Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Analysis of gastric microbiota by pyrosequencing in Korea

ABSTRACT: 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: Nayoung Kim, 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).

ORGANISM(S): human gut metagenome

PROVIDER: GSE61493 | GEO | 2014/09/18

SECONDARY ACCESSION(S): PRJNA261299

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Analysis of gastric microbiota by pyrosequencing in Korea

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

microRNA expressions in gastric cancer

Project description:The study was undertaken to identify microRNAs differently expressed by intestinal type of gastric cancer using miRNA microarray. The miRNA expression in the intestinal type of gastric cancer depending on H. pylori infection suggest that different gastric cancer pathogenesis could be exist between H. pylori-positive and -negative gastric cancer. Total RNA was extracted from cancerous region and non-cancerous regions in formalin fixed paraffin embedded tissues of intestinal type gastric cancer patients who were H. pylori-positive (n=8) or -negative (n=8). Corresponding author: Nayoung Kim, M.D., Department of Internal Medicine, Seoul National University Bundang Hospital (Tel., +82-31-787-7008; e-mail, nayoungkim49@empas.com).

2014-01-25 | E-GEOD-54397 | biostudies-arrayexpress

Transcriptomic analyses for the CSC-like properties under monolayer and sphere culture conditions in 293T and MCF-7 cells

Project description:In order to verify the CSC-like properties in 3D spheres of 293T cells as compared to monolayer, MCF-7 breast cancer cells under monolayer and sphere culture conditions were used as a control. Corresponding author: Chul Geun Kim, Department of Life Science, Hanyang University, Seoul 133-791, Korea (e-mail, cgkim@hanyang.ac.kr).

2016-10-12 | GSE86896 | GEO

Transcriptome sequencing for cancer stem cell properties in MCF-7 cells with knocked down CD24

Project description:CD24 is the one of cell surface protein that anchored via glycosyl phosphatidylinositol that links to cell surface and modulates growth and differentiation signal many of cell types. A small population of cells, namely ‘Cancer Stem Cells (CSCs)’, charges highly aggressive and metastatic character of cancer cells and shows conformational change of ‘epithelial to mesenchymal transition (EMT). To understand the role of CD24 in CSC and EMT, CD24 was knocked down using siRNA in the MCF7 cell line (MCF-7 hCD24 KD) and analyzed transcriptome profiles by mRNA-sequencing. Corresponding author: Chul Geun Kim, Department of Life Science, Hanyang University, Seoul 133-791, Korea (e-mail, cgkim@hanyang.ac.kr).

2014-10-15 | GSE61917 | GEO

Transcriptome sequencing for cancer stem cell properties in MCF-7 cells with knocked down CD24

Project description:CD24 is the one of cell surface protein that anchored via glycosyl phosphatidylinositol that links to cell surface and modulates growth and differentiation signal many of cell types. A small population of cells, namely M-bM-^@M-^XCancer Stem Cells (CSCs)M-bM-^@M-^Y, charges highly aggressive and metastatic character of cancer cells and shows conformational change of M-bM-^@M-^Xepithelial to mesenchymal transition (EMT). To understand the role of CD24 in CSC and EMT, CD24 was knocked down using siRNA in the MCF7 cell line (MCF-7 hCD24 KD) and analyzed transcriptome profiles by mRNA-sequencing. Corresponding author: Chul Geun Kim, Department of Life Science, Hanyang University, Seoul 133-791, Korea (e-mail, cgkim@hanyang.ac.kr). mRNA profiles of MCF-7 hCD24 KD cells [M-bM-^@M-^Xmonolayer (m) cultured MCF7 wild type (WT) and mMCF7 CD24KDM-bM-^@M-^Y and M-bM-^@M-^Xsphere-forming (s) MCF7 WT and sMCF7 CD24KDM-bM-^@M-^Y] were generated by deep sequencing using Illumina GAIIx.

2014-10-15 | E-GEOD-61917 | biostudies-arrayexpress

Genome-wide analysis of gene expression in human embryonic stem cells (hESCs) and their differentiated cells

Project description:In order to investigate the gene expression changes in human embryonic stem cells (hESCs) during differentiation, we performed a microarray analysis from RNAs isolated from undifferentiated hESCs and their differentiated cells incubated for 1 week or 2 weeks in ESC medium. Human SNUhES3 ESCs (Seoul National University Hospital, Seoul, Korea) were cultured on mitotically-arrested STO feeder cells (ATCC, Manassas, USA) in DMEM/F12 supplemented with 20% knockout serum replacement (KSR). The embryoid bodies were incubated for 1 or 2 weeks in the above ESC medium without bFGF. Cells were then lysed and RNA was isolated.

2012-12-31 | E-GEOD-36255 | biostudies-arrayexpress

Analysis of gene expression patterns of arabidopsis whitening mutant wn1 and wild-type

Project description:This data analyzes gene expression patterns in Arabidopsis whitening mutants, wn1, with defects in chloroplast development. We found that wn1 was a T-DNA insertion line of Arabidopsis AtPTAC10/PAP3 (At3g48500) and exhibited a lethal, albino-like phenotype in the seedling stages. pTAC10 was known as a component of RNA polymerase complex called plastid-encoded RNA polymerase, PEP, in mature chloroplasts. Because wn1 mutants were lethal, we extracted RNA from cotyledons of 7-day-old seedlings from wn1 mutants and Col-0. RNA seq analysis was commissioned by NICEM in Seoul National University, Korea and transcriptome resequencing was confirmed in Macrogen, Korea. Through analysis, we compared gene expression patterns of wn1 mutant and Col-0 seedlings.

2017-04-02 | GSE90159 | GEO

Transcription profiling of mouse parthenogenetic embryonic stem cells and normal embryos to investigate imprinting

Project description:To identify the imprinting loci, we designed microarray analysis on the parthenogenetic embryonic stem cells and normal embryos. We could predict 217 imprinting domains associated with embryo development and maternal imprinting. Experiment Overall Design: Five embryonic stem (ES) cell lines were derived from two F1 hybrid strains that were produced by mating female C57BL6 mice with male DBA2 or CBA/Ca mice. Two-week-old prepubertal female was used for follicle retrieval. All procedures for animal management, breeding, and surgery followed the standard protocols of Seoul National University, Korea. The Institutional Animal Care and Use Committee Review Board at Seoul National University approved our research proposal in April 2005 (approval number: SNU0050331-02). Three parthonogenetic ES embryo cell lines were established from parthenogenetic activation on naturally ovulated oocytes (OpB6D2-SNU-1) and in vitro-growth oocytes (FpB6CBA-SNU8 and FpB6D2-SNU2). Two normal ES embryo cell lines were derived from mating naturally ovulated female mice in estrus with male mice (NmB6D2-SNU-1) and purchased from ATCC. Detailed procedures, including establishment of ES cell lines can be found elsewhere (FpB6CBA-SNU8, FpB6D2-SNU2 and OpB6D2-SNU-1 for and NmB6D2-SNU-1 and OP1 for manuscript in preparation).

2009-01-14 | E-GEOD-10776 | biostudies-arrayexpress

Comprehensive molecular classification for adenocarcinoma of gastroesophageal junction between esophageal and gastric adenocarcinomas

Project description:Background and aims: The aim of this study was to analyze the molecular characteristics of adenocarcinoma of the gastroesophageal junction (AGEJ) compared to esophageal (EAC) and gastric adenocarcinomas (GCFB) from The Cancer Genome Atlas (TCGA) and Seoul National University (SNU) cohorts using next-generation sequencing. Methods: Based on mRNA expression of EAC (n=78) and GCFB (n=102) from the TCGA cohort, a molecular classification model using the Bayesian compound covariate predictor classified AGEJ/cardia (n=48) from the TCGA cohort and AGEJ/upper third gastric adenocarcinoma (n=46) from the SNU cohort into the EAC-like or GCFB-like groups. The molecular characteristics between the EAC-like and GCFB-like groups were compared.

2022-02-06 | GSE126304 | GEO

Comprehensive transcriptomic profiling of glioblastoma patient-derived primary tumor cell lines using bulk RNA-sequencing

Project description:Glioblastoma multiforme (GBM) is a highly aggressive primary brain cancer with significant transcriptomic heterogeneity among patients. Our study aims to contribute to the field of personalized medicine for GBM patients by providing comprehensive transcriptomic profiles of GBM patients (N = 45) who underwent concurrent chemoradiotherapy with temozolomide at Seoul National University Hospital. Additionally, we include transcriptomic profiles of normal brain tissue obtained from GBM patients. This dataset may add depth to existing knowledge by uncovering distinct transcriptomic signatures related to aggressiveness in GBM, and may inform future research on the molecular mechanisms underlying transcriptomic features of GBM and personalized treatment strategies.

2024-04-14 | GSE263588 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data