|
| Status |
Public on May 06, 2024 |
| Title |
Mouse8_TCRb_KO_co_housed |
| Sample type |
SRA |
| |
|
| Source name |
MouseNo.8
|
| Organism |
feces metagenome |
| Characteristics |
tissue: Fecal pellets
genotype: TCRb-/-
treatment: co_housed
|
| Treatment protocol |
Self-maintained as above or co-housed for 4 weeks.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Microbial genomic DNA were extracted with a QIAamp DNA Stool Mini Kit (Qiagen, 51504) following the manufacturer’s instructions and eluted into 200 uL ddH2O. DNA was concentrated with a Quick-DNA Microprep Kit (Zymo, D3020).
PCR for V3 and V4 hypervariable regions using barcoded primers. Sequencing adaptor were added to purified PCR product under manufacturers' guide.
DNA library
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina MiSeq |
| |
|
| Data processing |
16S data was trimmed by Cutadapt(v 4.1) and analyzed using QIIME2 (v2018.6). DADA2 procedure with default parameters was used for the pre-processing steps
The alpha and beta diversity analysis were calculated in R by using the phyloseq and microbiome package (http://microbiome.github.com/microbiome).
Differential abundance analysis was performed using Linear discriminant analysis effect size (LEfSe) with an LDA score threshold of > 3.8 and the Kruskal-Wallis test (α < 0.01), and the more stringent ANCOM were used to validate the results.
Assembly: SILVA 128
Supplementary files format and content: rds file containing colony OTU
Library strategy: 16s rRNA-seq
|
| |
|
| Submission date |
Dec 13, 2022 |
| Last update date |
May 06, 2024 |
| Contact name |
Xiaofei Yu |
| E-mail(s) |
xiaofei_yu@fudan.edu.cn
|
| Organization name |
Fudan University
|
| Street address |
2005 Songhu Rd
|
| City |
Shanghai |
| ZIP/Postal code |
200438 |
| Country |
China |
| |
|
| Platform ID |
GPL24116 |
| Series (2) |
| GSE220867 |
16S-seq analysis of the microbiota of WT and TCRb-/- mice |
| GSE220938 |
Hydrogen sulfide produced by the microbiota suppresses GLP-1 production |
|
| Relations |
| BioSample |
SAMN32193261 |
| SRA |
SRX18675039 |
