E-MTAB-3689
Ontology highlight
ABSTRACT:
PROVIDER: E-MTAB-3689 | ExpressionAtlas | 2019-05-14
REPOSITORIES: ExpressionAtlas
Similar Datasets
Project description:RNA-seq of gastric biopsies from subjects at different stages of gastric inflammation and histological changes.
| PRJEB9749 | ENA
Project description:In this study we performed RNA-seq analysis of gastric corpus biopsies to study transcriptional changes during early gastric carcinogenesis. We included patients with non-atrophic gastritis, with intermediate and extensive corpus atrophy, and patients with intestinal metaplasia. We also included a control group of H. pylori-negative subjects. All subjects were from Nicaragua, which has a population of high gastric cancer risk. Total RNA samples were treated with RiboZero Magnetic (Human/Mouse/Rat) Kit (Epicentre Biotechnologies) to deplete rRNA and the cDNA libraries were prepared using ScriptSeqTM v2 RNA-Seq Library Preparation Kit (Epicentre). Sequencing was performed on the Illumina HiScan2500 platform, 2*100bp reads.
2015-12-31 | E-MTAB-3689 | biostudies-arrayexpress
Project description:Hepatic lipid accumulation is an important complication of obesity linked to risk for type 2 diabetes. To identify novel transcriptional changes in human liver which could contribute to hepatic lipid accumulation and associated insulin resistance and type 2 diabetes (DM2), we evaluated gene expression and gene set enrichment in surgical liver biopsies from 13 obese (9 with DM2) and 5 control subjects, obtained in the fasting state at the time of elective abdominal surgery for obesity or cholecystectomy. RNA was isolated for cRNA preparation and hybridized to Affymetrix U133A microarrays. Human liver samples were obtained from 5 lean control subjects undergoing elective cholecystectomy and 13 obese subjects (with or without Type 2 diabetes) undergoing gastric bypass surgery. Subjects with diabetes were classified as either well-controlled or poorly-controlled.
2009-06-01 | E-GEOD-15653 | biostudies-arrayexpress
Project description:Gastric cancer is characterized by prolonged, well-defined precancerous stages. In our study, we performed the whole genome gene expression mircroarray of 22 gastric tissues at different pathological stages. We aim to find genes that closely related to the changes of TCR repertoire during gastric carcinogenesis. By integrative analysis of the microarray data and TCR variation degrees, we identified a 11-gene module that can predict the overall survival of gastric cancer patients.
2017-08-21 | GSE87666 | GEO
Project description:Recent advances in high throughput sequencing methodologies allow the opportunity to probe in depth the transcriptomes of organisms including N. caninum. In this project, we are using Illumina sequencing technology to analyze the transcriptome (RNA-Seq) of experimentally accessible stages (e.g. tachyzoites at different times points) of N. caninum NCLiv. The aim is to make transcriptional landscape maps at different time points at different life cycle stages of N. caninum and compare it with equivalent datasets from the closely related parasite Toxoplasma gondii. ArrayExpress Release Date: 2011-02-08 Person Roles: submitter Person Last Name: Service Person First Name: Submission Person Mid Initials: Person Email: datahose@sanger.ac.uk Person Phone: Person Address: The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom Person Affiliation: Wellcome Trust Sanger Institute Person Roles: Investigator Person Last Name: Reid Person First Name: Adam Person Mid Initials: Person Email: ar11@sanger.ac.uk Person Phone: 01223 834244 Person Address: Wellcome Trust Genome Campus,Hinxton,Cambridge. CB10 1SA UK Person Affiliation: Wellcome Trust Sanger Institute Person Roles: Project Coordinator Person Last Name: Sanders Person First Name: Mandy Person Mid Initials: J Person Email: mjs@sanger.ac.uk Person Phone: 01223 834244 Person Address: Wellcome Trust Genome Campus,Hinxton,Cambridge. CB10 1SA UK Person Affiliation: Wellcome Trust Sanger Institute
2011-07-14 | GSE30613 | GEO
Project description:Recent advances in high throughput sequencing methodologies allow the opportunity to probe in depth the transcriptomes of organisms including N. caninum and Toxoplasma gondii. In this project, we are using Illumina sequencing technology to analyze the transcriptome (RNA-Seq) of experimentally accessible stages (e.g. tachyzoites at different times points) of T. gondii VEG strain. The aim is to make comparative transcriptional landscape maps of Neospora and Toxoplasma at different time points at different life cycle stages and compare levels of expression of orthologous genes in these two organisms. ArrayExpress Release Date: 2011-02-08 Person Roles: submitter Person Last Name: Service Person First Name: Submission Person Mid Initials: Person Email: datahose@sanger.ac.uk Person Phone: Person Address: The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom Person Affiliation: Wellcome Trust Sanger Institute Person Roles: Investigator Person Last Name: Reid Person First Name: Adam Person Mid Initials: Person Email: ar11@sanger.ac.uk Person Phone: 01223 834244 Person Address: Wellcome Trust Genome Campus,Hinxton,Cambridge. CB10 1SA UK Person Affiliation: Wellcome Trust Sanger Institute Person Roles: Project Coordinator Person Last Name: Sanders Person First Name: Mandy Person Mid Initials: J Person Email: mjs@sanger.ac.uk Person Phone: 01223 834244 Person Address: Wellcome Trust Genome Campus,Hinxton,Cambridge. CB10 1SA UK Person Affiliation: Wellcome Trust Sanger Institute
2011-07-14 | GSE30614 | GEO
Project description:To investigate the changes in molecular expression, biological processes, stemness, immune microenvironment, tumor hallmark activities and co-expression relationships during intestinal-type gastric cancer carcinogenesis and to excavate the prognostic information contained in the carcinogenesis process. RNA expression profiles of ninety-four gastroscope biopsy samples with different stages of precancerous lesions or early gastric cancers and their paired controls were detected by Agilent Microarray.
2020-03-15 | GSE130823 | GEO
Project description:RNA sequencong of 9 upper GI gastric biopsies and resected gastric tissues
2017-04-18 | GSE80388 | GEO
Project description:The expression profiles of normal gastric mucosa were described by advanced technology such as SWATH and RNA-seq.
2018-07-25 | PXD047977 | iProX
Project description:Gastric cancer is the most common cancer in Asia and most developing countries. To identify the molecular underpinnings of gastric cancer in the Asian population, we applied an RNA-sequencing approach to gastric tumor and noncancerous specimens to quantitatively characterize the entire transcriptome of gastric cancer (including mRNAs and microRNAs). A multi-layer analysis was then developed to identify multiple types of transcriptional aberrations associated with different stages of gastric cancer, including differentially expressed mRNAs, recurrent somatic mutations and key differentially expressed microRNAs. Through this approach, we identified the central metabolic regulator AMPK-M-NM-1 as a potential functional target in Asian gastric cancer. Further, we experimentally demonstrated the translational relevance of this gene as a potential therapeutic target for early-stage gastric cancer in Asian patients. Together, our findings not only provide a valuable information resource for identifying and elucidating the molecular mechanisms of Asian gastric cancer, but also represent a general integrative framework to develop more effective therapeutic targets. Using Life Technologies SOLiDM-bM-^DM-" sequencing platform, we performed transcriptome-wide profiling of gastric cancer samples from 30 anonymous, unrelated Asians of both sexes. Included were six noncancerous gastric tissue samples and 24 gastric tumor samples that represented stages I through IV of tumor development. From the WT-seq protocol we generated a WT-seq dataset of 2.1 billion 50-nt short reads from the 30 samples; Applying the second small RNA-seq protocol to 19 gastric tumor samples (5 of the original 24 yielded insufficient sample amounts) and 6 noncancerous gastric tissue samples resulted in a small RNA-seq dataset.
2012-04-03 | E-GEOD-36968 | biostudies-arrayexpress