|
| Status |
Public on Nov 30, 2015 |
| Title |
STS135.F66 Space Shuttle 135 study |
| Sample type |
SRA |
| |
|
| Source name |
feces
|
| Organism |
mouse gut metagenome |
| Characteristics |
strain: C57BL/6
radiation: Mixed space radiation
diet: AEM
microgravity: Microgravity
|
| Treatment protocol |
Radiation, diet, microgravity
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Total DNA was isolated from fecal samples using Qiagen's protocol
Initial amplification of the V1-V2 region of the bacterial 16S rDNA was performed on total DNA isolated from fecal samples. Each sample was individually gel purified using the E-Gel Electrophoresis System. To ensure equal representation of each sample in the sequencing run, each barcoded sample was standardized by calculating equimolar amounts prior to pooling. Pooled samples of the 16S rDNA multiplexed amplicons were sequenced on a Roche 454 Genome Sequencer FLX Titanium instrument using the GS FLX Titanium XLR70 sequencing reagents and protocols.
|
| |
|
| Library strategy |
OTHER |
| Library source |
metagenomic |
| Library selection |
other |
| Instrument model |
454 GS FLX Titanium |
| |
|
| Description |
Space Shuttle 135 study
table.from_biom_w_taxonomyJSCSTS
|
| Data processing |
454 Life Sciences GS Data Analysis Software package using standard parameters
The combined raw sequencing data were de-multiplexed and filtered by QIIME
Data were denoised using Denoiser software
Sequences were grouped into OTUs at a 97% level to approximate species-level phylotypes using Uclust
Supplementary_files_format_and_content: Text file containing taxonomy classification and abundances from biom
|
| |
|
| Submission date |
May 11, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Nancy D. Turner |
| E-mail(s) |
n-turner@tamu.edu
|
| Organization name |
Texas A&M University
|
| Department |
Nutrition & Food Science
|
| Street address |
2253 TAMU
|
| City |
College Station |
| State/province |
TX |
| ZIP/Postal code |
77843-2253 |
| Country |
USA |
| |
|
| Platform ID |
GPL26358 |
| Series (1) |
| GSE68738 |
Space environmental factor impacts upon murine colon microbiota and mucosal homeostasis |
|
| Relations |
| BioSample |
SAMN03652383 |
| SRA |
SRX1023435 |
