SOERE_PRO_2014
soil metagenome
Soil from Colmar, sampled one year after organic waste product apllication
ENA first public
2017-06-01
ENA last update
2016-10-21
External Id
SAMEA4065980
INSDC center alias
INRA-CMSE
INSDC center name
UMR Agroecology, INRA - Burgundy University, Dijon, France
INSDC first public
2017-06-01T17:02:03Z
INSDC last update
2016-10-21T09:34:42Z
INSDC status
public
Submitter Id
B4T1_18S
city
Colmar
collection date
2012-03
common name
SOERE_PRO_2012
depth
0.2
environment (biome)
cropland biome
environment (feature)
microbial feature
environment (material)
arable soil
geographic location (country and/or sea)
France
geographic location (elevation)
175
geographic location (latitude)
48.0833
geographic location (longitude)
7.3667
geographic location (region and locality)
Alsace
history/previous land use
12 years of organic waste application (every 2 years)
horizon
A horizon
investigation type
metagenome
multiplex identifiers
CGATCGTATA
nucleic acid amplification
5ng of DNA were used for a 25µl PCR conducted under the following conditions: initial denaturation: 94degC_3min; 35 cycles of: denaturation: 94degC_1min; annealing: 52degC_1min; elongation: 72degC_1min, final elongation: 72degC_5min. 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.
nucleic acid extraction
DNA was extracted using a procedure slightly modified, developed by the GenoSol platform for application in large-scale soil surveys (Terrat et al., 2012)
organic waste product
Non-composted sewage sludge
pcr conditions
5ng of DNA were used for a 25 µl PCR conducted under the following conditions: initial denaturation:94degC_3.0min;35 cycles of denaturation:94degC_0.5min;annealing:52degC_1.0min;elongation:72degC_1.0min;final elongation:72degC_5.0min
pcr primers
FR1:5'-ANCCATTCAATCGGTANT-3';FF390:5'-CGATAACGAACGAGACCT-3'
project name
SOERE_PRO_2014
sample name
B4T1_18S
sample volume or weight for DNA extraction
1
sequencing method
Illumina
soil environmental package
soil
target gene
16S rRNA gene