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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.

  • 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.

  • Samples were collected from the slurry tank of a 200-cow dairy farm in the East Midlands once per month between June and October 2017 (n=5). Triplicate extractions were performed on each sample using two extraction kits: PowerFecal Kit (Qiagen) and Isolate II Fecal DNA kit (BioLine) (30 extractions in total). DNA was quantified using a Qubit fluorometer (Invitrogen) while quality was assessed via Nanodrop (ThermoFisher). Extracted DNA was stored at 4˚ C pending sequencing. Metagenomic shotgun sequencing of extracted slurry DNA was performed and demultiplexed by Edinburgh Genomics using the Illumina NovaSeq platform (150bp paired end library). Viral metagenomes were prepared firstly by homogenising cattle slurry in PBS. The homogenate was ultracentrifuged to pellet unwanted solids and bacteria. To further remove bacteria, the supernatant was passed sequentially through 0.45um and 0.22um filters. The filtrate was concentrated on an Amicon column and DNA was extracted using a standard phenol-chloroform extraction. Sequencing was conducted using Illumina Novaseq with a 2x150bp library. This data is NERC-funded but not held by the EIDC. This data is archived in the European Nucletotide Archive.

  • 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

  • Data comprise plot location (latitude, longitude, elevation), taxonomic family and species names and measurements of trees (diameter, height, health). Presence of lianas (vines) and their measurements were also recorded. Funder: NERC - Brazil (CONFAP) Newton Fund: “Dry forest biomes in Brazil: biodiversity and ecosystem services” (NE/N000587/1) Full details about this dataset can be found at https://doi.org/10.5285/aa3babe9-072c-42ce-9ea5-9dbb921a922d

  • 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

  • Dataset contains the partial sequence RNA gene from the Lycopodiella inundata, neighboring angiosperms (the grasses Holcus lanatus, Molinia caerulea, and the rush Juncus bulbosus), and a liverwort (Fossombronia foveolata). The samples were collected from Thursley National Nature Reserve, Surrey, United Kingdom, in June 2017. This data is NERC-funded but not held by the EIDC. Representative DNA sequences were deposited in the GenBank/EMBL data libraries under accession numbers MK673773–MK673803. https://www.ncbi.nlm.nih.gov/nuccore/MK673773,MK673774,MK673775,MK673776,MK673777,MK673778,MK673779,MK673780,MK673781,MK673782,MK673783,MK673784,MK673785,MK673786,MK673787,MK673788,MK673789,MK673790,MK673791,MK673792,MK673793,MK673794,MK673795,MK673796,MK673797,MK673798,MK673799,MK673800,MK673801,MK673802,MK673803

  • The data set is sequences of microorganisms that were isolated or determined by direct DNA extraction from the Eyjafjallajökull Iceland lava flows. The data is held in BLAST as follows: Clone 16S rRNA gene sequences have been deposited in GenBank under accession numbers HQ898914 to HQ900366.

  • This dataset contains DNA sequence data from reproductive Bombus terrestris audax workers brain and ovarian tissue (80 – 100 days post establishment), and from the tissue of male offspring of these workers at varying developmental stages, specifically stage 4 larval heads, pupal heads, adult (13 – 14 days old) male brains and adult male sperm. This data is NERC-funded but not held by the EIDC. This data is archived in the NCBI SRA under BioProject PRJNA573598

  • Dataset contains DNA sequencing from reciprocal crosses of B.terrestris dalmatinus and B.terrestris audax which were carried out by Biobest, Leuven. Four successful colonies (one of each cross direction) from two ’families’ were housed at the University of Leuven and kept in 21◦C with red light conditions, they were fed ad libitum with pollen and a sugar syrup. Callow workers were tagged in order to determine age. Worker reproductive status was confirmed by ovary dissection and entire bodies were then stored at -80◦C along with the original queen mothers and male fathers. Three reproductive workers, aged 16-17days, were selected from queen-less conditions from each of the crosses. This data is NERC-funded but not held by the EIDC. This data is archived in the NCBI SRA under BioProject PRJNA573820