Find research datasets worth reusing

opencc-by-4.0Oct 2022View details →

Co-seismic slip of the 18 April 2021 Mw 5.9 Genaveh earthquake in the South Dezful Embayment of Zagros (Iran) and its aftershock sequence

This public repository contains INSAR and other processed data for the manuscript : "Co-seismic slip of the 18 April 2021 Mw 5.9 Genaveh earthquake in the South Dezful Embayment of Zagros (Iran) and its aftershock sequence" <ul> <li>InSAR unwrapped and geocoded files, for the ascending track A101 and the descending track D35: <ul> <li>GDM_Asc101_InU_geo_20210414_20210426_sd_4rlks.tiff</li> <li>GDM_Desc35_InU_geo_20210410_20210422_sd_4rlks.tiff</li> </ul> </li> <li>Sampled quadtree data for the ascending and descending data with LOS vector: <ul> <li>a101_okinv_input</li> <li>d35_okinv_input</li> </ul> </li> <li>Slip distribution model for the fault dipping N and the fault dipping S: <ul> <li>SDM_dipN_oksar.dat</li> <li>SDM_dipS_oksar.dat</li> </ul> </li> </ul>

opencc-by-sa-4.0May 2023View details →

Multiview Video Test Sequences

Multiview video test sequences for video coding standardization and other related research efforts in this area. Introduction The MERL-MVC dataset includes a set of multiview video test sequences for video coding standardization and research. At a Glance <ul> <li>The size of the unzipped dataset is ~2.7GB</li> <li>The zip file includes three folders, each with 8 videos in YUV format. Each video file corresponds to a view in a linear camera array. Additionally, there are two documents that provide more details about the capture system and post-processing steps, as well as camera parameter information.</li> </ul> Citation If you use the MERL-MVC dataset in your research, please cite our contribution: <pre><code>@Misc{Vetro05 author = {Anthony Vetro and Morgan McGuire and Wojciech Matusik and Alexander Behrens and Jinho Lee and Hanspeter Pfister}, title = {Multiview Video Test Sequences from {MERL}}, howpublished = {{ISO/IEC JTC1/SC29/WG11 m12077, Busan, Korea}} month = {April}, year = {2005}, } </code></pre> Copyright and License The MERL-MVC dataset is released under <a href="https://creativecommons.org/licenses/by-sa/4.0/">CC-BY-SA-4.0 license</a>. All data: <pre><code>Created by Mitsubishi Electric Research Laboratories (MERL), 2002 SPDX-License-Identifier: CC-BY-SA-4.0</code></pre>

opencc-by-4.0May 2023View details →

75-kyr paired mean summer temperature (MST) and moisture balance (BIT-index) data for eastern equatorial Africa based on GDGT distributions in the DeepCHALLA sediment sequence

The DeepCHALLA (DCH) GDGT-based climate proxy data series consist of paired measurements on 373 discrete 2-cm-thick sediment samples, represented by their DCH event-free depth in meter (mefd). Section depth center refers to the distance (in cm) of the sample’s center from the top of the individual core section as represented by its DCH core code. Sediment age is based on the age model as presented in Fig. 2 in Baxter et al. (2023). Mean Summer Temperature (MST) was calculated from the distribution of sedimentary brGDGTs according to Pearson et al. (2011) and rescaled using an ensemble reconstruction for eastern Africa covering the last 25 ka (Extended Data Fig. 4 in Baxter et al., 2023). The branched versus isoprenoid tetraether (BIT) index of sedimentary brGDGTs from Lake Chala, reflecting lake water-balance variation, was calculated according to Hopmans et al. (2004).

opencc-by-4.0Apr 2023View details →

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

ncVarPred-1D3D: The data used for testing the inconsistency among genome sequence, epigenetic profile, and later, to show its relation to 3D chromatin structure can be found in sanity_check_data.tar.gz. Some trained model for noncoding mutation effect prediction (mapping genome sequence to epigenetic profile) can be found in CNN_MLP, CNN_GCN, CNN_RNN_MLP, CNN_RNN_GCN.tar.gz. The trained model for pathogenic variants prediction can be found in fewshot_pathogenic_model.tar.gz.  The training data can be found in training_data.tar.gz. Some noncoding variant effects prediction results, e.g. eQTL and pathogenic variants, can be replicated using the data shared in ncVar_data.tar.gz.

opencc-zeroMay 2023View details →

Data from: A comparison of non-destructive visceral swab and tissue biopsy sampling methods for genotyping-by-sequencing in the freshwater mussel Fusconaia askewi

Limiting harm to organisms via genetic sampling is an important consideration for rare species. Nondestructive sampling techniques have been developed to address this issue in freshwater mussels. Two methods, visceral swabbing and tissue biopsies, have proven to be effective for DNA sampling, though it is unclear as to which method is preferable for genotyping-by-sequencing (GBS). Tissue biopsies may cause undue stress and damage to organisms, while visceral swabbing potentially reduces the chance of such harm. Our study compared the efficacy of these two DNA sampling methods for generating GBS data for the Unionid freshwater mussel, Texas Pigtoe (Fusconaia askewi). Our results find both methods generate quality sequence data, though some considerations are in order. Tissue biopsies produced significantly higher DNA concentrations and larger numbers of reads when compared to swabs, though there was no significant association between starting DNA concentration and number of reads generated. Swabbing produced greater sequence depth (more reads per sequence) while tissue biopsies revealed greater coverage across the genome (at lower sequence depth). Patterns of genomic variation as characterized in principal component analyses were similar regardless of the sampling method, suggesting that the less invasive swabbing is a viable option for producing quality GBS data in these organisms.

opencc-zeroMay 2023View details →

Amplicon sequence variants (ASV) of gut pathogens in hooded cranes and domestic geese

Driven by habitat loss from anthropogenic activities, wintering migratory birds forage together with poultry in paddy fields, and thus impose risks of cross transmitting pathogens. To date, there is little evidence for such risks of pathogen transmission between wild birds and poultry. Using the high-throughput sequencing, we report on detected potential pathogens of both wild hooded cranes Grus monacha and sympatric domestic geese Anser anser domesticus during the wintering period and infer the possibility of cross-species pathogen transmission. The results revealed that the number of shared amplicon sequence variants (ASVs) of potential pathogens between the gut microbiota of the two species was low during the early wintering stage (17.2%; 5 ASVs shared) but increased to 56.3% (18 ASVs shared) during the late wintering stage. That is, potential pathogens in the gut microbial communities of the two species became more similar through co-foraging in paddy fields, supporting cross-transmission of pathogens between hooded cranes and domestic geese during the wintering period. Importantly, transmission appeared to be largely from wild hooded cranes to domestic geese, although some potential pathogens may have become specialized to the domestic goose in late wintering stage. Humans are also facing the risks of contracting these potential pathogens from migratory birds through their frequent contact with domestic poultry. It is, therefore, necessary to closely monitor this pathway of pathogen transmission from wild birds to domestic animals and even to humans.

opencc-zeroMay 2023View details →

Characterizing the diet of a threatened seabird, the Marbled Murrelet (Brachyramphus marmoratus), using high-throughput sequencing

Understanding prey consumption patterns is critical to understanding the ways in which seabirds cope with a changing ocean. However, characterizing the dietary habitats of seabirds can be challenging. In this study, we investigated the diet of the Marbled Murrelet (Brachyramphus marmoratus) population that lives in waters off California, Oregon, and Washington, USA, using fecal DNA, custom metabarcoding, and high-throughput sequencing. Murrelets were captured at sea by dip-netting at night. Across this region, murrelets consumed highly diverse prey types including 17 fish species and 10 invertebrate species, in accord with previous work indicating the species' forage on a wide range of prey. Pacific Herring (Clupea pallasii) was the most common prey in Washington and Oregon (frequency of occurrence = 0.84 and 0.69, respectively), replaced by Northern Anchovy (Engraulis mordax) in California (frequency of occurrence = 0.77). In Oregon, where our sample size was sufficient, diet composition differed between the 2017 and 2018 breeding seasons, with an apparent decline in the proportional consumption of energy-dense prey. Common and energy-dense prey were consumed in equal proportions by males and females, perhaps because of foraging in the same habitat. Diet did not vary between breeders and non-breeders. Our study offers the first detailed report on the diet of adult Marbled Murrelets in waters where they are listed as Threatened by the US federal government. This indicates that managing fisheries and conserving spawning habitat for high-occurrence prey species could benefit murrelet populations.

opencc-by-4.0May 2023View details →

Additional raw data in `Cell-type-specific co-expression inference from single cell RNA-sequencing data'.

This repository holds the additional raw data used to generate figures in the publication "Cell-type-specific co-expression inference from single cell RNA-sequencing data" (preprint version: <a href="http://source%20code%20repo%20for%20%60cell-type-specific%20co-expression%20inference%20from%20single%20cell%20rna-sequencing%20data%27./">https://www.biorxiv.org/content/10.1101/2022.12.13.520181v1</a>). Table of contents: <ul> <li>Figure_1B.rds:  <ul> <li>raw data of Figure 1B </li> <li>co-expression estimates of 500*499/2 gene pairs across 100 replicates for 7 methods under two settings of sequencing detph variations</li> </ul> </li> <li>Supplementary_Figure_1B.rds:  <ul> <li>raw data of Supplementary Figure 1B </li> <li>co-expression estimates of 500*499/2 gene pairs across 100 replicates for 7 methods under two settings of sequencing detph variations</li> </ul> </li> <li>Supplementary_Figure_2.rds:  <ul> <li>raw data of Supplementary Figure 2 </li> <li>empirical power evaluated for 4999 gene pairs and 6 methods</li> </ul> </li> <li>Figure_3B.rds:  <ul> <li>raw data of Figure 3B</li> <li>co-expression estimates of a network of 500 genes for 9 methods across 100 replicates</li> </ul> </li> <li>Additional_Raw_Data.xlsx <ul> <li>raw data of Figure 3A: (geometric mean expression levels, co-expression estimates) for 4999 gene pairs and 11 methods</li> <li>raw data of Figure 3C: running times for 11 methods</li> <li>raw data of Supplementary Figure 3: (geometric mean expression levels, co-expression estimates) for 4999 gene pairs and 11 methods under two settings of sequencing detph variations</li> </ul> </li> </ul>

opencc-by-4.0Jun 2023View details →

Triplets of core transmembrane alpha-helical seqments consecutive in sequence from a curated subset of OPM pdb files.

PDB structure files of triplets of transmembrane alpha-helical segments consecutive in sequence from a curated subset of alpha-helical polytopic membrane proteins from OPM. The structures originate from representatives with less than 40% sequence identity and at least 2.7 Angstrom resolution. All together 332 triplet structures are present from 94 membrane proteins. The PDB ID of each file is the first four characters of the file name.

A next-generation sequencing study of arthropods in the diet of Laysan Teal (Anas laysanensis)

The critically endangered Laysan Teal Anas laysanensis (known as koloa pōhaka in the Hawaiian language) in the Northwestern Hawaiian Islands has wild populations on Kamole (Laysan Island), Kuaihelani (Midway Atoll NWR), and Hōlanikū (Kure Atoll). The Laysan Teal faces a new risk on Sand Island, Kuaihelani: non-target poisoning via a pending House Mouse Mus musculus eradication. After mice were observed attacking and depredating Laysan Albatross Phoebastria immutabilis (mōlī) in 2015, plans to eradicate mice were developed to protect this seabird species. However, this approach risks poisoning the Laysan Teal. To reduce exposure, teal will be translocated during mouse eradication. Even so, there is a potential risk of secondary poisoning for teal by ingesting arthropods that feed on mouse bait. We therefore used next-generation sequencing (NGS) to identify which arthropods teal consume. From August 2019 to February 2020, we collected 71 fresh teal faecal samples on Sand Island, and successfully extracted DNA from 21 samples. Via NGS, we found that teal most frequently consume cockroaches (order: Blattodea), freshwater ostracods (Cyprididae), midges (Chironomidae), and isopods (Porcellionidae). To a lesser degree, teal also eat spiders (Araneae), moths (Lepidoptera), beetles (Coleoptera), springtails (Entomobryomorpha), thrips (Thysanoptera), and crabs (Decapoda). Notably, Sand Island's teal consume entirely different arthropods from teal on Kamole, which mainly eat flies (Diptera) and brine shrimp (Anostraca, Artemia sp.). Our study serves as a model for risk mitigation during invasive rodent eradications.

opencc-by-4.0Jun 2023View details →

179 high quality metagenome-assembled genomes sequences and annotations

We analyzed seven sediment samples collected adjacent to ferromanganese nodules from the Clarion–Clipperton Fracture Zone (CCFZ) in the eastern Pacific Ocean. Through deep metagenomic sequencing, assembly, and binning, we reconstructed 179 high quality metagenome-assembled genomes (MAGs). This archive contains these genomes sequences and annotations.

Fastq sequence files supporting: Assessing the degradation of environmental DNA and RNA based on genomic origin in a metabarcoding context

Molecular tools of species identification based on eNAs (environmental nucleic acids; eDNA and eRNA) have the potential to greatly transform biodiversity science. However, the ability of eNAs to obtain "real-time" biodiversity estimates may be complicated by the differential persistence and degradation dynamics of the molecular template (eDNA or eRNA) and the barcode marker used. Here, we collected water samples over a 28-day period to comparatively assess species detection using eDNA and eRNA metabarcoding of two distinct barcode markers—a mitochondrial mRNA marker (COI) and a nuclear rRNA marker (18S)—following complete removal of Arthropoda taxa in a semi-natural freshwater system. Our findings demonstrate that Arthropoda community composition was largely influenced by marker choice, rather than molecular template, individual microcosm, or sampling time point. Further, although eRNA may capture similar species diversity as the established eDNA method, this finding may be marker dependent. Although we found little to no difference in decay rates observed among sample groups (COI eDNA, COI eRNA, 18S eDNA, 18S eRNA), this result is likely due to limitations in the ability of eNA-based metabarcoding to provide a strong correlation between true eNA copy numbers present in the environment and final read counts obtained (following the metabarcoding workflow). Collectively, our findings provide further support for the use of multi-marker assessments in metabarcoding surveys to unravel the broadest taxonomic diversity possible, highlight the limitations of eNA metabarcoding methods in providing accurate decay rate estimates, as well as establish the need for further comparative studies using both metabarcoding and single-species detection methods to assess the persistence and degradation dynamics of eNAs for a diverse range of taxa.

opencc-by-4.0Mar 2023View details →

Review on Current Aspects of Technique in DNA Sequencing

International -E- Conference on Recent Trends in Chemical Science, Physical Science, Life Science and Computer Technology (ICRTCPLCT-2023) Organized by AIJ Degree College of Science Murud Janjira on 15th March 2023.

opencc-by-4.0Jun 2023View details →

Isolation, biochemical characterization, and genome sequencing of two high-quality genomes of a novel chitinolytic Jeongeupia species

Raw data sets for the microbiologyOpen research article "Isolation, biochemical characterization, and genome sequencing of two high-quality genomes of a novel chitinolytic Jeongeupia species" including ClustalW Trees and the respective input file; canB 3.0 results; TYGS phylogenetic tree results; PGAP genome annotation files and Canu 2.0 assembly reports of the two genomes.

Dataset from: The origin and fate of fungal mitochondrial horizontal gene transferred sequences in orchids (Orchidaceae)

The transfer of DNA among distantly related organisms is relatively common in bacteria but less prevalent in eukaryotes. Among fungi and plants, few of these events have been reported. Two segments of fungal mitochondrial DNA have been discovered in the mitogenome of orchids. Here, we build on their work to understand the timing of those transfer events, which orchids retain the fungal DNA, and the fate of the foreign DNA during orchid evolution. We update the content of the large DNA fragment and establish that it was transferred to the most recent common ancestor of a highly diverse clade of epidendroid orchids that lived ~28–43 Mya. Also, we present hypotheses of the origin of the small transferred fragment. Our findings deepen the knowledge of these interesting DNA transfers among organelles and we formulate a probable mechanism for these horizontal gene transfer events.

454-sequence data of Iron Age cattle from Althiburos – Tunisia

The Maghreb is a key region for understanding the dynamics of cattle dispersal and admixture with local aurochs following their earliest domestication in the Fertile Crescent more than 10,000 years ago. Here, we present data on mitochondrial D-loop sequences obtained for 12 archaeological specimens of Iron Age (~2,800 cal BP–2,000 cal BP) domestic cattle from the Eastern Maghreb, i.e. Althiburos (El Kef, Tunisia). Maternal lineages were assigned to the elusive R and ubiquitous African-T1 haplogroups found in two and ten Althiburos specimens, respectively. Our results corroborate the introgression of aurochs females into the domestic stock of cattle from Althiburos.

Dataset for: How eDNA data filtration, sequence coverage, and primer selection influence assessment of fish communities in northern temperate lakes

For nearly 15 years now, environmental DNA has demonstrated its effectiveness in monitoring biodiversity. Methodological and technical improvements have significantly enhanced the field. However, the effect of factors such as sequence coverage, bioinformatic filtration and primer choice have been less explored or need to be optimized according to specific survey objectives and study site characteristics. We evaluated these factors to help optimize monitoring fish biodiversity in North American temperate lakes. We sampled water for fish community eDNA analysis in 12 lakes from southwestern Québec, Canada. The lakes were selected to encompass a wide range of surface areas and species richness. We sampled water from a total of 520 sites (25 to 50 per lake) and analyzed three mitochondrial DNA regions (12S rRNA; 16S rRNA; and cytb) using NovaSeq sequencing. Our results, based on rarefied count matrices (from a sequencing depth of 100,000 to a minimum depth of 1,000 reads per sample), showed that keeping only species in each sample if they represented at least one thousandth (species minimum read proportion threshold = 0.001) of the sample's reads was adequate to remove false positives and had a limited negative impact on true positives with low read counts. The sequencing depth was found to have a negligible impact on the accuracy of fish community assessment in a given lake. With the same sequencing depth and a complete local reference database for each primer set, a single primer set produced similar species richness medians than the combination of two or three primer sets. Overall, 12S and 16S detected more species and provided more consistent community profiles than cytb. Based on our observations, we suggest using the 12S MiFish-U primer set and applying a minimum proportion of 0.001 reads per species and site to monitor north-temperate lentic freshwater fish communities.

Analyses of ergot alkaloid production in Aspergillus leporis and an easD knockout and sequences for phylogenetic analyses of rugulovasine-associated genes

Ergot alkaloids are fungal specialized metabolites that are important in agriculture and serve as sources of several pharmaceuticals. Aspergillus leporis is a soil saprotroph that possesses two ergot alkaloid biosynthetic gene clusters encoding lysergic acid amide production. We identified two additional, partial biosynthetic gene clusters within the A. leporis genome containing some of the ergot alkaloid synthesis (eas) genes required to make two groups of clavine ergot alkaloids, fumigaclavines and rugulovasines. Clavines possess unique biological properties compared to lysergic acid derivatives. Bioinformatic analyses indicated the fumigaclavine cluster contained functional copies of easA, easG, easD, easM, and easN. Genes resembling easQ and easH, which are required for rugulovasine production, were identified in a separate gene cluster. The pathways encoded by these partial, or satellite, clusters would require intermediates from the previously described lysergic acid amide pathway to synthesize a product. Chemical analyses of A. leporis cultures revealed the presence of fumigaclavine A. Rugulovasine was only detected in a single sample, however, prompting a heterologous expression approach to confirm functionality of easQ and easH. An easA knockout strain of Metarhizium brunneum, which accumulates the rugulovasine precursor chanoclavine-I aldehyde, was chosen as expression host. Strains of M. brunneum expressing easQ and easH from A. leporis accumulated rugulovasine as demonstrated through mass spectrometry analysis. These data indicate that A. leporis is exceptional among fungi in having the capacity to synthesize products from three branches of the ergot alkaloid pathway and for utilizing an unusual satellite cluster approach to achieve that outcome.

opencc-by-4.0Dec 2022View details →

Intergrated Multi-omics Sequencing Reveals Metabolic Reprograms in the Progression of ccRCC

ccRCC is a complex disease with remarkable immune and metabolic heterogeneity. Here, we present a TJ-RCC cohort, performing genomic, transcriptomic, proteomic, metabonomic and spatial multi-omic profiling on 100 ccRCC cases. Using the scRNA-seq-derived signature, we identify 4 subtypes. Multilevel profiling distinguishes a unique ccRCC subtype, De-clear cell differentiated (DCCD) -ccRCC, with distinctive metabolic features. DCCD cancer cells are characterized by fewer lipid droplets, extremely inhibited metabolic activity, enhanced nutrients uptake capability and a high proliferation rate, leading to poor prognosis. Using single-cell and spatial trajectory analysis, we demonstrate that DCCD is a common mode of ccRCC progression. Even among stage I patients, DCCD indicates worse outcomes and higher recurrence rate, indicating it cannot be cured by nephrectomy alone. This study provides a treatment strategy based on immune subtypes, which could enable precise clinical management of ccRCC.