|
Status |
Public on May 01, 2018 |
Title |
16S rRNA gene sequencing of Consortium A |
Sample type |
SRA |
|
|
Source name |
a 1,4-dioxane degrading consortium
|
Organism |
1,4-dioxane-degrading enrichment culture |
Characteristics |
strain: Bacterial Consortium A carbon source: 1,4-dioxane molecule subtype: 16S rRNA gene PCR product
|
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
|
|
|
Submission date |
Apr 13, 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 |
GPL23311 |
Series (2) |
GSE97756 |
Microbial community analyses of two 1,4-dioxane degrading consortia enriched from uncontaminated soils [16s rRNA] |
GSE97758 |
Microbial community and SDIMO analyses of two 1,4-dioxane degrading consortia |
|
Relations |
SRA |
SRX2734766 |
BioSample |
SAMN06745537 |