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| Status |
Public on Aug 30, 2023 |
| Title |
A2 |
| Sample type |
SRA |
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| Source name |
Human feces
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| Organism |
human feces metagenome |
| Characteristics |
tissue: Fecal
diagnosis: Moderate-OSA
treatment: No
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| Treatment protocol |
One gram of fresh fecal samples was collected in a sterile fecal tube on the first day after admission and were immediately stored in the -20℃ refrigerator of the department, then sent to the -80℃ refrigerator of the central laboratory of Nanfang Hospital for cold storage within 4 hours by the researchers.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Bead beading isolation was done to extract genomic DNA using the QIAamp DNA Kit (QIAGEN, Hilden, Germany), following the manufacturer's protocol. The extracted DNA concentration was measured by Qubit 2.0 Fluorometer (Life Technology, Carlsbad, CA). DNA quality was detected by 1.0% agarose gel electrophoresis. Then, the 16S rDNA gene regions (V3 and V4) were amplified by PCR.
The 16S rDNA libraries were sequenced on the Illumina MiSeq platform PE300 mode (Illumina, USA)
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina MiSeq |
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| Data processing |
Sequencing data were filtered to remove low-quality sequences.Sequence splicing was performed using FLASH (Fast Length Adjustment of Short reads, V1.2.11)
Remove the primer sequence from the Tags sequence using the software CUTADAPT (version 1.16).
Using UCHIME method in VSEARCH(V2.3.4) software and combined with Gold Database (V20110519) chimera database to remove chimera sequences to get high-quality Tags sequence.
The software VSEARCH (V2.3.4) was used to cluster high-quality Tags sequence into OTU, and the REPRESENTATIVE sequence of OTU was obtained.
Using RDP Classifer (V2.2) software combined with Silva (V128) database, species annotation was performed for OTU representative sequences.
Based on 16S data, Alpha(α) diversity index (Observed OTU richness and Shannon Diversity) and Beta(β) diversity index based on Principal Coordinate Analysis (PCoA) (unweighted-Unifrac distance, Adonis) was used to assess the differences between groups. Linear discriminant analysis (LDA) and LDA Effective Size (LEfSe) was used to assess the taxonomic differences among groups.The network was then utilized to present the relationship between intestinal microbiome, intestinal barrier biomarkers, and AHI (Cytoscape v3.7.2). Statistical analysis of data was conducted in SPSS (version 21.0) and R software (v3.5.1).
Genome_build: 16S rDNA Sequences were aggregated into operational taxonomic units (OTUs) using 97% identity of the Silva v128 database
Supplementary_files_format_and_content: ConnectTags_stat.txt
Supplementary_files_format_and_content: OTU_table_for_biom.txt
Supplementary_files_format_and_content: Genus.absolute_abundance.txt
Supplementary_files_format_and_content: Alpha_diversity_detail.txt
Supplementary_files_format_and_content: unweighted_unifrac_Beta_diversity.txt
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| Submission date |
Aug 01, 2021 |
| Last update date |
Aug 30, 2023 |
| Contact name |
Qianjun Li |
| E-mail(s) |
qqjun8@yeah.net, qqjun8@163.com
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| Phone |
13777221353
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| Organization name |
Nanfang Hospital, Southern Medical University
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| Department |
Sleep Medicine Center
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| Street address |
No. 1838, North Guangzhou Avenue
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| City |
Guangzhou |
| State/province |
Guangdong |
| ZIP/Postal code |
510515 |
| Country |
China |
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| Platform ID |
GPL29470 |
| Series (1) |
| GSE181270 |
Obstructive sleep apnea is related to alterations in intestinal microbiome and impaired intestinal barrier function |
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| Relations |
| BioSample |
SAMN20515137 |
| SRA |
SRX11623672 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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