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Biota

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  • This data is NERC-funded but not held by the EIDC. This data is archived in the NCBI Sequence Read Archive (SRA). The dataset contains unprocessed single cell sequence from hemocytes in Drosophila melanogaster populations highly resistant or highly susceptible to the parasitic wasp Leptopilina boulardi. Wild caught D. melanogaster females were collected from Cambridge, UK, to establish an outbreed population. From this, three replicated populations were selected for resistance to L. boulardi strain NSRef for 26 generations (Selection). Another three populations were maintained in the laboratory for 26 generations without being exposed to parasitoid-associated selection pressures (No Selection). At generation 26, second instar D. melanogaster larvae (48-63 hours after fertilization) from each population were infected with L. boulardi for three hours (Infection) or maintained without infection (No infection). 48 hours after, circulating hemocytes from third instar D. melanogaster larvae (96-111 hours after fertilization) from each population were collected in PBS and cleaned in OptiPrep solution (1.09g/ml). 10X Single Cell GEX v2 libraries were prepared and sequenced. CellRanger v2 was used to generate sample cell count matrices. Seurat v3 was used to integrate, normalise and cluster the cell types.

  • These data represent genomic datasets from LOFRESH project on 'Understanding the ecological relevance of eDNA in freshwater lotic ecosystems' These include metabarcoding datasets consisting of fastq files, forward and reverse reads, produced on an Illumina HiSeq platform. Metabarcoding datasets were produced using 18S, COI, 12S and rbcL multiplexed genetic markers. Also included is a metagenomic dataset consisting of fastq files, forward and reverse reads, produced on an Illumina HiSeq platform. Accession number of bioproject: PRJEB48362 This data is NERC-funded but not held by the EIDC. This data is archived in the European Nucleotide Archive (ENA) which is maintained by EMBL-EBI

  • Agilent gene expression microarrays (Bham Chlamydomonas reinhardtii Agilent-029192 15k v1) were used to profile transcriptional changes afeter exposure of Chlamydomonas reinardtii algae to cerium dioxide nanoparticles. The data are generated from NERC-funding but not held by EIDC. This data is held by ArrayExpress with accession reference E-MTAB-2454.

  • This data is NERC-funded but not held by the EIDC. This data is archived in the National Centre for Biotechnology Information (NCBI), BioProject accession number PRJNA777104. Multi ‘omics’ data were collected from lines of Daphnia magna resurrected from Lake Ring (Denmark). The genome, methylome, transcriptome, accessible chromatin (ATAC), and metabolome was characterized from these lines, spanning >100 years.

  • RNA sequence data (FASTq files) to identify the genes differentially expressed in response to cold in different Drosophila species. This data is NERC-funded but not held by the EIDC. This data is archived by NCBI under the BioProject accession number PRJNA822705 but access may be embargoed

  • The two Bioprojects contain RNA-Seq transcriptome sequences (fastQ files) resulting from studies investigating gene expression in wild field voles (Microtus agrestis). RNA sequences are derived from studies investigating the immune response of voles in relation to sex and genotype. Accession numbers PRJEB23617 and PRJEB51626 This data is NERC-funded but not held by the EIDC. This data is archived in the European Nucleotide Archive (ENA) which is maintained by EMBL-EBI

  • Genotype-by-sequencing and chloroplast genome sequencing were carried out for 192 accessions of wild and landrace wheat accessions. This produced 10 nuclear DNA sequences, each 10-20 kb in length, and one 80 kb chloroplast DNA sequence, from each of 192 accessions of wild or domesticated emmer wheat. NB The data are stored in the European Nucleotide Archive (ENA) with accession number Study PRJEB42105 ena-STUDY-UOM-23-08-2017-14:32:05:787-517 and can be accessed at https://www.ebi.ac.uk/ena/browser/view/PRJEB42105

  • This dataset contains reduced representation sequencing of 549 F2 Silene uniflora individuals from three experimental cross families. The parents for each family were grown from seed and crossed by hand to produce F1 hybrids. From each cross a single individual was then selfed to produce the F2 offspring suitable for linkage mapping which were grown into adult plants. The source locations for the parents for the three crosses were as follows: Priddy pools X Brean down (England); Grogwynion X South Aberystwyth (Wales); Ross Island (Ireland) X South Aberystwyth. Whole genomic DNA was extracted from leaf tissue of the F2 plants. The data are composed of 75bp single-end DNA sequences for each individual generated by the reduced representation SEQSNP library preparation method by LGC. The work was supported by the Natural Environment Research Council NE/R001081/1. This record describes NERC-funded data managed by NCBI Sequence Read Archive (SRA), Accession Number: PRJNA764594.

  • This dataset contains RNA sequencing of 12 Silene uniflora individuals grown under two experimental conditions in deep water culture (control and zinc contaminated). Cuttings from 3 individuals from 4 sites (Priddy pools, Grogwynion, Brean Down and South Aberystwyth) were propagated and grown under experimental conditions for each treatment (see https://doi.org/10.1101/2021.11.30.470425). Root tissue was frozen at -80C, total RNA extracted and sequenced using DNBseq technology. The data are composed of 100bp paired-end DNA sequences for each individual. The work was supported by the Natural Environment Research Council NE/R001081/1. This record describes NERC-funded data managed by NCBI Sequence Read Archive (SRA), Accession Number: PRJNA706929 .

  • The data describe: Genome sequencing of desiccating bdelloid rotifers Population genomics of bdelloid rotifers Comparative genomics of bdelloid rotifers: evaluating the effects of asexuality and desiccation tolerance on genome evolution This data is NERC-funded but not held by the EIDC. This data is archived in the Environmental Nucleotide Archive