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| Status |
Public on Jul 20, 2019 |
| Title |
Dissecting the single-cell transcriptome network underlying gastric premalignant lesions and early gastric cancer [10x genomics] |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| 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.
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| 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.
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| Contributor(s) |
Li S, Zhang P |
| Citation(s) |
31067475, 33521016 |
| Submission date |
Jul 19, 2019 |
| Last update date |
Feb 08, 2021 |
| Contact name |
Shao Li |
| E-mail(s) |
shaoli@mail.tsinghua.edu.cn
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| Organization name |
Tsinghua University
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| Street address |
Haidian district
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| City |
Beijing |
| State/province |
Beijing |
| ZIP/Postal code |
+86 |
| Country |
China |
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| Platforms (1) |
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| Samples (13)
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| Relations |
| BioProject |
PRJNA555477 |
| SRA |
SRP215370 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE134520_RAW.tar |
83.5 Mb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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