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opencc-by-4.0Oct 2022View details →

Methods for structural variant detection with long-read sequencing data

SV calls from different long-read based SV callers on sequencing data. SV results evaluated in Methods for structural variant detection with long-read sequencing data. NA24385_Pacbio_HiFi -> HiFi_L1 in paper NA24385_Pacbio_MtSinai -> CLR_L1 in paper NA24385_Pacbio_CLR_SRX7668835 -> CLR_L2 in paper NA24385_Pacbio_CLR_SRX6719924 -> CLR_L3 in paper NA24385_ONT_Promethion -> Nano_L1 in paper

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Data from: Haplotype sequence collection of ABO blood group alleles by long-read sequencing reveals putative A1-diagnostic variants

In the era of blood group genomics, reference collections of complete and fully-resolved blood group gene alleles have gained high importance. For most blood groups, however, such collections are currently lacking, as resolving full-length gene sequences as haplotypes (i.e. separated maternal/paternal origin) remains exceedingly difficult with both Sanger and short-read next-generation sequencing. Using the latest third-generation long-read sequencing, we generated a collection of fully-resolved sequences for all six main ABO allele groups: ABO*A1/A2/B/O.01.01/O.01.02/O.02. We selected 77 samples from an ABO genotype dataset (n=25,200) of serologically-typed Swiss blood donors. The entire ABO gene was amplified in two overlapping long-range PCRs (covering ~23.6 kb) and sequenced by long-read Oxford Nanopore sequencing. For quality validation, two samples per ABO group were re-sequenced using Illumina and PacBio technology. All 154 full-length ABO sequences were resolved as haplotypes. We observed novel, distinct sequence patterns for each ABO group. Most genetic diversity was found between, not within, ABO groups. Phylogenetic tree and haplotype network analyses highlighted distinct clades of each ABO group. Strikingly, our data uncovered four genetic variants putatively specific for ABO*A1, for which direct diagnostic targets are currently lacking. We validated A1-diagnostic potential using whole-genome data (n=4,872) of a multi-ethnic cohort. Overall, our sequencing strategy proved powerful for producing high-quality ABO haplotypes and holds promise for generating similar collections for other blood groups. The publicly available collection of 154 haplotypes will serve as a valuable resource for molecular analyses of ABO, as well as studies about the function and evolutionary history of ABO.

opencc-zeroOct 2022View details →

Supplementary material 2 from: Wayland MT, Vainio JK, Gibson DI, Herniou EA, Littlewood TDJ, Väinölä R (2015) The systematics of Echinorhynchus Zoega in Müller, 1776 (Acanthocephala, Echinorhynchidae) elucidated by nuclear and mitochondrial sequence data from eight European taxa. ZooKeys 484: 25-52. https://doi.org/10.3897/zookeys.484.9132

Maximum likelihood model parameters: Explanation note: Model parameters used in the maximum likelihood approach to phylogenetic reconstruction.

Supplementary material 4 from: Wayland MT, Vainio JK, Gibson DI, Herniou EA, Littlewood TDJ, Väinölä R (2015) The systematics of Echinorhynchus Zoega in Müller, 1776 (Acanthocephala, Echinorhynchidae) elucidated by nuclear and mitochondrial sequence data from eight European taxa. ZooKeys 484: 25-52. https://doi.org/10.3897/zookeys.484.9132

Patterns of COI sequence variation: Explanation note: Patterns of COI sequence variation. Graphs and discussion of patterns of nucleotide substitions in the COI data-set.

Supplementary material 1 from: Wayland MT, Vainio JK, Gibson DI, Herniou EA, Littlewood TDJ, Väinölä R (2015) The systematics of Echinorhynchus Zoega in Müller, 1776 (Acanthocephala, Echinorhynchidae) elucidated by nuclear and mitochondrial sequence data from eight European taxa. ZooKeys 484: 25-52. https://doi.org/10.3897/zookeys.484.9132

Aligned and concatenated partial sequences of COI and 28S rDNA: Explanation note: Aligned and concatenated partial sequences of COI and 28S rDNA in nexus format. Aligned partial sequences of COI and 28S rDNA from each acanthocephalan population have been concatenated. Gaps are indicated by '-'. The first 585 characters in each block correspond to COI and the remainder to 28S rDNA. The file contains data for all nine Echinorhynchus samples and the outgroup taxon, Acanthocephalus lucii. This nexus file was used in all phylogenetic analyses.

Supplementary material 3 from: Wayland MT, Vainio JK, Gibson DI, Herniou EA, Littlewood TDJ, Väinölä R (2015) The systematics of Echinorhynchus Zoega in Müller, 1776 (Acanthocephala, Echinorhynchidae) elucidated by nuclear and mitochondrial sequence data from eight European taxa. ZooKeys 484: 25-52. https://doi.org/10.3897/zookeys.484.9132

Nucleotide substitutions: Explanation note: Substitutions of nucleotides (transitions/transversions) for 28S rDNA (below the diagonal) and COI sequence data (above the diagonal).

opencc-by-4.0May 2024View details →

Rock-magnetic, paleomagnetic and multimethod paleointensity data from the Pliocene Khaveti lava flow sequence in Georgia

The folder “1 Rock magnetic data Khaveti.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 Pliocene volcanic rocks from a lava flow sequence in the Lesser Caucasus in Georgia . 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 “2 Paleomagnetic data Khaveti.zip” contains paleomagnetic thermal and alternating field demagnetisation data obtained on Pliocene volcanic rocks from a lava flow sequence in the Lesser Caucasus in Georgia. 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 “3 Paleointensity data Khaveti Thellier_Coe.zip” contains two folders with paleointensity determination data obtained with the Thellier-Coe method on Pliocene volcanic rocks from the Khaveti lava flow sequence in the Lesser Caucasus in Georgia. The two folders Thellier_Coe Khaveti_down and Thellier_Coe Khaveti_up contain paleointensity determination data obtained respectively in the 14 lower and 14 upper flows of the sequence. Experiments were carried out in the Paleomagnetics and Magnetic Materials Laboratory of the University of Hawai’i at Manoa. Data from each flow have been put in an own folder, and 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 “4 Paleointensity data Khaveti Multispecimen.zip” contains two folders with paleointensity determination data from Pliocene volcanic rocks from the Khaveti lava flow sequence in the Lesser Caucasus in Georgia. These data were obtained with the multispecimen method (Biggin and Poidras, 2006; Dekkers and Böhnel, 2006; Fabian and Leonhardt, 2010). The folder MS_Morelia contains determinations carried out at Laboratorio Interinstitucional de Magnetismo Natural, Instituto de Geofísica, Unidad Michoacán, UNAM, Mexico. The folder MS_Burgos contains determinations carried out at the paleomagnetic laboratory of the University of Burgos. All files are Excel files, and each one corresponds to a single sample subjected to multispecimen analysis. Data can be visualised and analysed with the VBA based software tool “MSP-Tool” (Monster et al.,2015) directly included in each one of the sample files.   <h3>REFERENCES</h3>   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., 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. Leonhardt, R., 2006. Analyzing rock magnetic measurements; The RockMagAnalyzer 1.0 software.Computers and Geosciences, 32, 1420-1431. 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

Supplementary information to the data note The genome sequence of the Sandhill Rustic moth Luperina nickerlii (Freyer, 1845) subspecies leechi Goater, 1976"

Supplementary information to the data note: "The genome sequence of the Sandhill Rustic moth Luperina nickerlii (Freyer, 1845) subspecies leechi Goater, 1976" . The LSU analysis of the Luperina nickerlii subsp. leechi genome, presenting evidence that this is a ZO female.

1000 Genomes Data: Sequencing Data in BAM Format - LPA Region

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Sample data for analysis of FFPE sequencing data

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Sequenced Raw Data: Untreated PTB (UTB) Cases, Completed ATT Treatment PTB (CTB) Cases, and Healthy Controls (HC)

The FastQ datasets were generated using the Illumina MiSeq sequencing platform, specifically targeting the v3-v4 hypervariable region of the 16S rRNA gene, to facilitate high-resolution profiling of microbial communities.

opencc-zeroJun 2024View details →

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Mutant Harmonia axyridis raw sequencing data of CRISPR/Cas9 induced mutations in the genes laccase2 and scarlet

Harmonia axyridis (Pallas), commonly known as the Asian lady beetle, is a native insect species of Asia that has been intentionally introduced to various regions for biocontrol purposes. However, its widespread presence beyond its original release sites suggests a high degree of invasiveness. In this study, we utilized the CRISPR-Cas9 approach to achieve precise genome editing in H. axyridis. Specifically, we targeted two genes in H. axyridis, laccase2 and scarlet, knockdown of which orthologs in other insects showed visible phenotypic changes. The knockout laccase2 resulted in an early-detectable phenotype but also in lethality. However, we successfully established a viable and genetically stable mutant colony by disrupting the scarlet gene, resulting in beetles with white eyes. Our findings contribute to the expanding knowledge of genetic manipulation in H. axyridis and provide insights into its potential for future research and practical applications for biocontrol and invasive species management.

Data and code for, "Predicting self-assembly of sequence-controlled copoly- mers with stochastic sequence variation"

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opencc-by-4.0Apr 2023View details →

Data used in the study "Application of nanopore sequencing for accurate identification of bioaerosol-derived bacterial colonies"

Data used in the study "Application of nanopore sequencing for accurate identification of bioaerosol-derived bacterial colonies." The datasets contain nanopore and Sanger sequencing data (including the electropherograms) as well as EPI2ME and NGSpeciesID analysis.

opencc-by-4.0Jul 2024View details →

16S Amplicon sequence variants (ASVs) data of NEREA Augmented Observatory

Metabarcoding - 16S ASV generation and taxonomic assignment. Raw 16S paired-end sequences were subjected to a data quality control step and subsequently imported into the QIIME2 pipeline v.2022.2.0. Leftover primers and adapter sequences were removed through cutadapt. The amplicon sequence variants (ASV) table, which represent true biological sequences within each sample, was generated using the denoised-paired method including truncation, denoising, dereplication, merging, and chimera filtering of the DADA2 (Divisive Amplicon Denoising Algorithm 2) plugin inside QIIME2. Default parameters were used with the exception of the forward and reverse sequence length (--p-trunc-len-f and --p-trunc-len-r), that were set to 220 and 180, respectively. Processed reads that passed all these filters were used for taxonomy classification. The V4-V5 regions were extracted from the pre-formatted reference sequences and taxonomy file built on the SILVA 138 99% OTUs database and the vsearch v.2.6.2 global alignment implemented in QIIME2 was used.

opencc-by-4.0Jul 2024View details →

U-Pb-Th SHRIMP & LA-ICP-MS complementary data of "The bimodal Fii-A2-type and calc-alkaline volcanic sequence of the Aljustrel brownfield region, Iberian Pyrite Belt, SW Iberian Massif"

U-Pb-Th complementary  data of  "The bimodal Fii-A2-type and calc-alkaline volcanic sequence of the Aljustrel brownfield region, Iberian Pyrite Belt, SW Iberian Massif" <a title="Persistent link using digital object identifier" href="https://doi.org/10.1016/j.chemer.2023.126049" target="_blank" rel="noreferrer noopener">https://doi.org/10.1016/j.chemer.2023.126049</a>

opencc-by-4.0Jul 2024View details →

Melanoma Cell Lines SLC22A17 Bisulfite Sequencing Raw Data

Bisulfite sequencing raw data of SLC22A17 gene obtained in melanoma cell lines. The data will be published in the article entitled "Identification of SLC22A17 DNA methylation hotspot as a potential biomarker in cutaneous melanoma" submitted to Journal of Translational Medicine

opencc-by-4.0Feb 2018View details →

Sequencing data for "Long read sequencing reveals poxvirus evolution through rapid homogenization of gene arrays"

Illumina and Oxford Nanopore sequencing datasets (in FASTQ format) generated for the manuscript "Long read sequencing reveals poxvirus evolution through rapid homogenization of gene arrays." Paired-end Illumina MiSeq data are uploaded as two separate files ("r1" and "r2") for each passaged population. BAM files, filtered to exclude reads that did not align to K3L, are provided for passaged populations analyzed in the manuscript.

opennotspecifiedOct 2018View details →

Fig. 4 in Pollen characters and DNA sequence data converge on a monophyletic genus Iresine (Amaranthaceae, Caryophyllales) and help to elucidate its species diversity

Fig. 4. Scanning electron photomicrographs of pollen grains from the Iresine clade (= Iresinoids). A, Iresine cassiniiformis (Borsch & al. 3792); B, Iresine type XXXIV (Borsch & al. 5412); C, Iresine rzedowskii (Borsch & al. 3793); D, Iresine ajuscana (Borsch & al. 5404); E, Iresine orientalis (Borsch & al. 5404); F, Iresine discolor (Purpus 3453); G, Magnification of aperture with details of mesoporium of pollen from the same plant; H, Iresine hartmanii (Tenorino 1864); I, Iresine type XXXIV (Borsch & al. 5390). — Scale = 10 µm apart from G where it is 4 µm.