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Sample GSM2577018 Query DataSets for GSM2577018
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

Supplementary file Size Download File type/resource
GSM2577018_Consortium_A_Genus_composition.xlsx 10.7 Kb (ftp)(http) XLSX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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