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| Status |
Public on Sep 18, 2014 |
| Title |
S957 |
| Sample type |
SRA |
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| Source name |
stomach_uncultured_bacteria
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| Organism |
human gut metagenome |
| Characteristics |
host organism: Human
host tissue: stomach
host tissue subsection: gastric antrum
biopsy type: gastric mucosal biopsy
helicobacter pylori status: HP positive cancer
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| Extracted molecule |
genomic DNA |
| Extraction 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.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
454 GS Junior |
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| Description |
Pyrosequencing
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| Data processing |
Pyrosequencing analysis was conducted according to the methods described in the previous studies (Hur M, Kim Y, Song HR, et al. Effect of genetically modified poplars on soil microbial communities during the phytoremediation of waste mine tailings. Appl Environ Microbiol 2011;77:7611-9.).
Any reads containing two or more ambiguous nucleotides, reads with low quality score (average score < 25), or reads shorter than 300 base pairs, were discarded. Potential chimeric sequences were detected by the Bellerophon method, which compares the BLASTN search results between the forward half and reverse half sequences.
The taxonomic classification of each read was assigned against the EzTaxon-e database (http://eztaxon-e.ezbiocloud.net), which contains the 16S rRNA gene sequence of type strains that have valid published names and representative species level phylotypes of either cultured or uncultured entries in GenBank public database with complete hierarchical taxonomic classification from the phylum to the species.
The species richness of samples was determined by the abundance-based coverage estimator (ACE), Chao1 estimator and Jackknife estimator. In addition, Simpson diversity index, Shannon diversity index, and Good's library coverage were calculated in the CLcommunity program (Chunlab Inc., Seoul, Korea).
Random subsampling was conducted to equalize the read size of samples for comparing different read sizes among samples. To compare the operational taxonomic units (OTUs) between samples, shared OTUs were obtained with the XOR analysis of the CLcommunity program.
Genome_build: EzTaxon-e database (http://eztaxon-e.ezbiocloud.net)
Supplementary_files_format_and_content: tab-delimited text files include ‘microbial phylotypes classification’ for each sample
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| Submission date |
Sep 17, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Jung Min Kim |
| E-mail(s) |
jmkim2010@korea.com
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| Phone |
82-10-3459-4776
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| Organization name |
NAR Center, Inc. & Genoplan, Inc.
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| Department |
Department of Health Genomics
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| Lab |
Genetics & Genomics
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| Street address |
Gangnam-gu Teheran-ro 216
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| City |
Seoul |
| ZIP/Postal code |
06221 |
| Country |
South Korea |
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| Platform ID |
GPL20020 |
| Series (1) |
| GSE61493 |
Analysis of gastric microbiota by pyrosequencing in Korea |
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| Relations |
| BioSample |
SAMN03071966 |
| SRA |
SRX702655 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1506189_S957.txt.gz |
2.9 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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