Data from: Host-parasite network structure is associated with community-level immunogenetic diversity

Pilosof S, Fortuna MA, Cosson J, Galan M, Kittipong C, Ribas A, Segal E, Krasnov BR, Morand S, Bascompte J

Date Published: October 20, 2014

DOI: http://dx.doi.org/10.5061/dryad.mq7n0

 

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Title Rodent DRB Alleles from Asia
Downloaded 7 times
Description Dataset of MHC class II DRB exon 2 allele sequences from rodents sampling in Thailand, Laos and Cambodia. The name of alleles include the species ID: Bain for Bandicota indica ; Basa for Bandicota savilei ; Bebe for Berylmys berdmorei ; Bebo for Berylmys bowersi ; Leed for Leopoldamys edwardsi ; Muca for Mus caroli ; Muce for Mus cervicolor ; Muco for Mus cookii ; Raex for Rattus exulans ; Rasa for Rattus sakaratensis ; Rata for Rattus tanezumi ; RaR3 for Rattus tanezumi mitochondrial lineage R3
Download Rodent DRB Alleles from Asia.fas (53.13 Kb)
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Title 454 raw sequences of the MHC class II DRB exon 2 gene from rodents - Run 1
Downloaded 16 times
Description This FASTA file contains 91,467 raw sequences produced using 454 GS-FLX pyrosequencing (first run). The 864 multiplexed amplicons were tagged using both forward and reverse primers. The list of the 864 multiplexed samples and associated tags are provided in the following file: 454_Reads_DRB_Asia_Run1.csv.
Download 454_Reads_DRB_Asia_Run1.fasta (24.61 Mb)
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Title 454 quality scores of the raw sequences of the MHC class II DRB exon 2 gene from rodents - Run 1
Downloaded 6 times
Description This file contains the quality scores for the 91,467 raw sequences produced using 454 GS-FLX pyrosequencing (first run). The 864 multiplexed amplicons were tagged using both forward and reverse primers. The list of the 864 multiplexed samples and associated tags are provided in the following file: 454_Reads_DRB_Asia_Run1.csv.
Download 454_Reads_DRB_Asia_Run1.qual.txt (63.81 Mb)
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Title 454 reads of the MHC class II DRB exon 2 gene from rodents including a correction for the reverse tags - Run 1
Downloaded 2 times
Description This FASTA file contains 91,467 raw sequences produced using 454 GS-FLX pyrosequencing (first run). The 864 multiplexed amplicons were tagged using both forward and reverse primers. The reverse tags forming a homopolymer GG with the "454-Adaptor" sequence were truncated. This file contains the raw sequences corrected (addition of a G at the end of the reads) for the concerned tags. The list of the 864 multiplexed samples and associated tags are provided in the following file: 454_Reads_DRB_Asia_Run1.csv.
Download 454_Reads_DRB_Asia_Run1_G_add_in_Rev_Tags.fasta (25.09 Mb)
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Title Information concerning the samples multiplexed in the 454 Run 1
Downloaded 3 times
Description This SESAME software formatted file contains the sample names, the forward and reverse tag sequences, the forward and reverse primer sequences, the gene name, the species name, the population name and the ploidy level for each of the 864 samples multiplexed in the 454 pyrosequencing run 1.
Download 454_Reads_DRB_Asia_Run1.csv (78.58 Kb)
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Title 454 raw sequences of the MHC class II DRB exon 2 gene from rodents - Run 2
Downloaded 3 times
Description This FASTA file contains 272,975 raw sequences produced using 454 GS-FLX Titanium pyrosequencing (second run). The 864 multiplexed amplicons were tagged using both forward and reverse primers. The list of the 864 multiplexed samples and associated tags are provided in the following file: 454_Reads_DRB_Asia_Run2.csv.
Download 454_Reads_DRB_Asia_Run2.fasta (78.84 Mb)
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Title 454 quality scores of the raw sequences of the MHC class II DRB exon 2 gene from rodents - Run 2
Downloaded 5 times
Description This file contains the quality scores for the 272,975 raw sequences produced using 454 GS-FLX Titanium pyrosequencing (second run). The 864 multiplexed amplicons were tagged using both forward and reverse primers. The list of the 864 multiplexed samples and associated tags are provided in the following file: 454_Reads_DRB_Asia_Run2.csv.
Download 454_Reads_DRB_Asia_Run2.qual (192.0 Mb)
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Title Information concerning the samples multiplexed in the 454 Run 2
Downloaded 4 times
Description This SESAME software formatted file contains the sample names, the forward and reverse tag sequences, the forward and reverse primer sequences, the gene name, the species name, the population name and the ploidy level for each of the 864 samples multiplexed in the 454 pyrosequencing run 2.
Download 454_Reads_DRB_Asia_Run2.csv (88.56 Kb)
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Title 454 standard flowgram format (SFF) file of the raw sequences of the MHC class II DRB exon 2 gene from rodents - Run 2
Downloaded 15 times
Description This SFF file contains the encoded results of each flowgram for the 272,975 raw sequences produced using 454 GS-FLX Titanium pyrosequencing (second run). The 864 multiplexed amplicons were tagged using both forward and reverse primers. Note: The SFF file for the run 1 is not available (not provide by the sequencing company).
Download 454_Reads_DRB_Asia_Run2.sff (671.7 Mb)
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When using this data, please cite the original publication:

Pilosof S, Fortuna MA, Cosson J, Galan M, Kittipong C, Ribas A, Segal E, Krasnov BR, Morand S, Bascompte J (2014) Host-parasite network structure is associated with community-level immunogenetic diversity. Nature Communications 5: 5172. http://dx.doi.org/10.1038/ncomms6172

Additionally, please cite the Dryad data package:

Pilosof S, Fortuna MA, Cosson J, Galan M, Kittipong C, Ribas A, Segal E, Krasnov BR, Morand S, Bascompte J (2014) Data from: Host-parasite network structure is associated with community-level immunogenetic diversity. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.mq7n0
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