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Study

Study Name: Simulated microbial communities from University of Calgary, Alberta, Canada

Projects

Biosamples

Organisms

Biosamples: 10 Seq. Projects: 10
STUDY INFORMATION
GOLD Study ID Gs0141988
Study Name Simulated microbial communities from University of Calgary, Alberta, Canada
Other Names
NCBI Umbrella Bioproject Name Mock community metagenomes and 16S rRNA amplicons
NCBI Umbrella Bioproject ID 383919
SRA Studies
SRA Study Id ERP021973  (Link to NCBI )
Study Title Quantification of mock microbial communities with metagenomes, 16S rRNA gene amplicons and metaproteomics
Study Abstract In this study we compared methods for quantifying taxonomic composition of microbial communities. The compared methods included metagenomics, 16S rRNA amplicon sequencing and metaproteomics. This ENA study contains the metagenomic and the 16S rRNA amplicon data. The metaproteomic data is available from ProteomeXchange via the PRIDE repository(PXD006118). For the comparison of the methods we analyzed three types of mock communities with all three methods. The communities contain between 28 to 32 species and strains of bacteria, archaea, eukaryotes and bacteriophage. For each community type 4 biological replicate communities were generated. All four replicates were analyzed by 16S rRNA sequencing. Three replicates of each community type were analyzed with metagenomics. The "C" type communities have same cell/phage particle number for all community members (C1 to C4). The "P" type communities have the same protein content for all community members (P1 to P4). The "U" (uneven) type communities cover a large range of protein amounts and cell numbers (U1 to U4). The 16S rRNA libraries were sequenced twice in independent runs. The prefixes "rep1_" and "rep2_" indicate the two individual runs. The 16S rRNA read files without prefix are rep1 and rep2 merged.
  
Legacy ER Study ID
Legacy GOLD ID
Added By xiaoli dong on 2019-03-18
Last Modified By Galina Ovchinnikova on 2020-04-27
PI
Description Quantification of mock microbial communities with metagenomes, 16S rRNA gene amplicons and metaproteomics
Relevance
Study Information Link
Study Information Visibility Public
Metagenomic Study Yes
Publication
Is GEBA No
Is HMP No
ECOSYSTEM CLASSIFICATION
Ecosystem Engineered
Ecosystem Category Modeled
Ecosystem Type Simulated communities (microbial mixture)
Ecosystem Subtype Unclassified
Specific Ecosystem Unclassified
STUDY COMPOSITION
Number of Biosamples 10
Number of Organisms 0
Number of Seq Projects 10
Number of Analysis Projects 8
Number of Related Studies 0

 

 

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