Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR26788702.fastq.gz | Fastqsanger.gz | |||
| SRR26788703.fastq.gz | Fastqsanger.gz | |||
| SRR26788704.fastq.gz | Fastqsanger.gz | |||
| SRR26788705.fastq.gz | Fastqsanger.gz | |||
| SRR26788706.fastq.gz | Fastqsanger.gz |
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Project description:The comprehensive DNA methylation status of gastric cancer cells obtained from an advanced Epstein-Barr virus-associated gastric cancer case, in which complete response to S-1 plus cisplatin chemotherapy was achieved, was analyzed with DNA methylation microarray (Illumina Infinium MethylationEPIC BeadChip). DNA was extracted from metastatic lesion (lymph node).
2019-06-08 | GSE132406 | GEO
Project description:Gastric cancer is one of the most aggressive cancers and is the second leading cause of cancer death worldwide. Approximately 40% of global gastric cancer cases occur in China, with peritoneal metastasis being the prevalent form of recurrence and metastasis in advanced disease (>50%). Currently, there are limited clinical approaches for predicting and treatment of peritoneal metastasis, resulting in a 6- month average survival time. By comprehensive genome analysis will uncover the pathogenesis of peritoneal metastasis. Here we describe a comprehensive whole-genome and transcriptome sequencing analysis of one advanced gastric cancer case, including non-cancerous mucosa, primary cancer and matched peritoneal metastatic cancer. The peripheral blood is used as normal control.
2019-06-12 | GSE64916 | GEO
Project description:Methylation analysis of Epstein-Barr virus-associated gastric cancer case
| PRJNA547827 | ENA
Project description:The goal of this project was to compare the metabolite profiles of the: mouse gastric antrum and the mouse gastric corpus, the mouse gastric antrum and the mouse gastric antrum isolated glands, and the mouse gastric corpus and the mouse gastric corpus isolated glands.
2016-02-09 | ST000354 | MetabolomicsWorkbench
Project description:Helicobacter pylori and risk of gastric cancer: a case-control study
| PRJNA1136026 | ENA
Project description:Because gastric cancer cells already had genetic and epigenetic alterations which can affect the gastric carcinogenesis, we tried to characterize genetic and epigenetic changes during gastric carcinogenesis. To do this, we performed MBD sequencing and RRBS sequencing. MBD and RRBS sequencing of gastric mucosa, intestinal metaplasia, and gastric cancer cells from one patient were generated by NGS using Illumina GAII.
2015-09-01 | E-GEOD-55159 | biostudies-arrayexpress
Project description:Because gastric cancer cells already had genetic and epigenetic alterations which can affect the gastric carcinogenesis, we tried to characterize genetic and epigenetic changes during gastric carcinogenesis. To do this, we performed MBD sequencing and RRBS sequencing. MBD and RRBS sequencing of gastric mucosa, intestinal metaplasia, and gastric cancer cells from one patient were generated by NGS using Illumina GAII.
2015-09-01 | E-GEOD-55157 | biostudies-arrayexpress
Project description:Background: Gastric cancer (GC) remains the third leading cause of cancer death worldwide due to the absence of sensitive and specific biomarkers for its early detection. 5-hydroxymethylcytosine (5hmC)-enriched gene profiles and regions show tissue-specific and tumor specific, and cell-free DNA (cfDNA) 5hmC modification feature sequencing provides a robust tool for gastric cancer detection.Methods: A matched case‒control study design with 50 gastric cancer patients and 50 controls was performed to sequence the 5hmC modification of cfDNA. Significantly differential 5hmC modification genes were identified to construct a gastric cancer diagnostic model. The data set from Gene Expression Omnibus consisted of 61 gastric cancer patients, 90 healthy individuals and 22 benign gastric disease controls was used as an external testing set to test the robustness of the diagnostic model. Results: The vast majority of 5hmC peaks were distributed in the gene body, accounting for more than 90% of the total 5hmC peaks in both the GC and control groups. The diagnostic model was developed based on five different 5hmC modification genes, FBXL7, PDE3A, TPO, SNTG2 and SXBP5. The model could clearly distinguish gastric cancer patients from controls in the training (AUC=0.95, sensitivity=88.6%, specificity=94.3%), validation (AUC=0.87, sensitivity=73.3%, specificity=93.3%) and testing (AUC=0.90, sensitivity=81.9%, specificity=90.2%) sets. The predicted risk scores of the controls were significantly lower than those of GC patients in our own data (P<0.001) or GEO external testing data (P<0.001), but no significant difference was observed between different TNM stage groups (P=0.09 and 0.66). Furthermore, the risk scores of healthy and benign gastric disease controls in the testing set were also not different (P=0.10). Conclusions: The characteristics of 5hmC in cfDNA are specific to GC patients, and the diagnostic model constructed by the 5hmC features of five genes could effectively identify GC patients.
2024-12-30 | GSE246110 | GEO
Project description:Helicobacter pylori infects the stomachs of half of all humans. It has a relatively benign relationship with most hosts, but produces severe pathology, including gastric cancer, in others. Identifying the relative contributions of host, microbial and environmental factors to the outcome of infection has been challenging. Here, we describe one approach for identifying microbial genes that affect the magnitude of host responses to infection. Single colony purified H. pylori isolates were obtained from 25 cases and 71 controls in a Swedish case-control study of gastric cancer. Strains were first phenotyped based on their ability to produce adhesins that recognize two classes of human gastric epithelial receptors. Thirteen binding strains and two non-binding controls were then subjected to whole genome genotyping using H. pylori DNA microarrays. A cohort of 'variable' genes was identified based on a microarray-determined call of 'absent' in at least one member of the strain panel. Each strain was subsequently introduced into two types of germ-free transgenic mice, each programmed to express a different host factor postulated to pose increased risk for development of severe pathology. Expression of biomarkers of host defense was quantitated 4 weeks after inoculation and magnitude of the response correlated with bacterial genotype. The proportion of genes encoding HsdS homologs (specificity subunit of hetero-oligomeric type I restriction-modification systems) was significantly higher in the pool of 18 variable genes whose presence directly correlated with a robust host response than their proportion in the remaining 352 members of the variable gene pool. This suggests that the functions of these HsdS homologs may include control of expression of microbial determinants that affect the extent of gastric responses to this potentially virulent pathogen. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Keywords: Logical Set
2005-09-09 | GSE3272 | GEO