organism: soil metagenome
attributes.tag: ENA-FIRST-PUBLIC
attributes.value: 2016-06-07T17:01:14Z
attributes.tag: ENA-LAST-UPDATE
attributes.value: 2018-03-09T13:25:05Z
attributes.tag: External Id
attributes.value: SAMEA3444892
attributes.tag: INSDC center name
attributes.value: INRA-CMSE
attributes.tag: INSDC first public
attributes.value: 2016-06-07T17:01:14Z
attributes.tag: INSDC last update
attributes.value: 2018-03-09T13:25:05Z
attributes.tag: INSDC status
attributes.value: public
attributes.tag: Submitter Id
attributes.value: 2010_P8_11_30_16S
attributes.tag: collection date
attributes.value: 2010
attributes.tag: depth
attributes.value: 0.2
attributes.tag: environment (biome)
attributes.value: cropland biome
attributes.tag: environment (feature)
attributes.value: farm
attributes.tag: environment (material)
attributes.value: agricultural soil
attributes.tag: geographic location (country and/or sea)
attributes.value: France
attributes.tag: geographic location (elevation)
attributes.value: 32
attributes.tag: geographic location (latitude)
attributes.value: 49.0166667
attributes.tag: geographic location (longitude)
attributes.value: 2.16666667
attributes.tag: investigation type
attributes.value: mimarks-survey
attributes.tag: multiplex identifiers
attributes.value: MID058
attributes.tag: nucleic acid extraction
attributes.value: This DNA extraction procedure was initially developed and optimized by the GenoSol platform (Terrat et al., 2012). Soil was added to a 15 mL Falcon tube containing 2.5 g of 1.4 mm diameter ceramic beads, 2 g of 106 µm diameter silica beads and and four glass beads of 4 mm diameter. Each soil sample was mixed with a solution of 100 mM Tris-HCl (pH 8), 100 mM EDTA (pH8), 100 mM NaCl, 2% (w/v) and 2% (w/v) sodium dodecyl sulfate. Tubes were then shaken for 3x30 s at 4 m/sec in a FastPrep-24 (MP-Biomedicals, NY, USA) before incubation for 30 min at 70degC and centrifugation at 7,000g for 5 min at 20degC. After removing the supernatant, proteins were precipitated with 1/10 volume of 3 M sodium acetate prior to centrifugation (14,000g for 5 min at 4degC). Finally, nucleic acids were precipitated by adding 1 volume of ice-cold isopropanol. The DNA pellets obtained after centrifugation (14,000g for 5 min at 4degC) were washed with 70% ethanol
attributes.tag: pcr conditions
attributes.value: 5ng of DNA were used for a 25µl PCR conducted under the following conditions: initial denaturation: 94degC_2.0min; 35 cycles of denaturation: 94degC_0.5min;annealing: 52degC_0.5min;elongation: 72degC_1.0min;final elongation: 72degC_7.0min. A second PCR of 9 cycles was then conducted under similar PCR conditions with purified PCR products and ten base pair multiplex identifiers added to the primers at 5' position to specifically identify each sample and avoid PCR biases
attributes.tag: pcr primers
attributes.value: F479:5-CAGCMGCYGCNGTAANAC-3; R888:5-CCGYCAATTCMTTTRAGT-3
attributes.tag: ph
attributes.value: 7.7
attributes.tag: project name
attributes.value: RESACOR
attributes.tag: sample name
attributes.value: 2010_P8_11_30_16S
attributes.tag: sample volume or weight for DNA extraction
attributes.value: 1
attributes.tag: scientific_name
attributes.value: soil metagenome
attributes.tag: sequencing method
attributes.value: 454-Pyrosequencing
attributes.tag: soil environmental package
attributes.value: soil
attributes.tag: target gene
attributes.value: 16S rDNA
attributes.tag: texture
attributes.value: 80/10.9/7.9
attributes.tag: total nitrogen
attributes.value: 1.61
attributes.tag: total organic carbon
attributes.value: 50.4