Find research datasets worth reusing

Satyrium longicauda (Orchidaceae) species complex: Morphometric characters and DNA sequences

Morphology.xlsx Morphological data obtained from 1802 individuals of the Satyrium longicauda (Orchidaceae) complex. Each entry has fifteen values representing both vegetative and reproductive characters. The full dataset or part of it has been used to perform univariate and multivariate analyses. Each data point was obtained by measuring fresh material either with a ruler or a pair of calipers or by counting the number of different structures. TS Alignment_130Samples.nex Dataset that contains 130 ITS sequences including 14 gaps codified. This dataset has been used to perform phylogenetic analyses using both parsimony and Bayesian inference. All sequences are publically available on Genbank.

Sequences of Orthorectified Images of the Water Surface of Two Rivers: River Sheaf (Sheffield, UK), and River Calder (Todmorden, UK)

This data set contains sequences of orthorectified images of the free surface of two rivers:  <ul> <li>River Sheaf, Sheffield, United Kingdom (Latitude: 53.373056° Longitude: -1.463913° (WGS 84)), recorded between January 2019 and February 2020;</li> <li>River Calder, Todmorden, United Kingdom (Latitude: 53.716198° Longitude: -2.097028°), recorded between 6 and 13 October 2020.</li> </ul> The images are extracted from videos of the water surface also included in the data set. They are complemented by Matlab files containing the corresponding average space-time Fourier spectra. Each measurement is associated with the corresponding measurement of the river depth and estimates of the discharge. Please refer to Documentation.pdf for further details.

opencc-zeroMay 2022View details →

Sequence conservation and structural features that are common within TRP channels

TRP proteins are a large family of cation-selective channels, surpassed in variety only by voltage-gated potassium channels. Detailed molecular mechanisms governing how membrane voltage, ligand binding, or temperature can induce conformational changes promoting the open state in TRP channels are still a matter of debate. Aiming to unveil distinctive structural features common to the transmembrane domains within the TRP family, we performed phylogenetic reconstruction, sequence statistics, and structural analysis over a large set of TRP channel genes. Here we report an exceptionally conserved set of residues. This fingerprint is composed of twelve residues localized at equivalent three-dimensional positions in TRP channels from the different subtypes. Moreover, these amino acids are arranged in three groups, connected by a set of aromatics located at the core of the transmembrane structure. We hypothesize that differences in the connectivity between these different groups of residues harbors the apparent differences in coupling strategies used by TRP subgroups.

Raw sequencing data of NGS of stomach contents of sympatric species of weakly electric fish (genus: Campylomormyrus)

This dataset contains the raw sequencing data of stomach contents of sympatric species of weakly electric fish (genus: Campylomormyrus) using next generation sequencing. Stomach content samples were collected from five Campylomormyrus species (C. alces, ; C. compressirostris, ; C. curvirostris, ; C. numenius, ; C. tshokwe) and samples of Gnathonemus petersii (G. petersii, ), a sister genus of Campylomormyrus. The fish specimens, from which these stomach content samples are extracted, were collected during an expedition to the Republic of the Congo in fall 2012. The dataset files are in FASTA format.

opencc-zeroMay 2022View details →

Genotyping-by-sequencing of Canada's Apple Biodiversity Collection

Canada's Apple Biodiversity Collection (ABC) is one of the most diverse collections of apples in the world, which was designed to enable genetic mapping. The ABC is located at the Agriculture and Agri-Food Canada (AAFC) Kentville Research and Development Centre in Nova Scotia, Canada. In addition to phenotypic descriptions of the ABC, sequencing the accessions in the collection provides a valuable resource not only for researchers working on the collection, but for those studying apples more broadly. With this in mind, we report and make publicly available genotyping-by-sequencing (GBS) data for over 1,000 apple accessions from the ABC. By using three SNP callers and imputation, we were able to genotype 278,231 SNPs from 1,175 diverse apple accessions from the ABC.

Basal Ganglia Neurons in Healthy and Parkinsonian Primates Generate Recurring Sequences of Spikes

These data are the source data for the manuscript entitled "Basal Ganglia Neurons in Healthy and Parkinsonian Primates Generate Recurring Sequences of Spikes", authored by Adriana Galvan and Thomas Wichmann (Emory University, Atlanta, GA).   The data are interspike interval measurements generated from electrophysiological recordings of spontaneous spiking activities of single neurons in the basal ganglia of awake monkeys, before and after rendering them parkinsonian by treatment with MPTP. THe animals were not engaged in any task or other structured activity. The data format is a one-column listing of successive interspike intervals, and are presented in milliseconds. The data are structured into different folders: GPe normal - data collected in the external pallidal segment, under normal conditions GPe MPTP - data collected in the external pallidal segment, under parkinsonian conditions STN normal - data collected in the subthalamic nucleus, under normal conditions STN MPTP - data collected in the subthalamic nucleus, under parkinsonian conditions GPi normal - data collected in the internal pallidal segment, under normal conditions GPi MPTP - data collected in the internal pallidal segment, under parkinsonian conditions A 'Read Me' file is included, containing these explanations. For questions, please contact the corresponding author, Dr. Thomas Wichmann (twichma@emory.edu).

Supplementary material (Sanger sequencing photo) of the case of THRB mosaicism presented in Clinically Symptomatic Resistance to Thyroid Hormone β Syndrome Because of THRB Gene Mosaicism of Donnars et al. (https://doi.org/10.1210/clinem/dgac347)

Supplementary material (Sanger photo) of the case of THRB mosaicism presented in "Clinically Symptomatic Resistance to Thyroid Hormone β Syndrome Because of THRB Gene Mosaicism", by Donnars et al. (https://doi.org/10.1210/clinem/dgac347)

Data for "Predicting aggregate morphology of sequence-defined macromolecules with Recurrent Neural Networks"

These are the data associated with the paper, "Predicting aggregate morphology of sequence-defined macromolecules with Recurrent Neural Networks" (DOI 10.1039/D2SM00452F). Three of the directories contains subdirectories with `GSD` files dumped from HOOMD. The other contains pretrained RNN models as TorchScript binaries exported from PyTorch.

RNA modification detection using direct RNA sequencing and nanoDoc2

The core of nanoDoc2 includes a machine-learning algorithm in which a 6-mer segmented raw current signal is compared by Deep-One-Class classification using a Wavenet-based neural network. As an output, an RNA modification is detected by a statistical score in each candidate position. Herein, we describe the detailed instructions on how to use nanoDoc2 for signal segmentation, train/test the neural network and finally predict RNA modifications present in nanopore direct RNA sequence data.

opencc-zeroDec 2021View details →

Data from: A genotyping-in-thousands by sequencing panel to inform invasive deer management using non-invasive fecal and hair samples

Studies in ecology, evolution, and conservation often rely on non-invasive samples, making it challenging to generate large amounts of high-quality genetic data for many elusive and at-risk species. We developed and optimized a Genotyping-in-Thousands by sequencing (GT-seq) panel using non-invasive samples to inform the management of invasive Sitka black-tailed deer (Odocoileus hemionus sitkensis) in Haida Gwaii (Canada). We validated our panel using paired high-quality tissue and non-invasive fecal and hair samples to simultaneously distinguish individuals, identify sex and reconstruct kinship among deer sampled across the archipelago, then provided a proof-of-concept application using field-collected feces on SGang Gwaay, an island of high ecological and cultural value. Genotyping success across 244 loci was high (90.3%) and comparable to that of high-quality tissue samples genotyped using restriction-site associated DNA sequencing (92.4%), while genotyping discordance between paired high-quality tissue and non-invasive samples was low (0.50%). The panel will be used to inform future invasive species operations (culls or eradications) in Haida Gwaii by providing individual and population information to inform management. More broadly, our GT-seq workflow that includes quality control analyses for targeted SNP selection and a modified protocol may be of wider utility for other studies and systems where non-invasive genetic sampling is employed.

A Monomeric Mycobacteriophage Immunity Repressor Utilizes Two Domains to Recognize an Asymmetric DNA Sequence

Supporting source data consisting of simulation topologies and trajectories in pdb and xtc file formats, respectively.

First large-scale quantification study of DNA preservation in insects from natural history collections using genome-wide sequencing

Insect declines are a global issue with significant ecological and economic ramifications. Yet we have a poor understanding of the genomic impact these losses can have. Genome-wide data from historical specimens has the potential to provide baselines of population genetic measures to study population change, with natural history collections representing large repositories of such specimens. However, an initial challenge in conducting historical DNA data analyses, is to understand how molecular preservation varies between specimens. Here, we highlight how Next Generation Sequencing methods developed for studying archaeological samples can be applied to determine DNA preservation from only a single leg taken from entomological museum specimens, some of which are more than a century old. An analysis of genome-wide data from a set of 113 red-tailed bumblebee (Bombus lapidarius) specimens, from five British museum collections, was used to quantify DNA preservation over time. Additionally, to improve our analysis and further enable future research we generated a novel assembly of the red-tailed bumblebee genome. Our approach shows that museum entomological specimens are comprised of short DNA fragments with mean lengths below 100 base pairs (BP), suggesting a rapid and large-scale post-mortem reduction in DNA fragment size. After this initial decline, however, we find a relatively consistent rate of DNA decay in our dataset, and estimate a mean reduction in fragment length of 1.9bp per decade. The proportion of quality filtered reads mapping our assembled reference genome was around 50 %, and decreased by 1.1 % per decade. We demonstrate that historical insects have significant potential to act as sources of DNA to create valuable genetic baselines. The relatively consistent rate of DNA degradation, both across collections and through time, mean that population level analyses - for example for conservation or evolutionary studies - are entirely feasible, as long as the degraded nature of DNA is accounted for.

Flash sequence duration

Unlike light input for forming images, non-image forming retinal pathways are optimized to convey information about the total light environment, integrating over time and space. It has been demonstrated in a variety of species that the retinohypothalamic pathway underlying circadian entrainment can effectively integrate the impact of individual flashes over time and convey this information as if continuous light exposure had occurred. In this study, we examine the extent to which this temporal integration can occur. A group of healthy, young (N=20) individuals took part in a series of 16-d protocols in which we examined the impact of different lengths of light flash exposure sequences on circadian timing. We find that a sequence as short as 15 minutes can engender as much change in circadian timing as sequences that last for 3.5 hours. Acute suppression of melatonin was also observed during short (15-minute) exposures, but not in exposures over one hour. Our data are consistent with the theory that responses to light flashes are mediated by the extrinsic, rod/cone pathway and saturate the response of this pathway within 15 minutes. Further excitation leads to no greater change in circadian timing and no longer can acutely suppress melatonin, indicating that this pathway may be in a refractory state following this brief light stimulation. As the light flash sequences can be administered while individuals are sleeping, and without waking an individual, these short, 15-minute exposures may be especially beneficial as a clinical intervention for a variety of circadian-based sleep disorders.

Zehneria neorensis: Additional phylogenies and sequence information

Basic data and supplement for Ranjan et al. 2022, Biogeography of Zehneria (Cucurbitaceae) and a New Species from India, Systematic Botany. Zehneria is one of the most diverse genera in Cucurbitaceae with 75 accepted species mainly in Southeast Asia and tropical Africa. We describe Zehneria neorensis, a new species from Neora Valley in the mountains of West Bengal, India, which has 7–10 cm long twisted fruiting pedicels, the longest pedicels reported in the genus so far. Based on morphological data, we also suggest the transfer of Melothria morobensis to the genus Zehneria. With a molecular phylogenetic and global biogeographic analysis based on 3856 nucleotides of plastid and nuclear ribosomal DNA, we demonstrate that the genus Zehneria most likely originated on the African continent 24 (30-19) million years ago and spread from there at least five times to Madagascar and three times to Asia. Zehneria neorensis represents an independent colonization event from Africa to India about 11 (15–7) million years ago. Three lineages reached New Guinea/Australia and finally moved into Polynesia. We infer a rate of at least 20 long-distance dispersal (LDD) events per 10 million years in the genus. This high LDD frequency is most likely a result of the small berry fruits and small flattened seeds of Zehneria, which seem perfectly adapted to long-distance bird dispersal. Field observations are needed to investigate a potential effect of the newly discovered extended and coiling pedicels in Zehneria neorensis on seed dispersal efficiency. The new species adds to a growing list of rather old Cucurbitaceae lineages in the Himalayan foothills, supporting the hypothesis of long climatic stability in the region.

Dataset from: Sequence grammar underlying unfolding and phase separation of globular proteins

Dataset related to the figures from the paper "Sequence grammar underlying unfolding and phase separation of globular proteins". The raw mass spectrometry proteomics data have been deposited via the PRIDE partner repository to the ProteomeXchange Consortium under the dataset identifier PXD033716.

Data for a preliminary molecular phylogeny of the family Hydroptilidae (Trichoptera): exploring the combination of targeted enrichment data and legacy Sanger sequence data

The purpose of this study is to provide a proof-of-concept that the use of molecular data, particularly targeted enrichment data, and statistically supported methods of analysis can result in the construction of a stable phylogenetic framework for the microcaddisflies (Trichoptera: Hydroptilidae). Here, we use a combination of targeted enrichment data for ca. 300 nuclear protein-coding genes and legacy (Sanger-based) sequence data for the mitochondrial COI gene and partial sequence from the 28S rRNA gene.

DNA metabarcoding sequence data for diet analysis of caribou

Woodland caribou (Rangifer tarandus caribou) are threatened in Canada due to the drastic decline in population size caused primarily by human-induced landscape changes that decrease habitat and increase predation risk. Conservation efforts have largely focused on reducing predators and protecting critical habitat, whereas research on dietary niches and the role of potential food constraints in lichen-poor environments is limited. To improve our understanding of dietary niche variability, we used a next-generation sequencing approach with metabarcoding of DNA extracted from faecal pellets of woodland caribou located on Lake Superior in lichen-rich (mainland) and lichen-poor (island) environments. Amplicon sequencing of fungal ITS2 region revealed lichen-associated fungi as predominant in samples from both populations, but amplification at the chloroplast trnL region, which was only successful on island samples, revealed primary consumption of yew based on relative read abundance (Taxus spp.; 83.68%) with dogwood (Cornus spp.; 9.67%) and maple (Acer spp.; 4.10%) also prevalent. These results suggest that conservation efforts for caribou need to consider the availability of food resources beyond lichen to ensure successful outcomes. More broadly, we provide a reliable methodology for assessing ungulate diet from archived faecal pellets that could reveal important dietary shifts over time in response to climate change.

Data in support of Using target sequence capture to improve the phylogenetic resolution of a rapid radiation in New Zealand Veronica

Includes alignments and trees for the analysis found in Thomas et al. 2021, Using target sequence capture to improve the phylogenetic resolution of a rapid radiation in New Zealand Veronica; American Journal of Botany, Special Issue: Exploring Angiosperms353: a Universal Toolkit for Flowering Plant Phylogenomics. Alignments comprise subsets of Angiosperms353 genes given each filtering scheme (full, intersection, sortadate_BP, sortadate_TL) and gene type/subset (exons, introns, supercontigs), and for markers downloaded from GenBank, as explained in the Methods section of Thomas et al. 2021. Trees were included for each of these alignments from IQtree and Astral; SVDquartets tree was only estimated for the full set of supercontigs. Gene trees were generated with IQtree. Tree files are named differently than the final manuscript; refer to the number of genes specified in Fig 1 of Thomas et al, 2021 and specified in each filename to identify filtering scheme. Raw sequence reads are available on the Sequence Read Archive at <a href="http://www.ncbi.nlm.nih.gov/bioproject/715342">http://www.ncbi.nlm.nih.gov/bioproject/715342</a>.

16S sequence of gut bacterial isolates B. adolescentis 269-1 and A. caccae 127-8-5

The 16S rRNA gene sequences of bacterial strains B. adolescentis 269-1 and A. caccae 127-8-5 determined by Sanger sequencing. Amplification primers were 8F and 1492R; 8F was used for sequencing.

Data and processing scripts for PRISM barcode sequencing data used in "Massively parallel pooled screening reveals genomic determinants of nanoparticle-cell interactions"

Sequencing data for the PRISM barcodes generated after nano-particle treatment is presented in this repository alongside the code to process the sequencing counts to generate the binning probabilities and weighted scores.  For the details please see the original publication or the bioarxiv preprint:  https://doi.org/10.1101/2021.04.05.438521 The raw data is provided in PILOT_DATA_COUNTS.csv and EXPERIMENT_DATA_COUNTS.csv files, for the pilot and the actual experiment.  For each of these files an R script is provided to process them, along with the output of the scripts (PILOT_DATA_PROBABILITIES.csv and EXPERIMENT_DATA_PROBABILITIES.csv)