NGDC - GSA for Human

HRA002917

Title:

Spatially-resolved expression landscape and gene-regulatory network of human gastric corpus epithelium

Release date:

2022-11-03

Description:

Molecular knowledge of human gastric corpus epithelium remains incomplete. Here, by integrated analyses using single-cell RNA sequencing (scRNA-seq), spatial transcriptomics and single-cell assay for transposase accessible chromatin sequencing (scATAC-seq) techniques, we uncovered the spatially-resolved expression landscape and gene-regulatory network of human gastric corpus epithelium. Specifically, we identified a stem/progenitor cell population in the isthmus of human gastric corpus, where EGF and WNT signaling pathways were activated. Meanwhile, LGR4, but not LGR5, was responsible for the activation of WNT signaling pathway. Importantly, FABP5 and NME1 were identified and validated crucial for both normal gastric stem/progenitor cells and gastric cancer cells. Finally, we explored the epigenetic regulation of critical genes for gastric corpus epithelium at chromatin state level, and identified several important cell type specific transcription factors.

Data Accessibility:

Open access

BioProject:

PRJCA011342

Study type:

Human gastric corpus epithelium cell atlas

Dataset Download

MetaData:

HRA002917.xlsx

Files:

HTTPS：https://download.cncb.ac.cn/gsa-human/HRA002917

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Files:

FTP：ftp://download.big.ac.cn/gsa-human/HRA002917

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Individuals & samples

Individual Accession	Individual Name	Gender	Sample Accession	Sample Name	Sample Description

Individual Accession	Individual Name	Gender	Sample Accession	Sample Name	Sample Description
HRI273699	P51	male	HRS437614	10x scRNA-seq of gastric corpus sample1	10x scRNA-seq of gastric corpus from pancreatic ductal adenocarcinoma patient
HRI273699	P51	HRI273699	P51	male	HRS437620	strt scRNA-seq of gastric corpus sample 1	strt scRNA-seq of gastric corpus from pancreatic ductal adenocarcinoma patient
HRI273700	P52	male	HRS437615	10x scRNA-seq of gastric corpus sample2	10x scRNA-seq of gastric corpus from right-sided colon adenocarcinoma patient
HRI273700	P52	HRI273700	P52	male	HRS437621	strt scRNA-seq of gastric corpus sample 2	strt scRNA-seq of gastric corpus from right-sided colon adenocarcinoma patient
HRI273701	P53	male	HRS437616	10x spatial transcriptomics of gastric corpus sample 1	10x spatial transcriptomics of gastric corpus from esophagogastric junction adenocarcinoma
HRI273702	P54	male	HRS437617	10x spatial transcriptomics of gastric corpus sample 2	10x spatial transcriptomics of gastric corpus from esophagogastric junction adenocarcinoma
HRI273703	P55	male	HRS437618	10x scATAC-seq of gastric corpus sample 1	10x scATAC-seq of gastric corpus from adenocarcinoma of gastric antrum patient
HRI273704	P56	female	HRS437619	10x scATAC-seq of gastric corpus sample 2	10x scATAC-seq of gastric corpus from adenocarcinoma of gastric antrum patient
HRI273705	SI-1	female	HRS437622	10x scRNA-seq of ileum sample 1	10x scRNA-seq of ileum from right-sided colon adenocarcinoma patient
HRI273706	SI-2	female	HRS437623	10x scRNA-seq of ileum sample 2	10x scRNA-seq of ileum from right-sided colon neuroendocrine adenocarcinoma patient

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Files

Download

Run accession	Files	Experiment	Experiment title	Platform	Sample

Run accession	Files	Experiment	Experiment title	Platform	Sample
HRR742248	HRR742248_f1.fastq.gz (4.91 GB)	HRX536339	10x scRNA of gastric corpus from pancreatic ductal adenocarcinoma patient	Illumina HiSeq 4000	HRS437614 (SAMC2292559)
HRR742248	HRR742248	HRR742248_r2.fastq.gz (6.65 GB)	HRX536339	10x scRNA of gastric corpus from pancreatic ductal adenocarcinoma patient	Illumina HiSeq 4000	HRS437614 (SAMC2292559)
HRR742249	HRR742249_f1.fastq.gz (4.26 GB)	HRX536339	10x scRNA of gastric corpus from pancreatic ductal adenocarcinoma patient	Illumina HiSeq 4000	HRS437614 (SAMC2292559)
HRR742249	HRR742249	HRR742249_r2.fastq.gz (5.58 GB)	HRX536339	10x scRNA of gastric corpus from pancreatic ductal adenocarcinoma patient	Illumina HiSeq 4000	HRS437614 (SAMC2292559)
HRR742250	HRR742250_f1.fastq.gz (4.21 GB)	HRX536339	10x scRNA of gastric corpus from pancreatic ductal adenocarcinoma patient	Illumina HiSeq 4000	HRS437614 (SAMC2292559)
HRR742250	HRR742250	HRR742250_r2.fastq.gz (5.54 GB)	HRX536339	10x scRNA of gastric corpus from pancreatic ductal adenocarcinoma patient	Illumina HiSeq 4000	HRS437614 (SAMC2292559)
HRR742251	HRR742251_f1.fastq.gz (2.12 GB)	HRX536339	10x scRNA of gastric corpus from pancreatic ductal adenocarcinoma patient	Illumina HiSeq 4000	HRS437614 (SAMC2292559)
HRR742251	HRR742251	HRR742251_r2.fastq.gz (2.79 GB)	HRX536339	10x scRNA of gastric corpus from pancreatic ductal adenocarcinoma patient	Illumina HiSeq 4000	HRS437614 (SAMC2292559)
HRR742252	HRR742252_f1.fastq.gz (3.47 GB)	HRX536340	10x scRNA of gastric corpus from right-sided colon adenocarcinoma patient	Illumina HiSeq 4000	HRS437615 (SAMC2292563)
HRR742252	HRR742252	HRR742252_r2.fastq.gz (4.44 GB)	HRX536340	10x scRNA of gastric corpus from right-sided colon adenocarcinoma patient	Illumina HiSeq 4000	HRS437615 (SAMC2292563)

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Submitter: Tang Fuchou / tangfuchou@pku.edu.cn

Organization: Peking University

Submission date: 2022-08-21

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