|
| Status |
Public on Dec 28, 2019 |
| Title |
F22 |
| Sample type |
SRA |
| |
|
| Source name |
Fecal bacteria
|
| Organism |
mouse gut metagenome |
| Characteristics |
host biomaterial_provider: Jackson Laboratory
host sex: Female
host tissue: Fecal
host strain: C57BL/6
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Fecal and cecal samples collected at the time of harvest contents using QIAmp DNA stool Mini Kit (Qiagen, CA) with bead-beating. DNA concentration and quality was measured using Cytation5 (Biotek)
The V3-V5 variable regions of the 16S rDNA were amplified using primers (forward F357: 5’-CCTACGGGAGGCAGCAG-3’ and reverse R926: 5’-CCGTCAATTCMTTTRAGT-3’)
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina MiSeq |
| |
|
| Data processing |
Paired-end reads were generated with the Illumina® MiSeq platform for each sample, at a read length of 250 nucleotides. The reads were demultiplexed and quality-filtered using Trimmomatic (version 0.30) with a Phred score cut-off of 33. Data analysis was performed through the QIIME pipeline (version 1.9.0). Operational taxonomical unit (OTU)-picking was performed by searching the Greengenes 16S rRNA gene database
Genome_build: Greengenes 16S rRNA gene database
Supplementary_files_format_and_content: There microbiome processed files represents the abundance of bacterial genera in each sample by percentage. One file is averaged by the group and the other has the results for every sample.
|
| |
|
| Submission date |
Jan 03, 2017 |
| Last update date |
Dec 28, 2019 |
| Contact name |
Karen Chen |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Illinois at Urbana-Champaign
|
| Department |
Division of Nutritional Sciences
|
| Lab |
ERML 359
|
| Street address |
1201 W Gregory St
|
| City |
Urbana |
| State/province |
IL |
| ZIP/Postal code |
61801 |
| Country |
USA |
| |
|
| Platform ID |
GPL21051 |
| Series (2) |
| GSE93096 |
Bazedoxifene and conjugated estrogen combination improves gut-liver axis health [microbiota] |
| GSE93137 |
Bazedoxifene and conjugated estrogen combination improves gut-liver axis health |
|
| Relations |
| BioSample |
SAMN06203176 |
| SRA |
SRX2463333 |
