title: FE11.Py.28
organism: soil metagenome
description: soil sample under the fallowing soil characteristics (land-use, environmant, geographical coordinates, provided on this datasheet)
attributes.tag: CaCO3
attributes.value: 47.5
attributes.tag: ENA-FIRST-PUBLIC
attributes.value: 2015-03-11T17:01:48Z
attributes.tag: ENA-LAST-UPDATE
attributes.value: 2018-03-09T12:41:54Z
attributes.tag: External Id
attributes.value: SAMEA3220661
attributes.tag: INSDC center name
attributes.value: INRA-CMSE
attributes.tag: INSDC first public
attributes.value: 2015-03-11T17:01:48Z
attributes.tag: INSDC last update
attributes.value: 2018-03-09T12:41:54Z
attributes.tag: INSDC status
attributes.value: public
attributes.tag: Land-use_cluster
attributes.value: Min. Tillage
attributes.tag: Submitter Id
attributes.value: FE11.Py.28
attributes.tag: collection date
attributes.value: 2011-09-26
attributes.tag: current land use
attributes.value: Culture
attributes.tag: depth
attributes.value: 0.2
attributes.tag: environment (biome)
attributes.value: temperate grasslands
attributes.tag: environment (feature)
attributes.value: field soil
attributes.tag: environment (material)
attributes.value: calcisol
attributes.tag: geographic location (country and/or sea)
attributes.value: France
attributes.tag: geographic location (elevation)
attributes.value: 243
attributes.tag: geographic location (latitude)
attributes.value: 5.04495
attributes.tag: geographic location (longitude)
attributes.value: 47.23036
attributes.tag: investigation type
attributes.value: metagenome
attributes.tag: multiplex identifiers
attributes.value: CATCGAGCAG
attributes.tag: nucleic acid extraction
attributes.value: DNA was extracted using a procedure slightly modified, developed by the GenoSol platform for application in large-scale soil surveys (Terrat et al., 2012). Briefly, in a 15 ml Falcon tube 1 g of each soil sample was mixed with 4 ml of a solution containing 100 mM Tris (pH 8.0), 100 mM EDTA (pH 8.0), 100 mM NaCl, and 2% (wt/vol) sodium dodecylsulphate. 2 g of 100 µm diameter silica beads, 2.5 g of 1.4 mm diameter ceramic beads and 4 glass beads of 4 mm diameter were added to the mixture. The samples were then homogenized for 3 x 30 s at 4 m sec-1 in a FastPrep®-24 (MP-Biomedicals, NY, USA) and incubated for 30 min at 70°C before centrifugation at 7000 x g for 5 min at 20°C. For the deproteination, 1 ml of the collected supernatants was incubated for 10 min on ice with 1/10 volume of 3 M potassium acetate (pH 5.5) and centrifuged at 14000 x g for 5 min. Finally, after precipitation with one volume of ice-cold isopropanol, the nucleic acids were washed with 70% ethanol. For purification, DNA extracts were loaded onto PVPP (polyvinyl polypyrrolidone) minicolumns (BIORAD, Marne la Coquette, France) and centrifuged at 1000 x g for 2 min at 10°C. The collected eluate was then purified with the Geneclean Turbo (Q Biogene®, IllKirch, France).
attributes.tag: pcr conditions
attributes.value: 5ng of DNA were used for a 25�l 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: 8.21
attributes.tag: project name
attributes.value: FENAY_landscape_bacterial_biodiversity
attributes.tag: sample name
attributes.value: FE11.Py.28
attributes.tag: sample weight for DNA extraction
attributes.value: 1
attributes.tag: scientific_name
attributes.value: soil metagenome
attributes.tag: sequencing method
attributes.value: pyrosequencing
attributes.tag: soil environmental package
attributes.value: soil
attributes.tag: storage conditions (fresh/frozen/other)
attributes.value: freeze-dried
attributes.tag: target gene
attributes.value: 16S rRNA gene
attributes.tag: texture
attributes.value: 9.6/53.7/36.7
attributes.tag: total n
attributes.value: 1.56
attributes.tag: total organic carbon
attributes.value: 15.9