|
| Status |
Public on May 06, 2024 |
| Title |
WT_MouseNo_1 |
| Sample type |
SRA |
| |
|
| Source name |
Fecal
|
| Organism |
feces metagenome |
| Characteristics |
genotype: WT
host: mouse
host tissue: feces
|
| Growth protocol |
TCRb-/- mice were freshly ordered from the Jackson laboratory
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Feces were collected and DNA was extracted by QIAGEN Power Fecal Pro DNA Kit following manufacturer's instruction.
mWGS DNA library was constructed using TruSeq DNA Library Prep Kit under manufacturer's instruction for metagenomic whole-genome shotgun sequencing (mWGS)
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Raw fastq files were first filtered by fastp (v0.22.0) to trim and remove sequencing adapters as well as low quality bases and reads.
Trimmed fastq files were then aligned to mm10 (UCSC) with bowtie2(v2.5.2) under default parameters.Reads that cannot aligned to mouse genome were extracted by samtools (v1.18)
Clean fastq files were analyzed by Kraken2 (v2.0.7-beta) software using Standard PlusPF (release 1/12/2024) database downloaded from index zone (https://benlangmead.github.io/aws-indexes/k2).
Assembly: mm10
Assembly: Kraken 2 / Bracken Refseq index
Supplementary files format and content: Table separated files containing taxonomy counts of each sample.
Supplementary files format and content: Table separated files containing KEGG orthology gene counts of each sample.
Library strategy: metagenome sequencing
|
| |
|
| Submission date |
Mar 25, 2024 |
| 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 |
GPL33160 |
| Series (1) |
| GSE262397 |
mWGS analysis of the fecal microbiota of WT and TCRb-/- mice |
|
| Relations |
| BioSample |
SAMN40603457 |
| SRA |
SRX24044158 |
