Metagenome-assembled genome: ERR1018286_bin.0_CONCOCT_v1.1_MAG
uncultured Collinsella sp.
This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run ERR1018286 of study ERP012177.
ENA-FIRST-PUBLIC
2023-01-03
ENA-LAST-UPDATE
2023-01-03
External Id
SAMEA14083315
INSDC center alias
EBI
INSDC center name
European Bioinformatics Institute
INSDC first public
2023-01-03T00:33:32Z
INSDC last update
2023-01-03T00:33:32Z
INSDC status
public
Submitter Id
ERR1018286_bin.0_CONCOCT_v1.1_MAG
assembly quality
Many fragments with little to no review of assembly other than reporting of standard assembly statistics
assembly software
metaspadesv3.11.1
binning parameters
Default
binning software
CONCOCT v1.1
broker name
EMG broker account, EMBL-EBI
collection date
2012-01-01
completeness score
96.77
completeness software
CheckM
contamination score
8.94
environment (biome)
Host-associated
environment (feature)
Human
environment (material)
Digestive system
geographic location (country and/or sea)
China
geographic location (latitude)
55.676098
geographic location (longitude)
12.568337
investigation type
metagenome-assembled genome
isolation_source
human gut metagenome
metagenomic source
human gut metagenome
project name
We performed a metagenome-wide association study on fecal samples from 74 CRC patients and 54 controls from China and validated the results in 16 patients and 24 controls from Denmark. We further validated the biomarkers in two published cohorts from France and Austria. Finally, we employed targeted quantitative PCR (qPCR) assays to evaluate the diagnostic potential of selected biomarkers in an independent Chinese cohort of 47 patients and 109 controls.
sample derived from
SAMEA3541570
sample name
ERR1018286_bin.0_CONCOCT_v1.1_MAG
scientific_name
uncultured Collinsella sp.
sequencing method
Illumina HiSeq 2000
taxonomic identity marker
multi-marker approach