2024-09-19
ENA first public
ERC000050
ENA-CHECKLIST
EMBL Heidelberg
INSDC center name
public
INSDC status
ERS21055800
SRA accession
spire_mag_00047496
Submitter Id
Many fragments with little to no review of assembly other than reporting of standard assembly statistics
assembly quality
megahit 1.2.9
assembly software
default
binning parameters
metabat 2.12.1
binning software
human digestive system
broad-scale environmental context
EBI-EMG
broker name
2012
collection date
93.98
%
completeness score
checkm2 0.1.3
completeness software
5.78
%
contamination score
This sample represents a Third Party Annotation (TPA) binned metagenome assembled from the metagenomic run ERR1018214 of study ERP012177.
description
stool
environmental medium
China
geographic location (country and/or sea)
55.67609700
DD
geographic location (latitude)
12.56833700
DD
geographic location (longitude)
metagenome-assembled genome
investigation type
human gut metagenome
isolation_source
human gut
local environmental context
human gut metagenome
metagenomic source
Phocaeicola vulgatus
organism
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.
project name
SAMEA3541498
sample derived from
Phocaeicola vulgatus
scientific_name
Illumina HiSeq 2000
sequencing method
multi-marker approach
taxonomic identity marker
binned metagenome: spire_mag_00047496
title