Find research datasets worth reusing

opencc-by-4.0Mar 2023View details →

Precise, NLL-SSST-coherence hypocenter catalog for the 2023 Mw 7.8 and Mw 7.6 SE Turkey earthquake sequence.

CSV catalog file and visualizations of NLL-SSST-coherence earthquake relocations for the 2023 Mw 7.8 and Mw 7.6, Kahramanmaraş - Gaziantep, Turkey earthquake sequence (28,264 events, M≥1.5, 2023-01-01 to 2023-06-24). NLL-SSST-coherence (<a href="https://doi.org/10.1029/2021JB023190">Lomax and Savvaidis, 2022</a>; <a href="https://doi.org/10.26443/seismica.v2i1.324">Lomax and Henry, 2023</a>) is an enhanced, absolute-timing earthquake location procedure which 1) iteratively generates spatially varying travel-time corrections to improve multi-scale location precision and 2) uses waveform similarity to improve fine-scale location precision. Relocations performed with merged phase arrival data available from AFAD (<a href="https://deprem.afad.gov.tr/event-catalog">https://deprem.afad.gov.tr/event-catalog</a>) and KOERI (<a href="http://www.koeri.boun.edu.tr/sismo/2/bultenler">http://www.koeri.boun.edu.tr/sismo/2/bultenler</a>) downloaded on 2023-06-23. All events in the AFAD catalog with M≥1.5 are used for relocation; for each AFAD event, arrival data for the corresponding events from KOERI is merged when available (epicenter within 10km, origin time within 10 sec). Seismic velocity model is a smoothed version of the "Final 1-D" velocity model from: Acarel, D., Cambaz, M.D., Turhan, F., Mutlu, A.K. & Polat, R., 2019. Seismotectonics of Malatya Fault, Eastern Turkey. Open Geosciences, 11, 1098–1111. Available at: <a href="https://doi.org/10.1515/geo-2019-0085">https://doi.org/10.1515/geo-2019-0085</a>. [For relocations of events starting from 2020-01-01 through 2023-03-04 and including the 2020 Mw 6.8 Elazığ, Turkey sequence, see v1.0 of this dataset: <a href="https://doi.org/10.5281/zenodo.7699882">https://doi.org/10.5281/zenodo.7699882</a>]   This repository archive file contains: Full catalog in CSV format:  X_Turkey_20230624A_Acarel2019smooth_NLL-SSST-coherence_M1.5.csv CSV file data columns correspond to selected fields of the of NonLinLoc Hypocenter format output <a href="http://alomax.free.fr/nlloc/soft7.00/formats.html#_location_hypphs_">http://alomax.free.fr/nlloc/soft7.00/formats.html#_location_hypphs_</a> Key NLL-SSST-coherence configuration files: NLL-SSST-coherence_config/ Visualization images:     Full catalog:  A_Turkey_20230624A_Acarel2019smooth_NLL-SSST-coherence_M1.5.png     Events with (68% location ellipsoid) err ≤ 8km, origin-time color scale:  B_Turkey_20230624A_Acarel2019smooth_NLL-SSST-coherence_M1.5_se8km_OTIME.png     Events with err ≤ 8km:  B_Turkey_20230624A_Acarel2019smooth_NLL-SSST-coherence_M1.5_se8km.png     Events with err ≤ 8km, depth ≤ 10km:  C_Turkey_20230624A_Acarel2019smooth_NLL-SSST-coherence_M1.5_se8km_z-10.png     Events with err ≤ 8km, depth ≥ 10km:  C_Turkey_20230624A_Acarel2019smooth_NLL-SSST-coherence_M1.5_se8km_z10-.png Symbol size is proportional to event magnitude. AFAD stations shown by light gray inverted pyramids. KOERI stations shown by dark gray inverted pyramids. Origin-time plot event colors: Blue: before 2023-02-06 M 7.8 event Yellow: from 2023-02-06  01h17 UTC M 7.8 event through 2023-02-06 10h24 UTC M 7.6 event Orange to Red: after 2023-02-06 10h24 UTC M 7.6 event Plot data: Background image from https://opentopography.org Mapped surface faults (light purple) from: Emre, Ö., Duman, T.Y., Özalp, S., Şaroğlu, F., Olgun, Ş., Elmacı, H. & Çan, T., 2018. Active fault database of Turkey. Bull Earthquake Eng, 16, 3229–3275. <a href="https://doi.org/10.1007/s10518-016-0041-2">https://doi.org/10.1007/s10518-016-0041-2</a> Surface Rupture Lines (green) from: Reitman, N.G., Briggs, R.W., Barnhart, W.D., Thompson Jobe, J.A., DuRoss, C.B., Hatem, A.E., Gold, R.D., Akçiz, S., Koehler, R.D., Mejstrik, J.D., Collett, C., 2023, Fault rupture mapping of the 6 February 2023 Kahramanmaraş, Türkiye, earthquake sequence from satellite data: U.S. Geological Survey data release, <a href="https://doi.org/10.5066/P985I7U2">https://doi.org/10.5066/P985I7U2</a>.   Thanks to Sinan Ozeren, Didem Cambaz, Fatih Turhan, Dogan Kalafat, Selda Altuncu Poyraz, Kıvanç Kekovalı, Onur Tan, Alberto Michelini and Pierre Henry for assistance and discussions.

opencc-zeroJun 2023View details →

Sequencing data for: Tracking climate-change induced biological invasions over 4 decades by metabarcoding archived natural eDNA samplers

In a time of unprecedented global environmental change, understanding the response of biodiversity is paramount. However, our knowledge of anthropogenic impacts on ecosystems is limited by a lack of standardized retrospective biomonitoring data. Here, we use four-decade time series of archived blue mussels to trace spatiotemporal biodiversity change in coastal ecosystems. The filter-feeding mussels can serve as natural eDNA samplers, carrying an imprint of the surrounding aquatic community at the time of sampling. By sequencing the preserved DNA, we characterize highly diverse mussel-associated communities and reconstruct the invasion trajectory of an invasive species to the detriment of native taxa uncovering repeated population collapses and reinvasions after cold winters. Time series of natural eDNA samplers provide highly resolved temporal data on community assembly and global warming-driven invasion processes and overcome critical shortfalls in our understanding of biodiversity change in the Anthropocene.

Massive Chinese domestic pigs provide missing sequences in reference genome and reveal non-coding sequence variations regulating gene expression across Eurasian boars

This dataset contains novel sequences in Chinese domestic pigs but is absent in Sscrofa 11.1 reference genome. The detailed information for each file is recorded in the README file.

Sequence Diagram case reengineering FRS web

sequence diagram dibuat berdasarkan use case specification yang telah disusun sebelumnya. Diagram ini menunjukkan urutan dan komunikasi antara objek-objek dalam sistem saat menjalankan skenario use case. Hal ini membantu dalam memvisualisasikan alur eksekusi sistem dan mengidentifikasi objek-objek yang terlibat dalam interaksi tersebut

opencc-zeroJul 2023View details →

Data from: Insight into the structural and magnetotransport properties of epitaxial alpha-Fe2O3/Pt(111) heterostructures: The role of the reversed layer sequence

We report on the chemical structure and spin Hall magnetoresistance (SMR) in epitaxial α-Fe2O3(hematite)(0001)/Pt(111) bilayers with hematite thicknesses of 6 nm and 15 nm grown by molecular beam epitaxy on a MgO(111) substrate. Unlike previous studies that involved Pt overlayers on hematite, the present hematite films were grown on a stable Pt buffer layer and displayed structural changes as a function of thickness. These structural differences (the presence of a ferrimagnetic phase in the thinner film) significantly affected the magnetotransport properties of the bilayers. We observed a sign change of the SMR from positive to negative when the thickness of hematite increased from 6 nm to 15 nm. For α-Fe2O3(15 nm)/Pt, we demonstrated room-temperature switching of the Néel order with rectangular, nondecaying switching characteristics. Such structures open the way to extending magnetotransport studies to more complex systems with double asymmetric metal/hematite/Pt interfaces.

Serratia fonticola EBS19 Whole genome sequence data fasta file annotated

Whole genome sequence data of Serratia fonticola EBS19 strain.

miRNA read counts and mature sequences

Guppy post-filtered miRNA discovery set. Includes mature read counts, and sequences for three tissues.

Characterising neutrophil subtypes in cancer using human and murine single-cell RNA sequencing datasets

Single cell RNA sequencing data generated by 10xGenomics for Neutrophils derived from colorectal cancer (CRC) KPN tumours (CRC_KPN_counts.csv) and normalised counts (CRC_KPN_NormalisedCounts.csv) as well as from other mouse models of CRC carrying AKPT, BPN, BP and KP mutations (CRC_other_counts.csv and CRC_other_NormalisedCounts.csv), together with the relevant metadata (CRC_KPN_metadata.csv and CRC_other_metadata.csv).

Sequences of target genes and probes for construction of exon-targeted libraries for Prunus spp.

(Files) "baits-selection-15171.fas": Sequences of 15,171 baits used for hybridization reaction. "Targets_mume.15171.xlsx": Sequences of target genes used for design baits.   (Protocol for bait design) To selectively retrieve libraries with exons, a myBaits Custom design kit was used to design 1–20-K probes (Arbor Biosciences, Ann Arbor, MI, USA), which uses biotinylated RNA probes to concentrate fragments carrying sequences of interest (Gnirke et al., 2009), based on the published genomic and coding sequences of P. mume (Zhang et al., 2012). We subjected 29,621 non-redundant coding loci to search for single hits with BLAST+ (MEGABLAST with -p 70) against the P. mume genome, for the subsequent bait design. A 120-mer bait with 25–55 GC% per locus was randomly designed for each locus, and finally we obtained a bait set targeting 15,171 coding loci.

Inverse folding for antibody sequence design using deep learning

Model weights of the <a href="https://arxiv.org/abs/2310.19513">AbMPNN model (arXiv:2310.19513)</a> presented at the <a href="https://icml-compbio.github.io/">2023 ICML Workshop on Computational Biology</a>, and csv files with the split between train, test and validation across the <a href="https://opig.stats.ox.ac.uk/webapps/sabdab-sabpred/sabdab/">SAbDab</a> and <a href="https://zenodo.org/record/7258553">ImmuneBuilder</a> datasets.This model is based on <a href="https://www.biorxiv.org/content/10.1101/2022.06.03.494563v1">ProteinMPNN</a> and can be run using the corresponding code: <a href="https://github.com/dauparas/ProteinMPNN">https://github.com/dauparas/ProteinMPNN</a>.

opencc-zeroJul 2023View details →

Mitochondrial ND2 sequences from 40 specimens of six Onychorhynchus coronatus lineages: swainsoni, coronatus, castelnaui, mexicanus, occidentalis, and fraterculus

We examined phylogeographic patterns and cryptic diversity within the royal flycatcher, Onychorhynchus coronatus (Aves: Onychorhynchidae), a widespread Neotropical lowland forest tyrant flycatcher. A phylogeny of the six recognized subspecies was constructed from mtDNA sequence data of the NADH dehydrogenase subunit two gene, using Bayesian Inference and Maximum Likelihood methods. Phylogenetic analyses revealed high levels of intraspecific divergence within O. coronatus, supporting the existence of at least six independent lineages. The phylogenetic results uncovered the following relationships: (O. c. swainsoni [Southern Atlantic Forest], (O. c. coronatus [western Amazonia], (O. c. castelnaui [eastern Amazonia], (O. c. mexicanus [Central America], (O. c. occidentalis [Tumbesian], O. c. fraterculus [extreme northwestern South America])))). Biogeographic and dating analyses suggest that vicariant and dispersal events acted across approximately six million years to influence lineage diversification within this genus. Some of those events include the formation of the Amazon River and its tributaries, Andean uplift, and climatically induced vegetational shifts. Phylogenetic and biogeographic analyses of O. coronatus lineages support a hypothesis of area relationships in which the first divergence event isolated the Southern Atlantic Forest from Amazonia during the Late Miocene/Early Pliocene. This event was followed by the split of western and eastern Amazonia at the Early/Late Pliocene, the divergence of cis- and trans-Andean lowland regions also at the Early/Late Pliocene, the split between Central America and the extreme northwestern South America/Tumbes at the Early/Middle Pleistocene, and the split between extreme northwestern South America and Tumbes at Middle/Late Pleistocene. Subsequent divergence of the southern and northern populations in the western and eastern Onychorhynchus lineages took place during the Pleistocene. Comparison of phylogenetic trees and patterns in Onychorhynchus with those from published work suggests that across large New World radiations such as the Suboscines, some co-distributed lineages began to diverge long before others, which exemplifies the complexity of their evolutionary history.

Read coverage information for analysis missing plasmid sequences

This file contains two directories: read_coverage, and read_coverage_contigs. This directories should be decompressed and located within ecoli-binary-classifier/2021_11_missing_sequences_analysis/results/ in order to reproduce results described the in the mansucript.

opencc-zeroJul 2023View details →

Sample extraction and SNP sequencing data for: Identification of sex-linked SNP markers in wild populations of monomorphic birds

Single-nucleotide polymorphism (SNP) analyses are a powerful tool for population genetics, pedigree reconstruction and phenotypic trait mapping. However, the untapped potential of SNP markers to discriminate the sex of individuals in species with reduced sexual dimorphism or of individuals during immature stages remains a largely unexplored avenue. Here, we develop a novel protocol for molecular sexing of birds based on the detection of unique Z- and W-linked SNP markers. Our method is based on the identification of two unique loci, one in each sexual chromosome. Individuals are considered males when they show no calls for the W-linked SNP and are heterozygotic or homozygotic for the Z-linked SNP, while females show both Z- and W-linked SNP calls. We validated the method in the Jackdaw (Corvus monedula). The reduced sexual dimorphism in this species makes it difficult to sex individuals in the wild. We assessed the reliability of the method using 36 individuals of known sex and found that their sex was correctly assigned in 100% of cases. The sex-linked markers also proved to be widely applicable to discriminate males and females from a sample of 927 genotyped individuals of different maturity stages with an accuracy of 99.5%. Given that SNP markers are increasingly used in quantitative genetic analyses of wild populations, the approach we propose has a great potential to be integrated into broader genetic research programmes without the need for additional sexing techniques.

sequences generated by TopoProgenerator

sequences generated by TopoProgenerator

Sheldon Nevada Earthquake Sequence Datasets

This repository contains two movie visualizations and three datasets related to the Sheldon, NV (USA) earthquake sequence. The movies are as follows: <ol> <li>movie_S1.mp4 provides a 3D visualization of the hypocentral locations of relocated Sheldon earthquakes, including the best fitting fault plane (a dipping normal fault) for the main part of the sequence. Events are color-coded by depth.</li> <li>movie_S2.mp4 shows a time-evolution of relocated earthquakes, with events plotting in map view and color-coded by the distance from the fault plane shown in movie_S1.mp4. </li> </ol>   The datasets consist of two ASCII text files: <ol> <li>vzmodel.nonlinloc.txt is the velocity model used in the absolute and relative relocations (<a href="http://alomax.free.fr/nlloc/soft6.00/index.html">NonLinLoc format</a>). </li> <li>growclust_relocations.txt is the relocated catalog for the sequence in <a href="https://github.com/dttrugman/GrowClust3D.jl/wiki/Documentation#output-files">GrowClust3D.jl output format</a>.</li> <li>sheldon_mt_compilation.csv is a compilation of moment tensor inversions for select larger earthquakes in the sequence. The columns are labeled in the file header:</li> </ol> <ul> <li>evid, datetime = NSL event id and centroid time</li> <li>lat, lon, depth = centroid position</li> <li>mw, mo: moment magnitude and moment in dyne-cm</li> <li>var: variance reduction of the fit</li> <li>mrr, mtt, mff, mrt, mrf, mtf: moment tensor components</li> <li>rlat, rlon, rdep: hypocentral position in relocated catalog</li> <li>reloc: indicator of a relocated event</li> <li>s1, d1, r1: strike, dip, rake of nodal plane 1</li> <li>s2, d2, d2: strike, dip, rake of nodal plane 2 </li> </ul>

opencc-by-4.0Apr 2023View details →

Multimodal learning of noncoding variant effects using genome sequence and chromatin structure

ncVarPred-1D3D: pretrained models of Sei (PMID: 35817977) + our 3D structure embedding models are shared. The models are trained and validated using DeepSEA (PMID: 26301843) selected 200 bp regions (we extended to 4K bp neighboring) to predict the epigenetic profile containing 21907 epigenetic events Sei processed. The pretrained DeepSEA (PMID: 26301843) and reproduced DanQ (PMID: 27084946) can be found in SOTA.tar.gz.

Whole-genome capture and sequencing of Francisella tularensis directly from clinical samples

This dataset comprises: 1. The design of RNA oligonucleotide baits for Agilent Technologies’ SureSelect target enrichment - 54756 RNA oligonucleotide "baits" (120 bp each) designed to perform whole-genome capture and sequencing of Francisella tularensis directly from clinical samples (DNA) using Agilent Technologies’ SureSelect target enrichment system following the Illumina paired-end multiplexed sequencing library protocol. RNA oligonucleotide “baits” were designed to span the Francisella tularensis chromosome and plasmid, accounting for the genetic variability among publicly available genome sequences. All resulting sequences were BLASTn searched against the Human Genomic + Transcript database to excluded homologous sequences to the human genome. Overall, a total of 54756 RNA probes were generated and this custom bait library was then uploaded to the SureDesign software (https://earray.chem.agilent.com/suredesign) and synthesized by Agilent Technologies. 2. Genome assemblies of 17 Francisella tularensis samples generated in the context of validation and application of SureSelect target enrichment for Whole-genome capture and sequencing of Francisella tularensis directly from clinical samples   File “Ft_assembly_metadata.xlsx” contains the genome assembly statistics for each isolate, including European Nucleotide Archive accession numbers. The archive “Ft_assemblies.zip” contains all the genome assemblies (.fasta format) of each isolate presented in the metadata file. More details can be found in the following publication: (available soon)

opencc-by-4.0Jun 2022View details →

MIR142 Sanger sequencing results in MPNs

To extend and complement knowledge about the occurrence and/or frequency of MIR142 mutations in hematologic cancers, we sequenced MIR142 in large panels of MPNs [including polycythemia vera (PV), essential thrombocythemia (ET), primary myelofibrosis (PMF), and chronic myeloid leukemia (CML)], blood disorders for which such mutations have never been tested, and in AML and CLL, for which the mutations have been reported. The dataset gathers Sanger sequencing results of the MIR142 locus.

opencc-zeroAug 2023View details →

White shark diet sequences and sequence library

The white shark (Carcharodon carcharias) is one of the world's largest apex predators found throughout the world's temperate and subtropical marine environments. However, the species has suffered significant declines in recent decades and effective conservation programs require a sound knowledge of white shark biology and ecology. In particular, information on white shark diet across life stages and the species' range is needed to identify critical trophic interactions supporting shark populations and to predict the resilience of white sharks to environmental changes. In this study, we reassess the diet and trophic ecology of white sharks via the genetic analyses of cloacal swabs from 214 juvenile and subadult sharks from eastern Australia. Our findings are largely consistent with those of previous studies based on visual analyses of gut contents but highlight the unprecedented taxonomic resolution of prey items offered by genomic assessments of shark cloacal swabs. Diets consisted primarily of ray-finned fishes, with Mugiliformes, Carangiformes, Perciformes, and Scombriformes being dominant prey taxa, but with elasmobranchs, marine mammals, and birds also being common dietary constituents. Statistical analyses revealed a significant effect of sex and sampling location on diet composition, indicating biological and spatial variability in diets and predatory behavior. Overall, these findings support the notion that juvenile and subadult white sharks are opportunistic predators, which may provide some level of resilience to shifts in marine resources. However, frequently consumed ray-finned fishes, many of which are commercially targeted, may be key to supporting white shark populations in eastern Australia. This study represents the most comprehensive analysis of juvenile and subadult white shark diets performed to date and provides added confidence in the genomic analysis of cloacal swabs for dietary assessments of predatory species. These results are expected to help inform management geared toward conserving this important marine predator across the world's oceans.