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DataSTORRE: Stirling Online Repository for Research Data.
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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. Faculty of Natural Sciences. Dataset. http://hdl.handle.net/11667/97 |
| Publisher: | University of Stirling. Faculty 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 (Biological and Environmental Sciences) Cardiff University Centre of Ecology and Hydrology Lyndhurst Gardens |
Files in This Item:
| File | Description | Size | Format | |
|---|---|---|---|---|
| lrubellus_lineageb.fa.gz | This is a gzipped fasta file (*.fa.gz). It is a standardised format for reporting nucleotide sequences for which no single piece of software is responsible | 285.87 MB | Unknown | View/Open |
| lrubellus_snps.zip | This data can be manipulated using the core software, PLINK v1.90 | 2.63 MB | Unknown | View/Open |
| DGCC.tar | 3.19 GB | Unknown | View/Open | |
| DGCM.tar | 2.1 GB | Unknown | View/Open | |
| CFM.tar | 1.41 GB | Unknown | View/Open | |
| CFC.tar | 718.8 MB | Unknown | View/Open | |
| CWMM.tar | 4.87 GB | Unknown | View/Open | |
| CWMC.tar | 5.77 GB | Unknown | View/Open |
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