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Please use this identifier to cite or link to this item: http://hdl.handle.net/11667/97
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dc.contributorAnderson, Craig-
dc.contributor.otherNERC - Natural Environment Research Councilen_GB
dc.coverage.spatialUnited Kingdomen_GB
dc.coverage.temporal2011-2017en_GB
dc.creatorAnderson, Craig-
dc.creatorKille, Peter-
dc.creatorSpurgeon, David-
dc.creatorCunha, Luis-
dc.creatorSechi, Pierfrancesco-
dc.date.accessioned2017-08-03T15:45:17Z-
dc.date.available2017-08-03T15:45:17Z-
dc.date.created2017-
dc.identifier.urihttp://hdl.handle.net/11667/97-
dc.description.abstractThe data represent RADseq data derived from individual Lumbricus rubellus earthworms that were sampled on contaminated former mine sites or nearby, proximal control sites. Specifically, a plink file in BED format contains the SNPs used to perform all analyses, while the version of the lineage B genome is also included. Finally RAW RADseq data is included, which is in FASTQ format.en_GB
dc.description.tableofcontentsFile “lrubellus_lineageb.fa.gz” is the reference genome for Lumbricus rubellus, derived from a single individual from lineage B. The genome for this work was assembled using sequence data derived from Illumina fastq reads and has been submitted to NCBI under bioproject SUB2807407. Professor Pete Kille (kille@cf.ac.uk) at Cardiff University is the PI directing this work and any future enquiries regarding further questions should be directed to him. The archive “lrubellus_snps.zip” contains the 219,545 SNPs derived from the analysis of RADseq data, in plink bed format. Site specific data incorporates abbreviations described below followed by a "C" or an "M", representing a control and a mine site, respectively. Earthworms were sampled in 2010 from three UK sites with known histories of metal pollution as well as a local control site with low soil metal concentrations. The three sites were Devon Great Consols (DGC, n=40), a former As and Cu mine in Devon, South West England; Carrock Fell (CF, n=29) an As and W mine located on the edge of the Lakes District of North West England, and also from Cwmystwyth (CWM, n=59), which is a former Pb mine located in Mid-Wales. Individuals included are listed in Supplementary Table S4 of the BMC Genetics paper. The remaining 6 compressed folders contain: Raw fastq format, paired-end sequences from RAD-sequencing of Lumbricus rubellus earthworms inhabiting contaminated former mine spoil across the UK, as well as from proximal control sites. File names consist of the acronym for a specific site, followed by a terminal initial associating those individuals with the mine (M) or control (C) soils.en_GB
dc.language.isoengen_GB
dc.publisherUniversity of Stirling. Faculty of Natural Sciencesen_GB
dc.relationAnderson, C; Kille, P; Spurgeon, D; Cunha, L; Sechi, P (2017): Raw RADseq data and down-stream SNPs from British Lumbricus rubellus, including the draft Lineage B reference genome. University of Stirling. Faculty of Natural Sciences. Dataset. http://hdl.handle.net/11667/97en_GB
dc.relation.isreferencedbyAnderson, C., Cunha, L., Sechi, P., Kille, P. and Spurgeon, D. (2017) Genetic variation in populations of the earthworm, Lumbricus rubellus, across contaminated mine sites. BMC Genetics, 18:97. DOI: https://doi.org/10.1186/s12863-017-0557-8 Available from: http://hdl.handle.net/1893/26181en_GB
dc.rightsRights covered by the standard CC-BY 4.0 licence: https://creativecommons.org/licenses/by/4.0/en_GB
dc.subjectRADseqen_GB
dc.subject.classification::Genetics and development::Population Genetics/Evolutionen_GB
dc.subject.classification::Animal science::Animal organisms::Invertebratesen_GB
dc.subject.classification::Pollution, waste and resources::Ecotoxicologyen_GB
dc.titleRaw RADseq data and down-stream SNPs from British Lumbricus rubellus, including the draft Lineage B reference genomeen_GB
dc.title.alternativeData from the paper: Genetic Variation in Populations of the Earthworm, Lumbricus rubellus, Across Contaminated Mine Sitesen_GB
dc.typedataseten_GB
dc.contributor.emailcraig.anderson@stir.ac.uken_GB
dc.identifier.projectidNE/G523571/1en_GB
dc.title.projectMechanistic bases of metal tolerance: linking phenotype to genotypeen_GB
dc.contributor.affiliationUniversity of Stirling (Biological and Environmental Sciences)en_GB
dc.contributor.affiliationCardiff Universityen_GB
dc.contributor.affiliationCentre of Ecology and Hydrologyen_GB
dc.contributor.affiliationLyndhurst Gardensen_GB
dc.date.publicationyear2017en_GB
Appears in Collections:University of Stirling Research Data

Files in This Item:
File Description SizeFormat 
lrubellus_lineageb.fa.gzThis is a gzipped fasta file (*.fa.gz). It is a standardised format for reporting nucleotide sequences for which no single piece of software is responsible285.87 MBUnknownView/Open
lrubellus_snps.zipThis data can be manipulated using the core software, PLINK v1.902.63 MBUnknownView/Open
DGCC.tar3.19 GBUnknownView/Open
DGCM.tar2.1 GBUnknownView/Open
CFM.tar1.41 GBUnknownView/Open
CFC.tar718.8 MBUnknownView/Open
CWMM.tar4.87 GBUnknownView/Open
CWMC.tar5.77 GBUnknownView/Open


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