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SRX702636: GSM1506170: S253; human gut metagenome; OTHER
1 LS454 (454 GS Junior) run: 9,622 spots, 5.2M bases, 10.6Mb downloads

Submitted by: NCBI (GEO)
Study: Analysis of gastric microbiota by pyrosequencing in Korea
show Abstracthide 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). Overall design: 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.
Sample: S253
SAMN03071918 • SRS702410 • All experiments • All runs
Library:
Instrument: 454 GS Junior
Strategy: OTHER
Source: GENOMIC
Selection: other
Layout: SINGLE
Construction protocol: Two pieces of gastric mucosa and gastric juice (500 ul) were excised and subjected to bacterial genomic DNA (gDNA) extraction using a commercial kit (iNtRON Biotechnology, Gyeonggi, Korea). Briefly, the tissues were treated with lysozyme at 37°C for 15 min and lysed with a buffer containing proteinase K and RNase A at 65°C for 15 min. The lysates were subsequently mixed with binding buffer and the gDNA was purified using resin columns. PCR amplification was performed using primers targeting the V1 to V3 regions of the 16S rRNA gene with extracted DNA. For bacterial amplification, barcoded primer of 9F (5'-CCTATCCCCTGTGTGCCTTGGCAGTC-TCAG-AC-AGAGTTTGATCMTGGCTCAG-3'; underlined sequence indicates the target region primer) and 541R (5'-CCATCTCATCCCTGCGTGTCTCCGAC-TCAG-X-AC-ATTACCGCGGCTGCTGG-3'; 'X' indicates the unique barcode for each subject). Pyrosequencing was performed on GS Junior Sequencing system; Chunlab, Inc., Seoul, Korea.
Experiment attributes:
GEO Accession: GSM1506170
Links:
Runs: 1 run, 9,622 spots, 5.2M bases, 10.6Mb
Run# of Spots# of BasesSizePublished
SRR15769299,6225.2M10.6Mb2014-09-19

ID:
990921

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