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Dissecting the single-cell transcriptome network underlying gastric premalignant lesions and early gastric cancer [10x genomics]


ABSTRACT: Intestinal-type gastric cancer is preceded by premalignant lesions including chronic atrophic gastritis and intestinal metaplasia. In this study, we performed a scRNA-seq survey of 56,440 cells from thirteen gastric antral mucosa biopsies from nine patients with Non-atrophic gastritis (NAG), CAG, IM or early gastric cancer (EGC), and constructed a single-cell transcriptome atlas for gastric premalignant and early-malignant lesions. The thirteen biopsies, including three wild superficial gastritis (NAG) ones, three CAG ones, six IM ones and one EGC , spanned the cascade from gastritis to early gastric cancer.For each biopsy, we isolated single cells without prior selection for cell types and utilized the 10x Chromium platform to generate RNA-seq data. After removing low-quality cells (Methods), a total of 32, 332 cells that passed the quality control were retained for subsequent analysis, which yielded a median of 1941 detected genes per cell. Overall design: a scRNA-seq survey of 56,440 cells from thirteen gastric antral mucosa biopsies from nine patients with Non-atrophic gastritis (NAG), Chronic atrophic gastritis (CAG), Intestinal metaplasia (IM) or early gastric cancer (EGC), using 10X genomics.

INSTRUMENT(S): HiSeq X Ten (Homo sapiens)

ORGANISM(S): Homo Sapiens

SUBMITTER: Shao Li  

PROVIDER: GSE134520 | GEO | 2019-07-20

REPOSITORIES: GEO

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Publications

Dissecting the Single-Cell Transcriptome Network Underlying Gastric Premalignant Lesions and Early Gastric Cancer.

Zhang Peng P   Yang Mingran M   Zhang Yiding Y   Xiao Shuai S   Lai Xinxing X   Tan Aidi A   Du Shiyu S   Li Shao S  

Cell reports 20190501 6


Intestinal-type gastric cancer is preceded by premalignant lesions, including chronic atrophic gastritis and intestinal metaplasia. In this study, we constructed a single-cell atlas for 32,332 high-quality cells from gastric antral mucosa biopsies of patients spanning a cascade of gastric premalignant lesions and early gastric cancer (EGC) using single-cell RNA sequencing. We then constructed a single-cell network underlying cellular and molecular characteristics of gastric epithelial cells acro  ...[more]

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