Please use this identifier to cite or link to this item: http://hdl.handle.net/11667/97
Appears in Collections:University of Stirling Research Data
Title: Raw RADseq data and down-stream SNPs from British Lumbricus rubellus, including the draft Lineage B reference genome
Other Titles: Data from the paper: Genetic Variation in Populations of the Earthworm, Lumbricus rubellus, Across Contaminated Mine Sites
Creator(s): Anderson, Craig
Kille, Peter
Spurgeon, David
Cunha, Luis
Sechi, Pierfrancesco
Contact Email: craig.anderson@stir.ac.uk
Keywords: RADseq
Date Available: 3-Aug-2017
Citation: Anderson, 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. Dataset. http://hdl.handle.net/11667/97
Publisher: University of Stirling. School of Natural Sciences
Dataset Description (Abstract): The 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.
Dataset Description (TOC): File “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.
Type: dataset
Contract/Grant Title: Mechanistic bases of metal tolerance: linking phenotype to genotype
Funder(s): NERC - Natural Environment Research Council
Contract/Grant Number: NE/G523571/1
Geographic Location(s): United Kingdom
Time Period: 2011-2017
URI: http://hdl.handle.net/11667/97
Rights: Rights covered by the standard CC-BY 4.0 licence: https://creativecommons.org/licenses/by/4.0/
Affiliation(s) of Dataset Creator(s): University of Stirling
Cardiff University
Centre of Ecology and Hydrology
Lyndhurst Gardens
Cardiff University

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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