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: 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).
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.
Project description:For the identification of miRNA biomarker of pancreatic cancer, total RNA containing miRNA was extracted from the serum samples using Affymetrix miRNA 4.0 and the serum miRNA purification kit (Genolution, Seoul, Korea)
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.
Project description:Gene expression profiles were examined in whole lung tissue collected from male and female Long-Evans rats at different time points after inoculation with Seoul virus (i.e., the species-specific hantavirus that infects Norway rats); We used microarray analyses to analyze global gene expression differences between the sexes during hantavirus infection Experiment Overall Design: Gonadally-intact male and female rats were inoculated with 10^4 pfu of Seoul virus (strain SR-11) and lung samples were collected 0, 3, 15, and 40 days post-inoculation (p.i.) to assess gene expression patterns during the acute (i.e., days 3-15 p.i.) and persistent (i.e., day 40 p.i.) phases of infection
Project description:This study is designed to understand whether Pravastatin (Pra) treatment alters the transcriptome of small intestine after radiation injury. RNA was extracted from 15 Gy abdominal irradiated Gottingen minipigs with PS treatment. A cDNA library was generated using a TruSeq Stranded mRNA sample prep kit (Illumina, San Diego, CA), and transcriptome sequencing was performed using a TruSeq 3000/4000 SBS kit and Illumina sequencer with 101 bp paired-end reads per sample (Macrogen, Seoul, Korea).