Data from: Landscape-scale distribution patterns of earthworms inferred from soil DNA

Pansu J, De Danieli S, Puissant J, Gonzalez J, Gielly L, Cordonnier T, Zinger L, Brun J, Choler P, Taberlet P, Cécillon L

Date Published: February 13, 2015

DOI: http://dx.doi.org/10.5061/dryad.27qf3

 

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Title Pansu_et_al_SBB_ewDE_sequence_data_alternative_sampling
Downloaded 15 times
Description This fasta file contains merged reads assigned to their original sample obtained with the alternative soil sampling scheme covering the entire plot surface. Amplicons were amplified using ewDE primers (ewD: 5’- ATTCGGTTGGGGCGACC-3’ and ewE: 5’- CTGTTATCCCTAAGGTAGCTT-3’) (Bienert et al., 2012). Sequences were obtained by a 2 x 100 bp paired-end sequencing on Illumina HiSeq platform. First filtering steps were performed using the OBITOOLS software (http://metabarcoding.org/obitools) following the data filtering description in supplementary material (Pansu et al., 2015 Soil Biology and Biochemistry). Direct and reverse reads corresponding to the same sequence were aligned and merged thanks to the IlluminaPairEnd program. Only merged sequences with a high alignment quality score were retained (>=40). Then, the ngsfilter program assigned each merged sequence to its original sample using the tags information previously added to primers. Only sequences containing both primers (with a maximum of 3 mismatches per primer) and exact tag sequences were selected. Sequences containing ambiguous nucleotides or shorter than 55 bp were discarded. Strictly identical sequences were merged together while keeping information about the origin of sequences. Strict singletons (i.e. sequences occurring only once in the dataset) were removed.
Download ewDE_vercors_alternative_sampling.fasta (46.76 Mb)
Download README (2.168 Kb)
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Title Pansu_et_al_SBB_ewDE_sequence_data_subplots_sampling
Downloaded 36 times
Description This fasta file contains merged reads assigned to their original sample obtained with the subplots soil sampling scheme. Amplicons were amplified using ewDE primers (ewD: 5’- ATTCGGTTGGGGCGACC-3’ and ewE: 5’- CTGTTATCCCTAAGGTAGCTT-3’) (Bienert et al., 2012). Sequences were obtained by a 2 x 100 bp paired-end sequencing on Illumina HiSeq platform. First filtering steps were performed using the OBITOOLS software (http://metabarcoding.org/obitools) following the data filtering description in supplementary material (Pansu et al., 2015 Soil Biology and Biochemistry). Direct and reverse reads corresponding to the same sequence were aligned and merged thanks to the IlluminaPairEnd program. Only merged sequences with a high alignment quality score were retained (>=40). Then, the ngsfilter program assigned each merged sequence to its original sample using the tags information previously added to primers. Only sequences containing both primers (with a maximum of 3 mismatches per primer) and exact tag sequences were selected. Sequences containing ambiguous nucleotides or shorter than 55 bp were discarded. Strictly identical sequences were merged together while keeping information about the origin of sequences. Strict singletons (i.e. sequences occurring only once in the dataset) were removed.
Download README (2.104 Kb)
Download ewDE_vercors_subplots_sampling.fasta.zip (15.30 Mb)
Details View File Details

When using this data, please cite the original publication:

Pansu J, De Danieli S, Puissant J, Gonzalez J, Gielly L, Cordonnier T, Zinger L, Brun J, Choler P, Taberlet P, Cécillon L (2015) Landscape-scale distribution patterns of earthworms inferred from soil DNA. Soil Biology and Biochemistry 83: 100–105. http://dx.doi.org/10.1016/j.soilbio.2015.01.004

Additionally, please cite the Dryad data package:

Pansu J, De Danieli S, Puissant J, Gonzalez J, Gielly L, Cordonnier T, Zinger L, Brun J, Choler P, Taberlet P, Cécillon L (2015) Data from: Landscape-scale distribution patterns of earthworms inferred from soil DNA. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.27qf3
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