Ena-DATASET-DUKE-NUS-18-07-2017-08:37:45:391-266 - samples
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00001003448 | EGA |
REPOSITORIES: EGA
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Project description:Gastric cancers account for the fourth most frequent cancer death worldwide. Although many differential gene expression profiles are reported for gastric cancers, their variation at the post-transcriptional level has not been provided yet. In this study, we compared the gene expressions of normal stomach vs. stomach cancer in an exon-wise manner and compared alternatively spliced transcripts. The RNA from normal and cancer tissues of gastric cancer patients were subjected to Exon 1.0 ST microarrays. Transcriptome analysis of RNAs from normal and cancer tissues of human stomach by exon array. We analyzed 30 pairs of normal-cancer stomach tissues using the Affymetrix Human Exon 1.0 ST platform. Array data was processed by the Affymetrix Exon Array Computational Tool.
2014-07-12 | E-GEOD-30727 | biostudies-arrayexpress
Project description:Gastric cancers account for the fourth most frequent cancer death worldwide. Although many differential gene expression profiles are reported for gastric cancers, their variation at the post-transcriptional level has not been provided yet. In this study, we compared the gene expressions of normal stomach vs. stomach cancer in an exon-wise manner and compared alternatively spliced transcripts. The RNA from normal and cancer tissues of gastric cancer patients were subjected to Exon 1.0 ST microarrays.
2014-07-12 | GSE30727 | GEO
Project description:Mist1+ cells and parietal cells in mouse stomach were separatedly sorted, and RNAs were isolated. Mist1 (also known as Bhlha15) is expressed in gastric chief cells and gastric stem cells in mice. However, more specific genes for each population needs to be identified to better understand the precise biology in these cell populations. In order to address cell specific gene signature, we separately sorted Mist1+ gastric chief cells and Mist1+ gastric stem cells by FACS, and performed microarray analysis. Mist1+ gastric chief cells were sorted by using Mist1-CreERT; R26-TdTomato mouse stomach, immediately after tamoxifen administration. Mist1+ gastric stem cells were sorted by chief cell-ablated Mist1-CreERT; R26-TdTomato mouse stomach, combining with Lgr5-DTR mice. Lgr5-expressing chief cells were ablated by giving DT into these mice. As a control, acid-secreting gastric parietal cell samples were used. Mice were treated with or without Lgr5-DT ablation before sorting.
2019-06-25 | GSE133205 | GEO
Project description:The mouse stomach secrets digestive enzymes and stomach acid, and plays a key role in food digestion. While there are a few studies on the morphological changes during the stomach development, a comprehensive, systematic omics study is still missing. Here, we present a comprehensive, temporal proteome atlas of the mouse stomach by sequential mapping stomach tissues at multiple developmental stages. The quantitative analysis of 12,108 gene products provides coverage sufficient to observe the protein dynamics of the developing stomach. The whole process of stomach development can be roughly divided into three phases according to changes of RNAs or proteins. The molecular functions of protein modules pinpoint the gain of stomach functions at the longitudinal scale. Dissection of 8 key signaling pathways identified master regulators in governing stomach development and gastric cancer. Remarkably, many proteins differentially expressed in stomach development are also significantly overexpressed in diffuse-type gastric cancer, suggesting a close correlation between development and tumorigenesis. The transcriptome of the developing stomach reveals functionally important isoforms relevant to development. When combined with the proteomes, several functionally unannotated novel splicing junction transcripts were identified and validated at the peptide level. Overall, our study provides a valuable resource to understand stomach development and its connection to gastric cancer.
2018-08-04 | GSE118083 | GEO
Project description: Not available
| S-EPMC7402390 | biostudies-literature
Project description:Gene expression profiling of apparently normal gastric tissue (obtained from patients undergoing gastric surgery for Non-gastric cancers), paired normals (obtained from the same stomach as the gastric cancer but confirmed by frozen section not to harbour any tumour cells) and gastric cancer, with an intent to identify genes involved in the malignant transformation of normal gastric mucosa and to identify genes which can be used as biomarkers for early diagnosis and potential targets for treatment Identification of novel prognostic markers using microarray gene expression studies. Keywords: Patient tissue samples
2010-11-30 | GSE17154 | GEO
Project description:Gene expression profiling of apparently normal gastric tissue (obtained from patients undergoing gastric surgery for Non-gastric cancers), paired normals (obtained from the same stomach as the gastric cancer but confirmed by frozen section not to harbour any tumour cells) and gastric cancer, with an intent to identify genes involved in the malignant transformation of normal gastric mucosa and to identify genes which can be used as biomarkers for early diagnosis and potential targets for treatment Identification of novel prognostic markers using microarray gene expression studies. Keywords: Patient tissue samples Two-dye experiments using Universal control RNA (Stratagene) and RNA from tissues. Biological replicates: Apparently Normal = 5; Paired Normal = 20; Gastric cancers = 24. One replicate per array.
2010-11-30 | E-GEOD-17154 | biostudies-arrayexpress
Project description:Gastric ulcer, which affect many of patients and is deeply related with gastric cancer, is caused by chronic gastric acid stimulation. Stomach fundus, the main body of stomach, is a major source of gastric acid and peptidase for food digestion. Recapturing the main body of stomach requires mainly 3 functionally differentiated cells; parietal (oxyntic) cells, chief (zymogenic) cells, and surface mucous foveolar (pit) cells. We have previously shown the induction of stomach tissue with functional secreting activities by directed differentiation of mouse embryonic stem cells (ES cells) to stomach primordium with both gut epithelium and splanchnic mesoderm. However, generating human stomach with fundus and such functions has been elucidated and a long-desired goal. Here, we describe the method for establishing human embryonic stem cell-derived stomach organoids with fundus gland structure. Along with mouse stomach development and de novo stomach generation from mouse ES cells in vitro, we observed gut-like structure formation from human embryonic stem cells by induction of both endoderm and mesoderm. These human embryonic gut could differentiate into stomach primordium by growth factor stimulation as well as stomach development, and form stomach tissue in three-dimensional organoid culture. Furthermore, these stomach organoids contain fundus-like gland with parietal cells and chief cells, some of secreting activities, and is transcriptionally close to human stomach. Human functional stomach derived from embryonic stem cells represent powerful tools for analying human stomach development, and gastric ulcer related disease including gastric tumorgenesis.
2017-08-31 | GSE79673 | GEO
Project description:As the important layer of the stomach wall, gastric mucosa is related to many functions of digestion. According to the anatomical location, the human stomach is divided into seven regions. In order to get an entire profiling of the 7 regions at proteomic and transcriptomic levels, we collected 7 biopsies from each health volunteer, 49 total were used for integrative analysis, and measured the regional-specific gene products to define the reference intervals of gene expression for outliers screening and prognostic gene detection. Collectively, we presented profiling of normal gastric mucosa at different levels and defined reference ranges of gene expression to study the specific characteristics of abnormal and cancer samples, providing a better understanding of stomach physiological function in studies of gastric disease mechanism.
2024-04-01 | GSE250499 | GEO
Project description:We previously established long-term 3D organoid culture systems for several murine tissues (intestine, stomach, pancreas and liver) as well as human intestine and pancreas. Here, we describe culture conditions to generate long-term 3D culture from human gastric stem cells. The technology can be applied to study the epithelial response to infection with Helicobacter pylori. Human gastric cultures can expand indefinitely in 3D Matrigel. Cultures can be generated from normal tissue, from single sorted stem cells, or from tumor tissue. Organoids maintain many characteristics of the respective tissue in terms of histology, marker expression and euploidy. Organoids from normal tissue express markers of four lineages of the stomach and self-organize in gland and pit-domains. They can be directed to specifically express either lineages of the gastric gland, or the gastric pit by addition of Nicotinamide and withdrawal of Wnt. While gastric pit lineages react marginally to bacterial infection, gastric gland lineages mount a strong inflammatory response. The gastric culture system provides a unique tool to study gastric pathologies.
2014-10-13 | GSE60557 | GEO