SAMN35889935
External Id
Helios Fachklinik Vogelsang Gommern
INSDC center name
2023-06-24T00:00:00Z
INSDC first public
2023-06-24T14:01:13.163Z
INSDC last update
SRS18056362
INSDC secondary accession
live
INSDC status
Metagenome or environmental
NCBI submission model
Metagenome.environmental.1.0
NCBI submission package
SRS18056362
SRA accession
2017-09-06T06:00:00Z
collection_date
DNA of the stool sample of patient MetS_06 was extracted and 16S, 18S, and ITS metagenome analysis was performed; tag sequences: 16S w/o; 18S: GCAAGAT; ITS: GCAAGAT
description
Germany: Berlin
geo_loc_name
Homo sapiens
host
feces
isolation_source
52.52 N 13.40 E
lat_lon
human gut metagenome
http://purl.obolibrary.org/obo/NCBITaxon_408170
organism
J. Clin. Med. 2023, 12, accepted
ref_biomaterial
immediately frozen at -70°C, stored at -20°C
samp_collect_device
collected on the ward; frozen at -70°C and stored at -20°C; Complete homogenization by mortaring in liquid nitrogen; DNA extraction with Quick-DNATM Fecal/Soil Microbe Miniprep Kit (Catalog No. D6010, Zymo Research, Brühl, Germany); quantified using with Qubit dsDNA HS (High-Sensitivity) Assay Kit (Thermo Fisher Scientific); 100ng amplified for 16S-, ITS- or 18S- amplicons (core primer Sequences; 16S Primer fw: ACCGCGGCTGCTGGCAC; 16S Primer rev: AGAGTTTGATCMTGGCTCAG; ITS Primer fw: GTCCCTGCCCTTTGTACAC; ITS Primer rev: CCTGGTTAGTTTCTTTTCCTCCGC; 18S Primer fw: AACCTGGTTGATCCTGCCAGT; 18S Primer rev: CTACGAGCTTTTTAACTGCAACAACTTTAATATACGC; Amplification: preincubation at 98°C for 5min, 30 cycles; denaturation: 94°C for 30sec, annealing cycle 1-5: 56°C; cycle 6-30: 65°C for 30sec; elongation 72°C for 60sec; final step: 72°C for 10min. Purification with Ampure-Beads, normalized via Sequelprep-Plates (Thermo Fisher Scientific); ligated to Illumina compatible adapter sequences with a NEB DNA LibraryPrep-Kit. Sequencing: MiSeq instrument with Illumina MiSeq Reagent Kit v3 600-cycle MS-102-3003; read1 and read2: 300 bases.
samp_mat_process
≈2 to 5g
samp_size
stool sample of patient MetS_06 with metabolic syndrom after breaking the fast
title