Summary: 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.
Single-cell RNA-seq using 10X genomics platform was performed using Chromium鈩?Single Cell 3' v2 Reagent Kits following the manufacturer' protocol. Libraries were constructed using Chromium鈩?Single Cell 3' v2 Reagent Kits following the manufacturer' protocol Libraries were sequenced on Illumina HiSeq X Ten platform to obtain 100 and 32-bp paired end reads using the following read length; read 1, 26 cycles, read 2, 98 cycles and i7 index, 8 cycles.; Single-cell R--seq using 10X genomics platform was performed using Chromium™ Single Cell 3' v2 Reagent Kits following the manufacturer's protocol. Libraries were constructed using Chromium™ Single Cell 3' v2 Reagent Kits following the manufacturer's protocol Libraries were sequenced on Illumi- HiSeq X Ten platform to obtain 100 and 32-bp paired end reads using the following read length; read 1, 26 cycles, read 2, 98 cycles and i7 index, 8 cycles.
Library Construction Protocol:
HiSeq X Ten
Sequencing
Molecule Type:
poly(A)+ RNA
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Library Layout:
PAIRED
Library Strand:
Forward
Platform:
ILLUMINA
Instrument Model:
Illumina HiSeq X Ten
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Specific
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Publications
Dissecting the Single-Cell Transcriptome Network Underlying Gastric Premalignant Lesions and Early Gastric Cancer.
