Find research datasets worth reusing

opencc-by-nd-4.0Jun 2010View details →

FIGURE 7 in Holothyrids And Ticks: New Insights From Larval Morphology And Dna Sequencing, With The Description Of A New Species Of Diplothyrus (Parasitiformes: Neothyridae)

FIGURE 7: Single most parsimonious tree using a combination of DNA sequence data for three genes (18S rRNA, 28S rRNA and EF-1α). Numbers above branches: Bremer support/jackknife support (parsimony analysis); below branches: posterior probability (Bayesian analysis). xx: branch not supported in Bayesian analysis.

Aligned DNA sequence matrix for phylogenetic analyses in the article "Our unknown neighbor: a new species of rain frog of the genus Pristimantis (Amphibia: Anura: Strabomantidae) from the city of Loja, southern Ecuador"

The aligned matrix is in fasta format. Genes are arranged as follows: 12S = 1–909 16S = 910–1787 RAG-1 = 1788–2399

Input Data for "Protein Function Prediction for newly sequenced organisms"

The input sequence files in FASTA format and the detailed list of all organisms excluded when testing each specific bacterium.

Extended data table 1: Taqman array card results showing all individual target hits with Ct values and whether validated by conventional microbiology and/or microbial sequencing.

Data from study, protocol published at 10.5281/zenodo.5081880 Extended Data Table 1: TAC results showing all individual target hits with Ct values and whether validated by conventional microbiology and/or microbial sequencing. (BAL: bronchoalveolar lavage.) *Not included in validation numbers as duplicate at sub-species or genus level detection, **MecA was not included in validation numbers. TAC hits which did not pass the internal quality control standards required for reporting are indicated by (not reported). Samples which did not undergo sequencing indicated by ND. (✓) indicates low confidence hits from sequencing.

AliSim: Ultrafast and Realistic Sequence Alignment Simulator for Phylogenetics - Supplementary Data

This supplementary data contains testing scripts, input/output data for validating and benchmarking AliSim.

opencc-zeroSep 2021View details →

Deep sequencing datasets from: Witnessing the structural evolution of an RNA enzyme

An RNA polymerase ribozyme that has been the subject of extensive directed evolution efforts has attained the ability to synthesize complex functional RNAs, including a full-length copy of its own evolutionary ancestor. During the course of evolution, the catalytic core of the ribozyme has undergone a major structural rearrangement, resulting in a novel tertiary structural element that lies in close proximity to the active site. Through a combination of site-directed mutagenesis, structural probing, and deep sequencing analysis, the trajectory of evolution was seen to involve the progressive stabilization of the new structure, which provides the basis for improved catalytic activity of the ribozyme. Multiple paths to the new structure were explored by the evolving population, converging upon a common solution. Tertiary structural remodeling of RNA is known to occur in nature, as evidenced by the phylogenetic analysis of extant organisms, but this type of structural innovation had not previously been observed in an experimental setting. Despite prior speculation that the catalytic core of the ribozyme had become trapped in a narrow local fitness optimum, the evolving population has broken through to a new fitness locale, raising the possibility that further improvement of polymerase activity may be achievable.

opencc-by-4.0Oct 2021View details →

Rock-magnetic, paleomagnetic and multimethod paleointensity data from an upper Miocene lava flow sequence from São Vicente (Cape Verde)

The folder “Praia Grande Paleomagnetism Data.zip” contains paleomagnetic thermal and alternating field demagnetisation data obtained on upper Miocene volcanic rocks from São Vicente (Cape Verde). Measurements were performed in the paleomagnetic laboratory of the University of Burgos (Spain). Data are in .txt format with the extension .rs3. Columns are separated by empty spaces. Data can be visualised and analysed with the Remasoft software (Chadima and Hrouda, 2006). The folder “Praia Grande rock magnetism Data.zip” contains data in .txt format of IRM acquisition curves (extension .irm), hysteresis curves (extension .hys), backfield curves (extension .coe) and thermomagnetic magnetisation versus temperature curves (extension .rmp) obtained on upper Miocene volcanic rocks from São Vicente (Cape Verde). Measurements were performed in the paleomagnetic laboratory of the University of Burgos (Spain). Columns are separated by tabs. Data can be visualised and analysed with the RockMagAnalyzer 1.0 software (Leonhardt, 2006). The folder “Praia Grande Thellier-Coe Data.zip”contains paleointensity determination data obtained with the Thellier-Coe method on upper Miocene volcanic rocks from São Vicente (Cape Verde). Measurements were performed in the paleomagnetic laboratory of the University of Burgos (Spain). Data are in .txt format with the extension .tdt separated by tabs. Data can be visualised and analysed with the ThellierTool software (Leonhardt et al.,2004). The folder “Praia Grande Multispecimen.zip” contains paleointensity determination data on upper Miocene volcanic rocks from São Vicente (Cape Verde) obtained with the multispecimen method (Biggin and Poidras, 2006; Dekkers and Böhnel, 2006; Fabian and Leonhardt, 2010) at Laboratorio Interinstitucional de Magnetismo Natural, Instituto de Geofísica, Unidad Michoacán, UNAM, Mexico. Two kinds of files can be found: Five .txt files (M0.txt, M1.txt, M2.txt, M3.txt, M4.txt) and five .jr6 files (M0.jr6, M1.jr6, M2.jr6, M3.jr6, M4.jr6). Both types of files are in .txt format. The .txt files directly provide the measurement data generated during the multispecimen experiments. The first columns of the .jr6 files display the following information: column 1: specimen name; column 2: experimental step (explanation below); columns 3, 4 and 5: three magnetisation components M(x), M(y) and M(z); column 6: exponent of the magnetisation components to obtain the magnetisation value in A/m. In the multispecimen experiments, the specimen-name (e.g.  PRG1-3) can be divided in two parts, the first three characters indicate the sample (flow), the last character the specimen number (1 to 7). Eight different experimental steps (column 2) can be distinguished: NRM, A10, A20, A30, A40, A50, A60 and A70.  They correspond to the measurement of the NRM and of steps in which fields of 10, 20, 30, 40, 50, 60 and 70 mT where respectively applied. Files M0 (.txt and .jr6) include only NRM measurements, files M1 include measurements of specimens heated with an applied field parallel to their NRM, files M2 include measurements of specimens heated with an applied field antiparallel to their NRM, files M3 include measurements of specimens heated in zero field and cooled down in an applied field parallel to their NRM, and files M4 include again include measurements of specimens heated with an applied field parallel to their NRM. REFERENCES Biggin, A., Poidras, T., 2006. First-order symmetry of weak-field partial thermoremanence in multi-domain ferromagnetic grains. 1. Experimental evidence and physical implications. Earth Planet. Sci. Lett. 245, 438–453. doi:10.1016/j.epsl.2006.02.035 Chadima, M. and Hrouda, F., 2006. Remasoft 3.0 a user friendly paleomagnetic data browser and analyzer. Travaux Géophysiques, XXVII, 20-21. Dekkers, M.J., Böhnel, H.N., 2006. Reliable absolute palaeointensities independent of magnetic domain state. Earth Planet. Sci. Lett. 248, 507–516. doi:10.1016/j.epsl.2006.05.040 Fabian, K., Leonhardt, R., 2010. Multiple-specimen absolute paleointensity determination: An optimal protocol including pTRM normalization, domain-state correction, and alteration test. Earth Planet. Sci. Lett. 297, 84–94. doi:10.1016/j.epsl.2010.06.006 Leonhardt, R., 2006. Analyzing rock magnetic measurements; The RockMagAnalyzer 1.0 software.Computers and Geosciences, 32, 1420-1431. Leonhardt, R., Heunemann, C. and Krása, D., 2004. Analyzing absolute paleointensity determinations: Acceptance criteria and the software ThellierTool4.0. Geochem. Geophys. Geosyst., Vol. 5, no. 12, doi.: 10.1029/2004GC000807. Monster, M.W.L., de Groot, L. V., Dekkers, M.J., 2015. MSP-Tool: A VBA-Based Software Tool for the Analysis of Multispecimen Paleointensity Data. Front. Earth Sci. 3, 1–9. https://doi.org/10.3389/feart.2015.00086

opencc-zeroOct 2021View details →

Emergence and radiation of distemper viruses in terrestrial and marine mammals - Input files, bash and R codes for analysing PDV and CDV sequence data

Canine distemper virus (CDV) and phocine distemper virus (PDV) are major pathogens to terrestrial and marine mammals. Yet little is known about the timing and geographical origin of distemper viruses and to what extent it was influenced by environmental change and human activities. To address this, we i) performed the first comprehensive time-calibrated phylogenetic analysis of the two distemper viruses; ii) mapped distemper antibody and virus detection data from marine mammals collected between 1972-2018; iii) and compiled historical reports on distemper dating back to the 18th century. We find that CDV and PDV diverged in the early 17th century. Modern CDV strains last shared a common ancestor in the 19th century with a marked radiation during the 1930s-50s. Modern PDV strains are of more recent origin, diverging in the 1970s-80s. Based on the compiled information on distemper distribution, the diverse host range of CDV and basal phylogenetic placement of terrestrial morbilliviruses, we hypothesize a terrestrial CDV-like ancestor giving rise to PDV in the North Atlantic. Moreover, given the estimated timing of distemper origin and radiation, we hypothesize a prominent role of environmental change such as the Little Ice Age, and human activities like globalisation and war in distemper virus evolution.

opencc-zeroDec 2020View details →

Improved library preparation protocols for amplicon sequencing-based noninvasive fetal genotyping for RHD-positive D antigen-negative alleles

We aimed to simplify our fetal RHD genotyping protocol by changing the method to attach Illumina's sequencing adaptors to PCR products from the ligation-based method to a PCR-based method, and to improve its quantitative accuracy by introducing unique molecular indexes, which allow us to count the numbers of DNA fragments used as PCR templates and to minimize the effects of PCR and sequencing errors. Both of the newly established protocols reduced time and cost compared with our conventional protocol. Removal of PCR duplicates using UMIs reduced the frequencies of erroneously mapped sequences reads likely generated by PCR and sequencing errors. The modified protocols will help us facilitate implementing fetal RHD genotyping for East Asian populations into clinical practice.

opencc-by-4.0Oct 2021View details →

epicPCR sequencing data, October 20th

Samples: Rhodo100dilWWMocksBC10e8SM16S Rhodo100dilWWMocksBC10e8SM16S Rhodo100dilWWMocksBC10e8SM18S Rhodo100dilWWMocksBC10e8SM18S Rhodo10dilWWMocksBC10e8SM16S Rhodo10dilWWMocksBC10e8SM16S Rhodo10dilWWMocksBC10e8SM18S Rhodo10dilWWMocksBC10e8SM18S RhodoMocksBC10e7MC16S RhodoMocksBC10e7MC16S RhodoMocksBC10e7MC18S RhodoMocksBC10e7MC18S RhodoMocksBC10e8SM16S RhodoMocksBC10e8SM16S RhodoMocksBC10e8SM18S RhodoMocksBC10e8SM18S RhodoNoMocksBC10e7MC16S RhodoNoMocksBC10e7MC16S RhodoNoMocksBC10e7MC18S RhodoNoMocksBC10e7MC18S RhodoWWMocksBC10e8SM16S RhodoWWMocksBC10e8SM16S RhodoWWMocksBC10e8SM18S RhodoWWMocksBC10e8SM18S WWMocksBC10e7MC16S WWMocksBC10e7MC16S WWMocksBC10e7MC18S WWMocksBC10e7MC18S WWMocksBC10e8SM16S WWMocksBC10e8SM16S WWMocksBC10e8SM18S WWMocksBC10e8SM18S WWNoMocksBC10e7MC16S WWNoMocksBC10e7MC16S WWNoMocksBC10e7MC18S WWNoMocksBC10e7MC18S

opencc-by-4.0Oct 2022View details →

TIL1383I TCR mutation sequencing and SPR binding data

Sequence and mutation sequence data for the TIL1383I TCR and surface plasmon resonance data and analysis files for TIL1383I binding to tyrosinase/HLA-A2.

opencc-zeroOct 2022View details →

Illumina next generation ddRAD sequencing SNP data from: Contrasting genetic diversity and structure between endemic and widespread damselfishes are related to differing adaptive strategies

Aim: Discerning when, where, and how processes of isolation lead to differing biogeography is especially complex for marine species with similar ecological niches and within the same geographic location. We assessed population genetics of congeneric and ecologically similar damselfishes within their overlapping distributions and across potential barriers to geneflow. Taxon: Dascyllus marginatus (endemic) and Dascyllus abudafur (widespread). Location: Coral reefs from the Red Sea, Djibouti, Yemen, Oman, and Madagascar. Methods: We used RADseq derived SNPs to investigate key differences in population genetics between both species and discuss barriers shaping genetic differentiation (neutral vs. selective) and biogeography. Results: Dascyllus marginatus inhabited the Red Sea, the coasts of Yemen (including Socotra), and the Gulf of Oman. Dascyllus abudafur species was present from the Red Sea to Madagascar but was absent from Yemen and Oman. Populations of D. marginatus had an order of magnitude higher genetic differentiation compared to D. abudafur, as well as several outlier loci (suggesting selective pressure), which were absent in D. abudafur despite equal sampling locations. In both species, specimens from the Red Sea and Djibouti formed one genetic cluster separated from all other locations. Main conclusions: The stronger genetic structure at smaller geographic scale of the endemic species seems associated to faster adaptation to environmental differences; whereas the widespread species only experienced reduced geneflow and neutral differentiation at much larger geographic scales. Restrictive transitions (between the Gulf of Aqaba and the Red Sea or the Red Sea and the Gulf of Aden) did not affect the genetic architecture of either species, while the environmental shift within the Red Sea (at 22°N/20°N) affected the endemic but not the widespread species. Samples from continental Yemen revealed that a genetic break in the Gulf of Aden likely reflects historical colonization processes and not contemporary environmental regimes.

opencc-by-4.0Oct 2022View details →

Primers for whole genome sequencing of the Sars-Cov-2 virus

Here is the primer sequence for amplification and sequencing of the whole genome of the Sars-Cov-2 virus.

opencc-by-4.0Oct 2022View details →

TIGRFAM protein sequences named by taxonomy

A set of 411 TIGRFAM protein families originally used for benchmarking sequence clustering programs. Sequences were downloaded from <a href="https://www.ncbi.nlm.nih.gov/genome/annotation_prok/tigrfams/">NCBI</a> and renamed by their original name (accession number) followed by their semi-colon separated NCBI taxonomy. For example, the first sequence in TIGRFAM00005.fas.gz is named: <blockquote> WP_000005837.1 RluA family pseudouridine synthase, partial [Bacillus anthracis];TIGR00005(group);cellular organisms(no rank);Bacteria(superkingdom);Terrabacteria group(clade);Firmicutes(phylum);Bacilli(class);Bacillales(order);Bacillaceae(family);Bacillus(genus);Bacillus cereus group(species group);Bacillus anthracis(species) </blockquote>

opencc-by-4.0Nov 2022View details →

S and Z loci nucleotide sequences of Lolium multiflorum cultivar Rabiosa

Nucleotide sequences of two scaffolds spanning the S-locus and two scaffolds the Z-locus in Lolium multiflorum cultivar Rabiosa

Cephalopod retinal development shows vertebrate-like mechanisms of neurogenesis: Multiple sequence alignments and phylogenetic trees

Coleoid cephalopods, including squid, cuttlefish and octopus, have large and complex nervous systems and camera-type eyes that are comparable only to features that have independently evolved in the vertebrate lineage. The changes in development that result in the evolution of nervous system size and diversity of neural cell-types are not well understood. Here, we have pioneered live-imaging techniques and performed functional interrogation to show the squid, Doryteuthis pealeii, utilizes mechanisms during retinal neurogenesis that are hallmarks of vertebrate processes. Given the convergent evolution of elaborate visual systems in cephalopods and vertebrates, these results reveal common mechanisms that underlie the growth of highly proliferative neurogenic primordia that may alter ontogenetic allometry and contribute to the evolution of complex nervous systems.

Higher-order sequences of vocal mimicry performed by male Albert's lyrebirds are socially transmitted and enhance acoustic contrast

Most studies of acoustic communication focus on short units of vocalisation such as songs, yet these units are often hierarchically organised into higher-order sequences, and outside human language, little is known about the drivers of sequence structure. Here we investigate the organisation, transmission, and function of vocal sequences sung by male Albert's lyrebirds (Menura alberti), a species renowned for vocal imitations of other species. We quantified the organisation of mimetic units into sequences and examined the extent to which these sequences are repeated within and between individuals and shared among populations. We found that individual males organised their mimetic units into stereotyped sequences. Sequence structures were shared within and to a lesser extent among populations, implying that sequences were socially transmitted. Across the entire species range, mimetic units were sung with immediate variety and a high acoustic contrast between consecutive units, suggesting that sequence structure is a means to enhance receiver perceptions of repertoire complexity. Our results provide evidence that higher-order sequences of vocalisations can be socially transmitted, and that the order of vocal units can be functionally significant. We conclude that, to fully understand vocal behaviours, we must study both the individual vocal units and their higher-order temporal organisation.

Efficient Real-Time Selective Genome Sequencing on Resource-Constrained Devices

This dataset contains the curated nanopore raw signal data in <a href="https://www.nature.com/articles/s41587-021-01147-4">BLOW5 format </a>used to benchmark <a href="https://github.com/beebdev/HARU/">Hardware Accelerated Read Until (HARU)</a>. This dataset was created by using the publicly available datasets: <a href="https://community.artic.network/t/links-to-raw-fast5-fastq-data-for-artic-protocol/17">SARS-CoV-2 SP1</a> (1.382M reads) and <a href="https://ncbi.nlm.nih.gov/sra/SRX11368475">NA12878 PromethION subset</a> (500,000 reads). The tarball when extracted will have the following directory structure: haru-data ├── na12878-rfc1 │   ├── blow5-rawsignal │   │   ├── na12878_dna_0.blow5 │   │   ├── na12878_dna_100.blow5 │   │   ├── na12878_dna_101.blow5 │   │   ├── na12878_dna_102.blow5 │   │   ├── ... │   └── reference │       └── rfc1.fa └── SARS-CoV-2-sp1     ├── blow5-rawsignal     │   ├── readgroup0     │   │   ├── reads_0_0.blow5     │   │   ├── reads_0_10.blow5     │   │   ├── reads_0_11.blow5     │   │   ├── reads_0_12.blow5     │   │   ├── ...     │   └── readgroup1     │       ├── reads_1_0.blow5     │       ├── reads_1_10.blow5     │       ├── reads_1_11.blow5     │       ├── ....     └── reference         └── nCoV-2019.reference.fasta nCoV-2019.reference.fasta is the SARS-CoV-2 MN908947.3 reference genome. rfc1.fa is the genomic region hr4:39262456-39391375 extracted from hg38 human genome.

opencc-zeroDec 2021View details →

Sanger sequences of marpissoid salticids for Kelawakaju placement

The genus Kelawakaju Maddison & Ruiz, gen. nov., is described for a lineage of bark-dwelling Asian marpissine jumping spiders that represent a dispersal to Eurasia separate from that of the Marpissa-Mendoza lineage, according to the phylogeny recovered from analysis of four gene regions. All of the species of Kelawakaju are new except K. frenata (Simon, 1901), comb. nov., which is here transferred from Ocrisiona Simon, 1901. K. frenata is known from Hong Kong, Guangdong, Guangxi, and likely Taiwan. The five new species are Kelawakaju mulu Maddison & Ruiz (type species of Kelawakaju, from Sarawak, Malaysia, ♂♀), K. intexta Maddison & Ruiz (from Sarawak, ♂), K. leucomelas Maddison & Ng (Singapore and Johor Bahru, ♂♀), K. sahyadri Vishnudas, Maddison, & Sudhikumar (India, ♂♀), and K. singapura Maddison & Ng (Singapore, ♂♀), all sp. nov.

Genome sequence and silkomics of the spindle ermine moth, Yponomeuta cagnagella, representing the early diverging lineage of the ditrysian Lepidoptera

Many lepidopteran caterpillars produce silk, cocoons, feeding tubes, or nests for protection from predators and parasites. Yet, the number of lepidopteran species whose silk composition has been studied in detail is very small, because the genes encoding the major structural silk proteins tend to be large and repetitive, making their assembly and sequence analysis difficult. Here we have analyzed the silk of Yponomeuta cagnagella, which represents one of the early diverging lineages of the ditrysian Lepidoptera thus improving the coverage of the order. To obtain a comprehensive list of the Y. cagnagella silk genes, we sequenced, assembled, and annotated the draft genome using Oxford Nanopore and Illumina technologies. The 626 Mb assembly with N50 of 96.5 kb contained 96.9% insect orthologs recovered by BUSCO and 30,003 predicted gene models. We then used a silk-gland transcriptome and a silk proteome to identify major silk components and verified the tissue specificity of the expression of individual genes.