 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Apr 04, 2023 |
| Title |
severe group 7 |
| Sample type |
SRA |
| |
|
| Source name |
intestinal lavage fluid
|
| Organism |
gut metagenome |
| Characteristics |
tissue: intestinal lavage fluid
group: severe
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Extraction of total genomic DNA through the DNA Extraction Kit (Tiangen Biotechnology Company, Beijing, China) was conducted following the instructions of the kit.
DNA libraries for 16s-rDNA sequencing were prepared using SMARTER DNA-Seq Library Prep Kit following manufacturer's protocols.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina MiSeq |
| |
|
| Data processing |
Using FLASH v1.2.7 software, the reads of each sample are spliced by overlap, and the spliced sequence is the raw Tags.Using Trimmomatic v0.33 software, the Raw Tags obtained by splicing were filtered to obtain high-quality Tags data (Clean Tags)
Using UCLUST in QIIME(version 1.8.0) software to cluster Tags at the similarity level in ninety-seven percent, OTU was obtained, and the OTU was taxonomically annotated based on Silva (bacteria) and UNITE (fungi) taxonomic databases.
Comparing the representative sequence of the OTUs with a microbial reference database to obtain species classification information corresponding to each OTU, and counting the composition of each sample community at each level,
The Alpha diversity index of samples was evaluated using the Mothur (version v.1.30) software. In general, the index of diversity was compared among samples, and the number of sequences contained in samples was standardized for analysis.
The PICRUSt software was used to deduce the functional gene composition in samples by comparing the species composition information obtained from 16S sequencing data, so as to analyze the functional differences between different samples or subgroups.
Assembly: mm10
Library strategy: 16s-rDNA
|
| |
|
| Submission date |
Mar 06, 2023 |
| Last update date |
Apr 04, 2023 |
| Contact name |
Yunjie Shi |
| E-mail(s) |
shiyunpengjie@126.com
|
| Organization name |
Naval Medical University
|
| Street address |
No.800 Xiangyin Road
|
| City |
Shanghai |
| ZIP/Postal code |
200433 |
| Country |
China |
| |
|
| Platform ID |
GPL29420 |
| Series (1) |
| GSE226706 |
Interaction between the microbiome and the severity of diversion colitis after low anterior resection of rectal cancer |
|
| Relations |
| BioSample |
SAMN33598354 |
| SRA |
SRX19577978 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7082421_severe_group_7.xlsx |
11.6 Kb |
(ftp)(http) |
XLSX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
