characteristics.text: GSC:MIxS v2.1
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2012-04-17T08:25:43Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: GSC, MIxS, MIMS
characteristics.characteristic: ENA-KEYWORD
characteristics.text: 2018-03-09T09:54:58Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA1317685
characteristics.characteristic: External Id
characteristics.text: United States
characteristics.characteristic: Geographic location (country:region,area)
characteristics.text: Texas A&M University
characteristics.characteristic: INSDC center name
characteristics.text: 2012-04-17T08:25:43Z
characteristics.characteristic: INSDC first public
characteristics.text: 2018-03-09T09:54:58Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS075404
characteristics.characteristic: SRA accession
characteristics.text: BMS 8
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0006612
characteristics.characteristic: Submitter Id
characteristics.text: 3 months
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/UO_0000035
characteristics.characteristic: age
characteristics.text: 250 mg
characteristics.unit: g
characteristics.characteristic: amount or size of sample collected
characteristics.text: EMG
characteristics.characteristic: broker name
characteristics.text: 2007
characteristics.characteristic: collection date
characteristics.text: Stool sample from a 3 month old baby whose diet was only breast milk from birth. Genomic DNA was extracted using a modification of the method of Yu and Morrison. Deviation from the protocol included the use of glass beater steps. Briefly, 250 mg (wet weight) of feces was weighed into a 2 mL tube containing glass matrix E (MP Biomedicals, Solon, OH). One mL of lysis buffer (500 mM NaCl, 50 mM Tris-HCl, 50 mM EDTA, 4% sodium dodecyl sulfate) was added to the tube and shaken for 30 sec. Samples were then incubated at 70°C for 15 min. After centrifugation at 16,000 g for 5 min, supernatants were collected into 2.0 mL tubes. Lysis buffer (300 µL) was subsequently added and the above steps were repeated. Nucleic acids in the supernatant were precipitated sequentially with ammonium acetate and isopropanol, and dissolved in TE buffer. The precipitated nucleic acids were then treated with DNase-free RNase, proteinase K, and further purified on a QIAamp spin column from QIAgen DNA Mini Stool Kit (Qiagen, Valencia, CA). DNA quality was checked on a 1% agarose gel following ethidium bromide staining. DNA from 3 to 4 extractions per sample were pooled and concentration quantified on a NanoDrop 1000 spectrophotometer (NanoDrop Technologies, Wilmington DE).
characteristics.characteristic: description
characteristics.text: breast milk
characteristics.characteristic: diet
characteristics.text: human-gut
characteristics.characteristic: enviornmental package
characteristics.text: human gut
characteristics.characteristic: environment (biome)
characteristics.text: human-associated habitat
characteristics.characteristic: environment (featurel)
characteristics.text: feces
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/NCIT_C13234
characteristics.characteristic: environment (material)
characteristics.text: MIMS
characteristics.characteristic: investigation type
characteristics.text: human gut metagenome
characteristics.characteristic: organism
characteristics.text: Baby microbiome
characteristics.characteristic: project name
characteristics.text: human gut metagenome
characteristics.characteristic: scientific_name
characteristics.text: Pyrosequencing
characteristics.characteristic: sequencing method
characteristics.text: Female
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/PATO_0000383
characteristics.characteristic: sex
characteristics.characteristic: title