|
| Status |
Public on Apr 12, 2022 |
| Title |
AL-V2 |
| Sample type |
SRA |
| |
|
| Source name |
AL-V_microbial genomic DNA from cecum content
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
age: 6-8 weeks old
treatment: 10 days of ad libitum food co-treated with vancomycin in the drinking water (AL-V)
tissue/molecule: microbial genomic DNA from cecum content
|
| Treatment protocol |
Mice (6-8 weeks) underwent following procedures: a) 10 days of ad libitum food supply b) 10 days of intermittent fasting c) 10 days of ad libitum food co-treated with vancomycin in the drinking water (50mg/kg/day; 214.27 mg/l) d) 10 days of intermittent fasting food cotreated with vancomycin in the drinking water
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cecum content was collected from mice and immediately frozen in liquid nitrogen. Samples were stored at -80 °C. Faecal DNA was extracted using Fast DNA spin kit (MP Biomedicals).
Libraries were prepared using the 16S Metagenomic Sequencing Library Preparation protocol for the Illumina MiSeq System. In brief, PCR primers (16S Amplicon PCR Forward Primer = 5' TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGCCTACGGGNGGCWGCAG; 16S Amplicon PCR Reverse Primer = 5' GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGGACTACHVGGGTATCTAATCC) directed at the V3/V4 region of bacterial rRNA genes were used to generate libraries and libraries were validated by the Agilent 2100 Bioanalyzer. Sequencing was performed with 250 bp paired-end reads on Illumina Miseq2500
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
AL-V2_S18_L001
|
| Data processing |
Primers were trimmed off demultiplexed R1 sequence reads using cutadapt v1.18.
Reads were processed via the DADA2 pipeline using the following parameters for filtering and trimming: truncLen=125, maxN=0, maxEE=2, truncQ=2, rm.phix=TRUE, compress=TRUE, verbose = TRUE, multithread=FALSE.
Errors were estimated, samples variants were inferred and chimeras were removed from the data to yield an amplicon sequence variant (ASV) table and taxonomy was assigned using the SILVA reference database (v132).
Data was further processed in phyloseq (v1.26.1) for alpha and beta diversity as well as relative abundance investigations. Data was not normalised for alpha diversity (results are identical to using rarefied data) but was normalised by log transformation with a pseudo-count of +1 for beta diversity. Alpha diversity was calculated as Shannon index and visualised as a box plot. Beta diversity was calculated by Bray-Curtis dissimilarity and visualised in a PCoA plot. Statistical significance of beta diversity was calculated by PERMANOVA and variance calculated by betadisper function in the vegan package (v2.5-5). Data was agglomerated by taxa level and plotted as relative abundance bar charts.
Differential abundance was estimated using DESeq2 package (v1.22.2). Output tables are ASVs that attain statistically significant differences between groups that were compared. Alpha was set at p = 0.05. P adjustment method = Benjamini-Hochberg FDR.
Supplementary_files_format_and_content: DESeq2 output
|
| |
|
| Submission date |
Dec 07, 2020 |
| Last update date |
Apr 12, 2022 |
| Contact name |
Elisabeth Serger |
| E-mail(s) |
e.serger16@imperial.ac.uk
|
| Phone |
07803362113
|
| Organization name |
Imperial College London
|
| Department |
Brain Sciences
|
| Lab |
Simone Di Giovanni
|
| Street address |
Du Cane Road
|
| City |
London |
| State/province |
London |
| ZIP/Postal code |
W12 0NN |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL16417 |
| Series (1) |
| GSE162763 |
16S sequencing of mouse gut microbial DNA after 10 days of intermittent fasting or ad libitum with and without vancomycin treatment |
|
| Relations |
| BioSample |
SAMN17015027 |
| SRA |
SRX9640798 |
