|
| Status |
Public on May 01, 2018 |
| Title |
SDIMO gene sequencing of Consortium B Before Enrichment |
| Sample type |
SRA |
| |
|
| Source name |
Bacterial consortium
|
| Organism |
1,4-dioxane-degrading enrichment culture |
| Characteristics |
function: degrade 1,4-dioxane
strain: Bacterial Consortium B
molecule subtype: SDIMO gene PCR product
carbon source: 1,4-dioxane
|
| Growth protocol |
AMS medium amended with 1,4-dioxane as the sole carbon source
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Ultra clean Microbial DNA extraction kit (MO BIO)
Illumina DNA library for Miseq
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
PCR product produced using genomic DNA as the template
|
| Data processing |
Remove the barcodes, primers and short sequences<150bp
Remove ambigous base calls
Denoise sequences
Define Operational Taxonomic Units(OUT):97% similarity
Classify OTUs Using BLASTn against NCBI, GreenGenes, RDPII databases
Supplementary_files_format_and_content: Excel file, the genus level percentage of the bacteria contained in each consortium; the predominance of SDIMOs in each consortium
|
| |
|
| Submission date |
Jul 10, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Ya He |
| E-mail(s) |
yh38@rice.edu
|
| Phone |
8329752665
|
| Organization name |
Rice University
|
| Department |
Department of Civil and Environmental Engineering
|
| Street address |
6100 MAIN ST, MS-519
|
| City |
Houston |
| State/province |
Texas |
| ZIP/Postal code |
77005 |
| Country |
USA |
| |
|
| Platform ID |
GPL23690 |
| Series (2) |
| GSE97757 |
SDIMO gene analysis of two 1,4-dioxane degrading consortia enriched from uncontaminated soils |
| GSE97758 |
Microbial community and SDIMO analyses of two 1,4-dioxane degrading consortia |
|
| Relations |
| BioSample |
SAMN07340528 |
| SRA |
SRX2994309 |
