characteristics.text: 2024-01-01
characteristics.characteristic: ENA first public
characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: Oxford Centre for Microbiome Studies, Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics Rheumatology Musculoskeletal Sciences
characteristics.characteristic: INSDC center name
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS19832834
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-14061:PartID_5_24
characteristics.characteristic: Submitter Id
characteristics.text: ArrayExpress
characteristics.characteristic: broker name
characteristics.text: not collected
characteristics.characteristic: collection date
characteristics.text: Protocols: Study participants received a sample collection kit with instructions (manuscript supplementary section 2) and a collection tube with >99% ethanol for fixed faecal sample collection and storage. Sample collection kit provided by Oxford Centre for Microbiome Studies Faecal samples were extracted manually using the QIAamp PowerFecal Pro DNA kit (Qiagen, 51804) according to the manufacturer’s instructions. Sample homogenization in PowerBead tubes was performed using a Qiagen Vortex adapter coupled to a Vortex Genie 2 for 20 minutes at maximum speed. Initial DNA quantification was performed on a NanoDrop (Thermo Scientific) and DNA concentration was adjusted to within the desired mass range for sequencing and plated on a 96 well, low profile, skirted PCR plate (4titude) for sequencing submission For bacterial 16S rRNA gene amplicon sequencing, the variable V3 and V4 regions of the 16S rRNA gene were amplified from genomic DNA using the primers (standard IUPAC nucleotide nomenclature): Forward Primer = 5' TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGCCTACGGGNGGCWGCAGTCGTCGGCAGCGTCAGATGTGTATAAGAGACAGCCTACGGGNGGCWGCAG, Reverse Primer = 5’ GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGGACTACHVGGGTATCTAATCC The amplicons were then attached with indices and Illumina sequencing adapters using the Nextera XT index kit. The 16S amplicon libraries were pooled and sequenced in an Illumina MiSeq v3 flowcell as 300 paired end reads
characteristics.characteristic: description
characteristics.text: metabolic disease
characteristics.characteristic: disease
characteristics.text: not collected
characteristics.characteristic: geographic location (country and/or sea)
characteristics.text: not applicable
characteristics.characteristic: isolate
characteristics.text: human gut metagenome
characteristics.characteristic: organism
characteristics.text: human gut metagenome
characteristics.characteristic: organism
characteristics.text: faeces
characteristics.characteristic: organism part
characteristics.text: PartID_5
characteristics.characteristic: participant id
characteristics.text: human gut metagenome
characteristics.characteristic: scientific_name
characteristics.text: WTCHG_946783_71575133
characteristics.characteristic: sequencing id
characteristics.text: PartID_5_24
characteristics.characteristic: title