Data from: Exposing the structure of an Arctic food web

Vesterinen EJ, Wirta HK, Hambäck PA, Weingartner E, Rasmussen C, Reneerkens J, Schmidt NM, Gilg O, Roslin T

Date Published: August 24, 2015

DOI: http://dx.doi.org/10.5061/dryad.cv8cr

 

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Title Raw labeled reads from faecal samples of Calidris alpina, C. alba and Plectrophenax nivalis
Downloaded 1 time
Description Collected while handling the birds or from the field while observing the birds. DNA extracted from individual pellets using Zymo Research Faecal Mini Kit. Sequenced using Ion Torrent PGM. FASTQ file header stands for: @READNUMBER;barcodelabel=SAMPLEID_COLLECTIONLOCALITY_DAY-MONTH-YEAR_BIRDSPECIES_BIRDAGE.
Download README.txt (607 bytes)
Download labeled_reads_birds.fastq (1.036 Gb)
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Title Raw labeled reads from samples of Pardosa glacialis, Xysticus deichmanni, X. labradorensis, Erigone arctica, and Emblyna borealis
Description Collected from the field. DNA extracted from half individuals using Qiagen Animla Tissue Kit. Sequenced using Ion Torrent PGM. FASTQ file header stands for: @READNUMBER;barcodelabel=SAMPLEID. SampleID: Xd =
Download labeled_reads_spiders.fastq (1.989 Gb)
Download README.txt (385 bytes)
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Title OTU sequences
Description Clustered to OTUs using USEARCH algorithm with default (97%) similarity. This way there is a little bit of oversplitting, and OTUs belonging to same biological species are clustered subsequently.
Download label_otus.fa (37.68 Kb)
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Title Readmap linking trimmed reads and samples
Description The readmap shows read count for each sample. The readmap is constructed using USEARCH software.
Download readmap.tab (83.98 Kb)
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Title Technical data sheet for IonTorrent PGM runs
Description The data generated by Ion Torrent PGM for each run in the study.
Download IonTorrent_Data_Sheet.pdf (1.256 Mb)
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Title Command pipeline used for bioinformatics
Description The file contains all the commandds used in this study to generate the final data. The bioinformatics was carried out at servers on CSC - IT Center for SCience in Finland <www.csc.fi>.
Download Arctic_FoobWeb_commands_unix_csc.sh (8.738 Kb)
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Title The final readmap
Downloaded 1 time
Description This readmap contains the final read counts for each sample. The difference to raw readmap is that some OTU's in this version have been clumped together. The information in this sheet was used as presense/absence data in the study.
Download Readmap_final.xlsx (128.9 Kb)
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Title Q20 reads from Spider samples for Spider data2
Description Collected from the field. DNA extracted from half individuals. Sequenced using 454 pyrosequencing.
Download Spider2_data.fas (21.17 Mb)
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Title OTU sequences for Spider data2
Description Clustered to OTUs using USEARCH algorithm with default (97%) similarity. This way there is a little bit of oversplitting, and OTUs belonging to same biological species are clustered subsequently.
Download Spider2_label_otus.fa (74.38 Kb)
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Title Readmap linking trimmed reads and samples for Spider data2
Description The readmap shows read count for each sample. The readmap is constructed using USEARCH software.
Download Spider2_readmap.tab (19.44 Kb)
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Title Command pipeline used for bioinformatics for Spider data2
Description The file contains all the commands used in this study to generate the final data. The bioinformatics was carried out at servers on CSC - IT Center for SCience in Finland <www.csc.fi>.
Download Spider2_commands_unix_csc.sh (3.626 Kb)
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When using this data, please cite the original publication:

Wirta HK, Vesterinen EJ, Hambäck PA, Weingartner E, Rasmussen C, Reneerkens J, Schmidt NM, Gilg O, Roslin T (2015) Exposing the structure of an Arctic food web. Ecology and Evolution 5(17): 3842–3856. http://dx.doi.org/10.1002/ece3.1647

Additionally, please cite the Dryad data package:

Vesterinen EJ, Wirta HK, Hambäck PA, Weingartner E, Rasmussen C, Reneerkens J, Schmidt NM, Gilg O, Roslin T (2015) Data from: Exposing the structure of an Arctic food web. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.cv8cr
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