Data from: 16S rRNA amplicon sequencing for epidemiological surveys of bacteria in wildlife

Galan M, Razzauti M, Bard E, Bernard M, Brouat C, Charbonnel N, Dehne-Garcia A, Loiseau A, Tatard C, Tamisier L, Vayssier-Taussat M, Vignes H, Cosson J

Date Published: July 19, 2016

DOI: http://dx.doi.org/10.5061/dryad.m3p7d

 

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Title Informations concerning the samples and positive and negative controls multiplexed in the two MiSeq runs
Description This XLSX file contains the run names, the sample IDs, the sample types, the PCR IDs, the PCR replicate numbers, the localities, the rodent species and the fastq file names for each of the 1560 PCR products multiplexed in the two Illumina MiSeq runs.
Download Table_of_the_samples_and_fastq_informaions.xlsx (145.0 Kb)
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Title MiSeq raw sequences (Run 1) of the V4 region 16S rRNA gene from the spleens of 355 murinae from Senegal and 21 positive and negative controls (part 1 to 4)
Description This ZIP file contains the FASTQ files of the paired-end reads (R1: reads 1; R2: reads 2) produced for each individual in duplicate or triplicate using the MiSeq platform (Run 1). The 823 multiplexed PCR products were indexed using both forward and reverse indices. The list of the 355 multiplexed samples and the 21 positive and negative controls are provided in the following XLSX file titled: Information concerning the samples multiplexed in the MiSeq Run 1 & 2.
Download MiSeq_Reads_16Sv4_Murinae_Run1_part1.zip (977.6 Mb)
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Title MiSeq raw sequences (Run 1) of the V4 region 16S rRNA gene from the spleens of 355 murinae from Senegal and 21 positive and negative controls (part 2 to 4)
Description This ZIP file contains the FASTQ files of the paired-end reads (R1: reads 1; R2: reads 2) produced for each individual in duplicate or triplicate using the MiSeq platform (Run 1). The 823 multiplexed PCR products were indexed using both forward and reverse indices. The list of the 355 multiplexed samples and the 21 positive and negative controls are provided in the following XLSX file titled: Information concerning the samples multiplexed in the MiSeq Run 1 & 2.
Download MiSeq_Reads_16Sv4_Murinae_Run1_part2.zip (893.8 Mb)
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Title MiSeq raw sequences (Run 1) of the V4 region 16S rRNA gene from the spleens of 355 murinae from Senegal and 21 positive and negative controls (part 3 to 4)
Description This ZIP file contains the FASTQ files of the paired-end reads (R1: reads 1; R2: reads 2) produced for each individual in duplicate or triplicate using the MiSeq platform (Run 1). The 823 multiplexed PCR products were indexed using both forward and reverse indices. The list of the 355 multiplexed samples and the 21 positive and negative controls are provided in the following XLSX file titled: Information concerning the samples multiplexed in the MiSeq Run 1 & 2.
Download MiSeq_Reads_16Sv4_Murinae_Run1_part3.zip (988.5 Mb)
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Title MiSeq raw sequences (Run 1) of the V4 region 16S rRNA gene from the spleens of 355 murinae from Senegal and 21 positive and negative controls (part 4 to 4)
Description This ZIP file contains the FASTQ files of the paired-end reads (R1: reads 1; R2: reads 2) produced for each individual in duplicate or triplicate using the MiSeq platform (Run 1). The 823 multiplexed PCR products were indexed using both forward and reverse indices. The list of the 355 multiplexed samples and the 21 positive and negative controls are provided in the following XLSX file titled: Information concerning the samples multiplexed in the MiSeq Run 1 & 2.
Download MiSeq_Reads_16Sv4_Murinae_Run1_part4.zip (794.8 Mb)
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Title MiSeq raw sequences (Run 2) of the V4 region 16S rRNA gene from the spleens of 348 murinae from Senegal and 26 positive and negative controls (part 1 to 3)
Description This ZIP file contains the FASTQ files of the paired-end reads (R1: reads 1; R2: reads 2) produced for each individual in duplicate using the MiSeq platform (Run 2). The 746 multiplexed PCR products were indexed using both forward and reverse indices. The list of the 355 multiplexed samples and the 26 positive and negative controls are provided in the following XLSX file titled: Information concerning the samples multiplexed in the MiSeq Run 1 & 2.
Download MiSeq_Reads_16Sv4_Murinae_Run2_part1.zip (761.0 Mb)
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Title MiSeq raw sequences (Run 2) of the V4 region 16S rRNA gene from the spleens of 348 murinae from Senegal and 26 positive and negative controls (part 2 to 3)
Description This ZIP file contains the FASTQ files of the paired-end reads (R1: reads 1; R2: reads 2) produced for each individual in duplicate using the MiSeq platform (Run 2). The 746 multiplexed PCR products were indexed using both forward and reverse indices. The list of the 355 multiplexed samples and the 26 positive and negative controls are provided in the following XLSX file titled: Information concerning the samples multiplexed in the MiSeq Run 1 & 2.
Download MiSeq_Reads_16Sv4_Murinae_Run2_part2.zip (790.2 Mb)
Details View File Details
Title MiSeq raw sequences (Run 2) of the V4 region 16S rRNA gene from the spleens of 348 murinae from Senegal and 26 positive and negative controls (part 3 to 3)
Description This ZIP file contains the FASTQ files of the paired-end reads (R1: reads 1; R2: reads 2) produced for each individual in duplicate using the MiSeq platform (Run 2). The 746 multiplexed PCR products were indexed using both forward and reverse indices. The list of the 355 multiplexed samples and the 26 positive and negative controls are provided in the following XLSX file titled: Information concerning the samples multiplexed in the MiSeq Run 1 & 2
Download MiSeq_Reads_16Sv4_Murinae_Run2_part3.zip (720.2 Mb)
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Title Raw output files generated by the mothur program
Description This ZIP file contains seven output files (.groups, .names, .table, .taxonomy, .list, .fasta and .log) generated by the mothur program for the whole 16S rRNA dataset. The .log file contains all the mothur command lines used for the processing of the raw sequences.
Download mothur_raw_output_files.zip (250.9 Mb)
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Title OTU table of raw abundance
Description This XLSX file contains the number of reads obtained for the Operational Taxonomic Units (OTU ≥ 100 reads due to file size limits for Excel) of the two MiSeq runs and each PCR product before the data filtering.
Download Table_of_abundance.xlsx (7.378 Mb)
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Title Table of presence and absence for the twelve pathogenic OTUs in the 704 analysed rodents
Description This XLSX file shows the presence (1) or absence (0) for the twelve pathogenic OTUs in the spleen of the 704 analysed rodents after the data filtering.
Download Table_of_presence_absence.xlsx (92.19 Kb)
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Title Sequence alignment file of the 16S rRNA PCR primers and 41,113 sequences from 79 bacterial zoonotic genera
Description This FASTA file contains 41,113 sequences of the V4 hypervariable region from 79 bacterial zoonotic genera extracted from the Silva SSU database v119, and the forward and reverse primers used in our 16S rRNA amplicon sequencing experiment.
Download 16Sv4_primers_and_zoonotic_genera.fasta (73.44 Mb)
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Title Perl script for the extraction of the most abundant sequences for each OTU and each sample
Description This ZIP file contains a script called GOMS: Get OTU Main Sequence. GOMS is a Perl program based on mothur files. It thus requiers several files from mothur (http://www.mothur.org/wiki/454_SOP or http://www.mothur.org/wiki/MiSeq_SOP): .list file, .names file, .groups file and .fasta file. The user must also provide the number of the OTU and the treshold used to form the OTUs. GOMS generates a fasta file with, for each sample, the highly representative sequence of a given OTU, meaning the unique sequence which has the most important number of copies. Some information are also provided within the fasta file like the number of sequences and unique sequences assigned to the OTU and the number of copies of the main unique sequence.
Download README.TXT (3.263 Kb)
Download GOMS.zip (6.753 Kb)
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Title Sequence alignment files of the V4 hypervariable region of the 16S rRNA used for the phylogenetic analysis
Description This ZIP file contains the FASTA files of the most abundant sequences from the 12 pathogenic OTUs (Bartonella, Borrelia, Ehrlichia, Orientia, Rickettsia, Streptobacillus and Mycoplasma_OTU_1 to Mycoplasma_OTU_6) and reference sequences from Silva ribosomal database v119 for the same genera.
Download Alignment_files_for_phylogenetic_analysis.zip (11.61 Kb)
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When using this data, please cite the original publication:

Galan M, Razzauti M, Bard E, Bernard M, Brouat C, Charbonnel N, Dehne-Garcia A, Loiseau A, Tatard C, Tamisier L, Vayssier-Taussat M, Vignes H, Cosson J (2016) 16S rRNA amplicon sequencing for epidemiological surveys of bacteria in wildlife. mSystems 1(4): e00032-16. http://dx.doi.org/10.1128/mSystems.00032-16

Additionally, please cite the Dryad data package:

Galan M, Razzauti M, Bard E, Bernard M, Brouat C, Charbonnel N, Dehne-Garcia A, Loiseau A, Tatard C, Tamisier L, Vayssier-Taussat M, Vignes H, Cosson J (2016) Data from: 16S rRNA amplicon sequencing for epidemiological surveys of bacteria in wildlife. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.m3p7d
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