|
| Status |
Public on May 31, 2024 |
| Title |
Colon tissue, model_1, rep2 |
| Sample type |
SRA |
| |
|
| Source name |
WT C57BL/6J with DSS water
|
| Organism |
mouse gut metagenome |
| Characteristics |
tissue: Colon
disease state: induced acute colitis
strain: C57BL/6J
treatment: normal saline
|
| Treatment protocol |
Mice were randomly divided into 6 groups with 10 mice per group: the untreated normal control, model group, low-dose MG group (50 mg/kg), medium-dose MG group (100 mg/kg), high-dose MG group (200 mg/kg) and SASP-positive group (500 mg/kg) that were orally administered once daily for 6 days.
|
| Growth protocol |
Acute colitis was induced in mice via administration of 2.5% (w/v) DSS in drinking water. Mice received either regular drinking water (normal group) or 2.5% DSS drinking water (model group and treatment groups) for 8 days followed by regular drinking water for 6 days.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
the E.Z.N.A.® Soil DNA Kit (Omega Bio-Tek, Norcross, GA, USA) was used to extract the total genomic DNA from the colon.
The RNA-seq transcriptome library was prepared following the TruSeqTM RNA Sample Preparation Kit from Illumina using 1 μg of total RNA
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
DNA concentrations were quantified by a Nanodrop spectrophotometer (Thermo Scientific Inc., Waltham, MA, USA), and the purity was tested on 1% agarose gel
Qualified samples were subsequently amplified the hypervariable region V3-V4 of the bacterial 16S rRNA gene with the primer pairs 338F (5’-ACTCCTACGGGAGGCAGCA-3’) and 806R (5’-GGACTACHVGGGTWTCTAAT-3’) by an ABI GeneAmp® 9700 PCR thermocycler
Following that, the samples were sequenced on an Illumina MiSeq PE300 platform
Operational taxonomic units (OTUs) clustering was identified at 97% sequence identity
The similarity among the microbial communities in different samples was determined by principal coordinate analysis (PCoA) based on Bray‒Curtis
The PERMANOVA test was used to assess the percentage of variation explained by the treatment along with its statistical significance using Vegan v2.5-3 package
The linear discriminant analysis (LDA) effect size (LEfSe) was performed to identify the significantly abundant taxa (phylum to genera) of bacteria among the different groups
Library strategy: 16S rRNA seq
|
| |
|
| Submission date |
Oct 24, 2022 |
| Last update date |
May 31, 2024 |
| Contact name |
Lai Jia |
| E-mail(s) |
laijiazoe@126.com
|
| Organization name |
Southwest Medical University
|
| Street address |
Xianglin Road
|
| City |
Luzhou |
| ZIP/Postal code |
646000 |
| Country |
China |
| |
|
| Platform ID |
GPL32553 |
| Series (2) |
| GSE216433 |
Methyl Gallate Alleviates Acute Ulcerative Colitis by Modulating Gut Microbiota and Inhibiting TLR4/NF-κB Pathway [16S] |
| GSE216435 |
Methyl Gallate Alleviates Acute Ulcerative Colitis by Modulating Gut Microbiota and Inhibiting TLR4/NF-κB Pathway |
|
| Relations |
| BioSample |
SAMN31428229 |
| SRA |
SRX18014855 |
