2024-09-20
ENA first public
ERC000050
ENA-CHECKLIST
EMBL Heidelberg
INSDC center name
public
INSDC status
ERS21065434
SRA accession
spire_mag_02988721
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
2017
collection date
60.52
%
completeness score
checkm2 0.1.3
completeness software
2.61
%
contamination score
This sample represents a Third Party Annotation (TPA) binned metagenome assembled from the metagenomic run SRR12326817 of study SRP273603.
description
stool
environmental medium
not provided
geographic location (country and/or sea)
-33.52000000
DD
geographic location (latitude)
151.20000000
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
The project examines the direct effect of the microbiome on the peripheral immune response in patients with NAFLD-HCC. The project employs shotgun metagenomics and metabolomics to present novel insights to the structure, function and metabolomic capability of the gut microbiome in patients with NAFLD-cirrhosis, with and without HCC compared to healthy controls. Next, we examine in an ex-vivo cell culture model the effect of NAFLD-HCC-associated microbiome and metabolome on the peripheral immune response.
project name
SAMN15589133
sample derived from
Phocaeicola vulgatus
scientific_name
Illumina NovaSeq 6000
sequencing method
multi-marker approach
taxonomic identity marker
binned metagenome: spire_mag_02988721
title