1c38de04-c8b3-45f5-9058-a8851006ee6a - samples
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00001010166 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:Collagenous gastritis (CG) is a rare disease characterized by thick bands of subepithelial collagen within the stomach and presents with a variety of symptoms ranging from anemia to vomiting. Gastric biopsies were collected from six CG patients, including one patient before and after glucocorticoid steroid treatment, and several matched controls. Single-cell RNA- and T-cell receptor (TCR)-sequencing was performed on gastric biopsies.
2025-11-16 | GSE254513 | GEO
Project description:We combined the tissue preservation and single-cell resolution of laser capture with an improved preamplification procedure enabling RNA sequencing of 10 microdissected cells. This in situ 10-cell RNA sequencing (10cRNA-seq) can exploit fluorescent reporters of cell type in genetically engineered mice and is compatible with freshly cryoembedded clinical biopsies from patients. By using small pools of microdissected cells, 10cRNA-seq thus results in improved per-cell reliability and sensitivity beyond existing approaches for single-cell RNA sequencing (scRNA-seq). Accordingly, in multiple tissue and tumor settings, we observe 1.5–2-fold increases in genes detected and overall alignment rates compared to scRNA-seq. Combined with existing approaches to deconvolve small pools of cells, 10cRNA-seq offers a reliable, unbiased, and sensitive way to measure cell-state heterogeneity in tissues and tumors.
2019-03-24 | GSE120261 | GEO
Project description:This dataset contains bulk RNA sequencing data from primary tumor biopsy samples of patients with prostate adenocarcinoma. TPM-normalized expression values are provided along with sample metadata. The data were generated to support transcriptomic profiling of human prostate tumors and are related to a companion single-cell RNA-seq dataset from the same cohort.
2025-11-19 | GSE297742 | GEO
Project description: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.
2019-07-20 | GSE134520 | GEO
Project description:Sequencing of 16S ribosomal RNA (rRNA) gene, which has improved the characterization of microbial community, has made it possible to detect a low level Helicobacter pylori (HP) sequences even in HP-negative subjects which were determined by a combination of conventional methods. This study was conducted to obtain a cutoff value for HP colonization in gastric mucosa biopsies and gastric juices by the pyrosequencing method. Corresponding author: Department of Internal Medicine, Seoul National University Bundang Hospital, Seoungnam, Gyeonggi-do, Korea; Department of Internal Medicine and Liver Research Institute, Seoul National University College of Medicine, Seoul, Korea (Tel., +82-31-787-7008; e-mail, nayoungkim49@empas.com). Microbial DNA from gastric mucosal samples [gastric antrum (n=63, mucosal biopsy), follow-up sample on gastric antrum (n=16, mucosal biopsy), and gastric body (n=18, mucosal biopsy)] and gastric juices (n=4, not mucosal biopsy) was amplified by nested PCR using universal bacterial primers, and the 16S rRNA genes were pyrosequenced.
2014-09-18 | E-GEOD-61493 | biostudies-arrayexpress
Project description:This dataset was applied to evaluate the performance of a deep learning framework, FFPERescuer, specifically designed to reconstruct gene expression profiles from RNA sequencing data derived from FFPE (formalin-fixed, paraffin-embedded) tumor tissues. The dataset includes a total of 12 RNA-Seq samples, comprising 10 FFPE tumor tissue samples from colorectal cancer (CRC) cases collected in Amsterdam, the Netherlands, with 2 duplicate samples included for reproducibility assessment. The corresponding gene expression profiles from fresh-frozen tumor tissues for these 10 cases are available in the dataset GSE33113, generated using microarray technology.
2025-07-31 | GSE299799 | GEO
Project description:RNA Sequencing performed on EBV positive gastric cancer biopsies and cells lines to study expression of EBV specific genes.
2015-07-16 | GSE70513 | GEO
Project description:This dataset contains single-cell RNA sequencing (scRNA-seq) data generated from patients with M1-stage metastatic prostate cancer, comprising two complementary sample types: metastatic lesion biopsies from five patients and peripheral blood mononuclear cells (PBMCs) from seven patients. Together, these datasets support integrated profiling of the metastatic tumor microenvironment and the systemic immune landscape. The processed data include log-normalized gene expression matrices and detailed cell-level metadata, enabling analyses of tumor–immune interactions, circulating immune phenotypes, and molecular features associated with metastatic disease progression. A related bulk RNA-seq dataset from primary tumor biopsies is available (see Related Series: GSE297742), providing opportunities for comparative transcriptomic analyses between primary and metastatic disease states.
2025-11-19 | GSE297652 | GEO
Project description:We have employed whole microRNA microarray with the potential to distinguish H.pylori infection.Among the 470 human miRNAs represented on the array chip, 228 were undetectable or expressed below the background and so were eliminated, leaving 242 miRNAs for the supervised analysis. When comparing 10 H. pylori-negative and nine H. pylori-positive subjects, 55 miRNAs were deemed significantly different on the basis of microRNA arrays. During endoscopy, a biopsy specimen was obtained from the gastric antrum along the lesser curvature. Biopsies of 10 H. pylori-negative and nine H. pylori-positive patients' subjects were performed.Exclusion criteria were: age <18 or >80 y, pregnancy, body mass index (BMI) >30 kg/m2, diabetes mellitus, cachectic state (including cancer), systemic infection, liver disease, renal impairment, use of medications effective against H. pylori during the preceding 3 months, alcohol abuse, drug addiction, and chronic corticosteroid or nonsteroidal anti-inflammatory drug use. None of the subjects had undergone gastrointestinal surgery.
2010-05-16 | E-GEOD-19769 | biostudies-arrayexpress
Project description:Reliable modelling of human stomach development and in vitro derivation of mature subsets of gastric epithelial cells has been challenging to achieve in 3D cultures. We derived fetal gastric organoid cultures from 8-20 post-conception week (PCW) stomachs, and post-natal controls from pediatric biopsies.
2020-10-01 | GSE153698 | GEO