2 GEO: GSE210347 Software and algorithms 10X Cell Ranger ARC pipeline,
Techniques: Sequencing, Biomarker Discovery