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Single-cell transcriptome landscape in colorectal cancer

ABSTRACT: One tumor tissue specimen pathologically diagnosed as adenocarcinoma undergoing radical colorectal surgery without any preoperative treatment at our center was collected, and the single cell transcriptome sequencing was performed, which was consistent with the inclusion and exclusion criteria for the prospective observational clinical study.The detailed procedures of pre-processing and quality control were as follows: (1) Raw data quality control; (2) Data comparison and mapping; (3) Cell Barcode Correction; (4) UMI disaggregation; (5) Count matrix generation; (6) Quality control indicators; (7) Data standardization and normalization; (8) Identification of highly variable genes (HVGs); (9) Filtering condition settings: nCount_RNA > 1000 & nFeature_RNA < 3000 & percent.mt < 10 & nFeature_RNA > 200. The t-Distributed Stochastic Neighbor Embedding (t-SNE) algorithm was used for downscaling and cell clustering, and the "SingleR" R package was used for cell annotation. The "CellChat" and "NicheNet" R packages were used for cell communication. The "monocle2" was used for cell trajectory analysis.

ORGANISM(S): Homo sapiens

PROVIDER: GSE277669 | GEO | 2024/12/13

REPOSITORIES: GEO

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| PRJNA393319 | ENA

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