Find research datasets worth reusing

opencc-by-4.0Dec 2022View details →

Data to reproduce analysis in the WCDT metastatic prostate tumor subtypying paper

Systemic targeted therapy in prostate cancer is primarily focused on ablating androgen signaling. Androgen deprivation therapy and second-generation AR-targeted therapy selectively favor the development of treatment-resistant subtypes of metastatic castration resistant prostate cancer (mCRPC), defined by whether the tumor expresses either AR or neuroendocrine markers. Among the subtypes of mCRPC, the molecular drivers of double-negative (AR-/NE-) mCRPC are poorly defined. In this study, we comprehensively characterize genomic and epigenomic features of treatment-emergent mCRPC subtypes in 210 tumors by integrating matched RNA sequencing, whole-genome sequencing, and whole-genome bisulfite sequencing. We show that AR-/NE- tumors exhibit a clinically and molecularly distinct phenotype. Patients with AR-/NE- mCRPC tumors have the shortest survival, and these tumors preferentially harbor amplification of the chromatin remodeler CHD7 and loss of PTEN. We demonstrate that methylation changes in CHD7 candidate enhancers are linked to elevated CHD7 expression in AR-/NE+ tumors. Moreover, we use genome-wide methylation analysis to nominate the Krüppel-like factor gene KLF5 as a driver of the AR-/NE- phenotype and link its activity to loss of the tumor supressor RB1. These observations reveal the aggressiveness of the AR-/NE- tumors and elucidate genomic and epigenomic drivers of mCRPC subtypes, which may facilitate the identification of novel therapeutic targets in this highly aggressive disease.

opencc-by-4.0Jan 2023View details →

Data files for Constraints on axionlike particles from a combined analysis of three flaring Fermi flat-spectrum radio quasars

In this repository, we provide data files in connection to our publication “Constraints on axionlike particles from a combined analysis of three flaring Fermi flat-spectrum radio quasars” submitted for publication in Physical Review D and available on the Arxiv: <a href="https://arxiv.org/abs/2211.03414">https://arxiv.org/abs/2211.03414</a> In the paper, we analyze data from the Fermi Large Area Telescope (LAT) of three flat spectrum radio quasars (FSRQs): 3C454.3, 3C279, and CTA102, to search for signatures of oscillations between photons and axion-like particles (ALPs). In this repository, we provide the following data: <ul> <li>Files ending on *_data_seds.npy contain the spectral energy distributions (SEDs) measured with the Fermi LAT and extracted using the fermipy software</li> <li>Files ending on *_LLs.npy contain the log-likelihood values of our fits over a grid of ALP masses and photon-ALP couplings</li> <li>Files ending on *_Lambdas.npy contain the log-likelihood ratio test values of our fits over a grid of ALP masses and photon-ALP couplings</li> <li>Files ending on *_LL_thresh.npy contain the threshold values for the log-likelihood ratio test for which we can claim an exclusion at the 95% confidence level over a grid of ALP masses and photon-ALP couplings</li> <li>Files ending on*_contours.npy contain the upper limit contours.</li> </ul> Files starting with "ALL" contain the likelihoods combined over all sources We also provide a minimal jupyter notebook, analysis_arrays.ipynb, that demonstrates how to read in the files.

opencc-by-4.0Jan 2023View details →

Are Nonhuman Animals Averse to Inequity? A Meta-Analysis [Code and Data]

Code and (anonymized) data for the manuscript "Are Nonhuman Animals Averse to Inequity? A Meta-Analysis"

opencc-by-4.0Jan 2023View details →

N-TIMP2 CD loop extension NGS data and analysis script

NGS data and analysis script for the YSD sorts described in Bonadio et al. "Using designed loop extension and combinatorial screening to enhance specificity of a broad matrix metalloproteinase inhibitor"

Raw Data for the article: Analysis of the Specific Immune Response after the Third Dose of mRNA COVID-19 Vaccines in Organ Transplant Recipients: Possible Spike-S1 Reactive IgA Signature in Protection from SARS-CoV-2 Infection

Background: Several studies have indicated that anti-SARS-CoV-2 mRNA vaccinations are less effective in inducing robust immune responses among solid organ transplant recipients (SOTRs) compared with the immunocompetent. The third dose of vaccine in SOTRs showed promising results of immunogenicity, even though clinical studies have suggested that immunocompromised subjects are less likely to build a protective immune response against SARS-CoV-2 resulting in lower vaccine efficacy for the prevention of severe COVID-19. Methods: Serological IgG and IgA were analyzed through CLIA or ELISA, respectively, while Spike-specific T cells were detected by ELISpot assay after the second and third dose of vaccine in 43 SOTRs. Results: The third dose induced an improvement in antibody response against SARS-CoV-2. We also reported a strong correlation between specific humoral and cellular responses after the third dose, even though we did not see significant changes in the magnitude of the SARS-CoV-2-specific T cell response. SOTRs who contracted the SARS-CoV-2 infection after the third dose, despite eliciting a positive IgG response, failed to mount an anti-Spike-S1 IgA response, both after the third dose and after SARS-CoV-2 infection. Conclusions: We can conclude that serum IgA detection can be helpful, along with IgG detection, for the evaluation of vaccine efficacy, principally in fragile subjects at high risk of infection.

Data from: A phylogenomic analysis of Lonicera and its bearing on the evolution of organ fusion

PREMISE: The ~140 species of Lonicera are characterized by variously fused leaves, bracteoles, and ovaries, making it a model system for studying the evolution and development of organ fusion. However, previous phylogenetic analyses, based mainly on chloroplast DNA markers, have yielded uncertain and conflicting results. A well-supported phylogeny of Lonicera will allow us to trace the evolutionary history of organ fusion. METHODS: We inferred the phylogeny of Lonicera using Restriction-site Associated DNA Sequencing (RADSeq), sampling all major clades and 18 of the 23 subsections. This provided the basis for inferring the evolution of five fusion-related traits. RESULTS: RADSeq data yielded a well-resolved and well-supported phylogeny. The two traditionally recognized subgenera (Periclymenum and Chamaecerasus), three of the four sections (Isoxylosteum, Coeloxylosteum, and Nintooa), and half of the subsections sampled were recovered as monophyletic. However, the large and heterogeneous section Isika was strongly supported as paraphyletic. Nintooa, a clade of ~22 mostly vine-forming species, including L. japonica, was recovered in a novel position, raising the possibility of cytonuclear discordance. We document the parallel evolution of fused leaves, bracteoles, and ovaries, with rare reversals. Most strikingly, complete cupules, in which four fused bracteoles completely enclose two unfused ovaries, arose at least three times. Surprisingly, these appear to have evolved directly from ancestors with free bracteoles instead of partial cupules. CONCLUSIONS: We provide the most comprehensive and well-supported phylogeny of Lonicera to date. Our inference of multiple evolutionary shifts in organ fusion provides a solid foundation for in-depth developmental and functional analyses.

Data for: Multilevel analysis of integration and disparity in the mammalian skull

Biological variation is often considered in a scalable hierarchy, e.g., within the individual, within the populations, above the species level. Morphological integration, the concept of covariation among constituent parts of an organism, is also hierarchical; the degree to which these 'modules' covary is a matter of the scale of the study as well as underlying processes driving the covariation. Multilevel analyses of trait covariation are a valuable tool to infer the origins and historical persistence of morphological diversity. Here we investigate concordance in patterns of integration and modularity across three biological levels of variation: within a species, within two genera-level radiations, and among species at the family level. We demonstrate this approach using the skull of mammalian family Leporidae (rabbits and hares), which is morphologically diverse and has a rare-among-mammals functional signal of locomotion adaptation. We tested three alternative hypotheses of modularity; from the most supported we investigated disparity and integration of each module to infer which is most responsible for patterns of cranial variation across these levels, and whether variation is partitioned consistently across levels. We found a common pattern of modularity underlies leporid cranial diversity, though there is inconsistency across levels in each module's disparity and integration. The face module contributes the most to disparity at all levels, which we propose is facilitating evolutionary diversity in this clade. Therefore, the distinctive facial tilt of leporids is an adaptation to locomotory behavior facilitated by a modular system that allows lineages to respond differently to selection pressures.

Galaxy Training Data for "End-to-End Tissue Microarray Image Analysis with Galaxy-ME"

This dataset provides the inputs used in the Galaxy Training Network (GTN) training 'End-to-End Tissue Microarray Image Analysis with Galaxy-ME'. The tutorial demonstrates how to use the Galaxy-ME tool suite for primary image processing, data analysis, and interactive visualization of multiple tissue imaging datasets. Original data was published by <a href="https://pubmed.ncbi.nlm.nih.gov/34824477/">Schapiro et al</a>.

Raw Data for the article: High-Resolution Secretome Analysis of Chemical Hypoxia Treated Cells Identifies Putative Biomarkers of Chondrosarcoma

Chondrosarcoma is the second most common bone tumor, accounting for 20% of all cases. Little is known about the pathology and molecular mechanisms involved in the development and in the metastatic process of chondrosarcoma. As a consequence, there are no approved therapies for this tumor and surgical resection is the only treatment currently available. Moreover, there are no available biomarkers for this type of tumor, and chondrosarcoma classification relies on operator-dependent histopathological assessment. Reliable biomarkers of chondrosarcoma are urgently needed, as well as greater understanding of the molecular mechanisms of its development for translational purposes. Hypoxia is a central feature of chondrosarcoma progression. The hypoxic tumor microenvironment of chondrosarcoma triggers a number of cellular events, culminating in increased invasiveness and migratory capability. Herein, we analyzed the effects of chemically-induced hypoxia on the secretome of SW 1353, a human chondrosarcoma cell line, using high-resolution quantitative proteomics. We found that hypoxia induced unconventional protein secretion and the release of proteins associated to exosomes. Among these proteins, which may be used to monitor chondrosarcoma development, we validated the increased secretion in response to hypoxia of glyceraldehyde 3-phosphate dehydrogenase (GAPDH), a glycolytic enzyme well-known for its different functional roles in a wide range of tumors. In conclusion, by analyzing the changes induced by hypoxia in the secretome of chondrosarcoma cells, we identified molecular mechanisms that can play a role in chondrosarcoma progression and pinpointed proteins, including GAPDH, that may be developed as potential biomarkers for the diagnosis and therapeutic management of chondrosarcoma.

Data for: Phylogenetically controlled life history trait meta-analysis in cetaceans reveals unexpected negative brain size and longevity correlation

The identification of patterns in trait evolution is essential to understand the interaction of evolutionary forces, and provides useful information for species management. Cetaceans are a phylogenetically well-resolved infraorder that exhibit distinct trait variation across behavioural, molecular and life history dimensions, yet few researchers have applied a meta-analytic or comparative approach to these traits. To understand cetacean trait evolution, we used a phylogenetic generalised least squares approach to examine the cognitive buffer hypothesis (CBH). A large brain should buffer individuals against environmental challenges through increasing survival rates, and a longer lifespan should buffer individuals against the cost of extended development for larger brains according to the CBH, leading to an expected positive correlation between brain size and lifespan. In contrast to this expectation, previously observed in taxa including primates, we found a negative correlation between brain size and lifespan in cetaceans. This suggests cetaceans experience selective pressures different from most other mammals in these traits but may be more similar to some social mammalian carnivores that display alloparenting. We also provide a comprehensive dataset to explore additional aspects of trait evolution but which would greatly benefit from studies on behavioural ecology across cetaceans and increased focus on data-deficient species.

Data from: Meta-analysis of the effects of insect pathogens: Implications for plant reproduction

Despite extensive work on both insect disease and plant reproduction, there is little research on the intersection of the two. Insect-infecting pathogens could disrupt the pollination process by affecting pollinator population density or traits. Pathogens may also infect insect herbivores and change herbivory, potentially altering resource allocation to plant reproduction. We conducted a meta-analysis to 1) summarize the literature on the effects of pathogens on insect pollinators and herbivores and 2) quantify the extent to which pathogens affect insect traits, with potential repercussions for plant reproduction. We found 39 articles that fit our criteria for inclusion, extracting 218 measures of insect traits for 21 different insect species exposed to 25 different pathogens. We detected a negative effect of pathogen exposure on insect traits, which varied by host function: pathogens had a significant negative effect on insects that were herbivores or carried multiple functions but not on insects that solely functioned as pollinators. Particular pathogen types were heavily studied in certain insect orders, with 7 of 11 viral pathogen studies conducted in Lepidoptera and 5 of 9 fungal pathogen studies conducted in Hymenoptera. Our results suggest that most studies have focused on a small set of host–pathogen pairs. To understand the implications for plant reproduction, future work is needed to directly measure the effects of pathogens on pollinator effectiveness.

Data and analysis of proteomic responses to hexokinase-II depletion in GAL80 and gal80Δ Saccharomyces cerevisiae with an engineered sesquiterpene-pathway

Dataset 1: <a href="https://zenodo.org/api/files/ece3309f-0ca2-4773-b2e3-b1c5c839faa4/GAL80_HXK2_Vs._dhxk2p_20200324_T2_004.xlsx">GAL80_HXK2_Vs._dhxk2p_20200324_T2_004.xlsx</a> The comparison between strain ILHA o128R+pJT9RFR (dHxk2p) and ILHA o401R+ pJT9RFR (HXK2) under the conditions with the addition of 1-Naphthaleneacetic acid and in the exponential growth phase and the ethanol growth phase.    Dataset 2: <a href="https://zenodo.org/api/files/ece3309f-0ca2-4773-b2e3-b1c5c839faa4/gal80%CE%94_HXK2_Vs._dhxk2p_20200219_T1_004.xlsx">gal80Δ_HXK2_Vs._dhxk2p_20200219_T1_004.xlsx</a> The comparison between strain ILHA NLD128-1 (dHxk2p) and ILHA NLD401 (HXK2) under the conditions with the addition of 1-Naphthaleneacetic acid and in the exponential growth phase (EXP) and the ethanol growth phase (ETH).

opencc-zeroMar 2023View details →

Data from: Sensitivity analysis of collision risk at wind turbines based on flight altitude of migratory waterbirds

This dataset contains information on the distribution of geese and swans and the three-dimensional flight trajectories. The former was obtained through vehicle field surveys, interviews, and a literature review. The latter was obtained using ornithodolites.

Supplementary data for "Revised and extended analysis of Ar VI"

Supplementary data for "Revised and extended analysis of Ar VI," Table 4. The table contains the four least-squares adjustment calculations mentioned in the article. The input and output files of these calculations are available here. The file names contain the set to which it belongs, the program to which it refers, whether it is an input or output file, and the name of the file as generally used in Cowan's package of programs.

Data Set "Efficient automatic construction of atom-economical QM regions with point-charge variation analysis"

This data set accompanies the publication "Efficient automatic construction of atom-economical QM regions with point-charge variation analysis" by Felix Brandt and Christoph R. Jacob (TU Braunschweig, Germany)  It contains the following files: - PDB files of the reactant and product starting structure - modified AMBER95 force field file - AMS fragment files for the ligands and ions - AMS input files for all geometry optimizations and single point calculations

opencc-zeroMar 2023View details →

Data from: Quantitative genetic analysis of floral traits shows current limits but potential evolution in the wild

The vast variation in floral traits across angiosperms is often interpreted as the result of adaptation to pollinators. However, studies in wild populations often find no evidence of pollinator-mediated selection on flowers. Evolutionary theory predicts this could be the outcome of periods of stasis under stable conditions, followed by shorter periods of pollinator change that provide selection for innovative phenotypes. We asked if periods of stasis are caused by stabilizing selection, absence of other forms of selection, or by low trait ability to respond even if selection is present. We studied a plant predominantly pollinated by one bee species across its range. We measured heritability and evolvability of traits, using genome-wide relatedness in a large wild population, and combined this with estimates of selection on the same individuals. We found evidence for both stabilizing selection and low trait heritability as potential explanations for stasis in flowers. The area of the standard petal is under stabilizing selection, but the variability is not heritable. A separate trait, floral weight, presents high heritability, but is not currently under selection. We show how a simple pollination environment coincides with the absence of current prerequisites for adaptive evolutionary change, while heritable variation remains to respond to future selection pressures.

GRAND-SLAM analysis of simulated nucleotide conversion in Illumina TruSeq data sets for grandRescue

These are processed data sets from the simulation of nucleotide conversions (T>C) in single-end and paired-end Illumina TruSeq reads for the purpose of investigating 4sU-induced mapping impairment by read lengths and library preparation methods and the potential of grandRescue to alleviate these effects. The original data set is from: Sarantopoulou, D. et al. (https://doi.org/10.1038/s41598-019-49889-1) GEO Accession:GSE124167 (samples: GSM3523316 - GSM3523318)   The zip files contain the full output from the processing pipeline (including the mapped reads, the scripts to run the pipeline and the output) for single-end (R1) and paired-end before and after rescue. The *.tsv.gz files are the GRAND-SLAM output tables. To generate the GRAND-SLAM output yourself, first prepare the mouse genomes. Then run the following command with the respective cit-files, prefixes (*.cit) and genome: gedi -e Slam -trim5p 15 -reads *.cit -genomic m.ens102 -prefix grandslam_t15/* -plot  -D -modelall To generate the cit file you have to modify the first lines in start.bash to match the paths on your file system, and then run it.   Software versions:     gedi toolkit 1.0.5     GRAND-SLAM 2.0.7     STAR version 2.7.10b

GRAND-SLAM analysis of simulated nucleotide conversion in QuantSeq data sets for grandRescue

These are processed data sets from the simulation of nucleotide conversions (T>C) in QuantSeq reads for the purpose of investigating 4sU-induced mapping impairment by read lengths and library preparation methods and the potential of grandRescue to alleviate these effects. The original data set is from: Lee, J. W. et al. (https://doi.org/10.1038/s41586-019-1004-y) GEO Accession: GSE109480 (Samples: GSM2944116 – GSM2944120)   The zip files contain the full output from the processing pipeline (including the mapped reads, the scripts to run the pipeline and the output) before and after rescue. The *.tsv.gz files are the GRAND-SLAM output tables. To generate the GRAND-SLAM output yourself, first prepare the mouse genome. Then run the following command with the respective cit-files, prefixes (*.cit) and genome: gedi -e Slam -trim5p 15 -reads *.cit -genomic m.ens102 -prefix grandslam_t15/* -plot  -D -modelall To generate the cit file you have to modify the first lines in start.bash to match the paths on your file system, and then run it.   Software versions:     gedi toolkit 1.0.5     GRAND-SLAM 2.0.7     STAR version 2.7.10b

Data and analysis result for "A scalable variational approach to characterize pleiotropic components across thousands of human diseases and complex traits using GWAS summary statistics"

Data set and analysis results from our paper "A scalable variational approach to characterize pleiotropic components across thousands of human diseases and complex traits using GWAS summary statistics" (pre-print). This file contains GWAS summary statistics of 2,483 traits and 51,399 SNP variants from European individuals, originally downloaded and processed from Pan-UK Biobank (https://pan.ukbb.broadinstitute.org/). Additionally, we include results of 100 pleiotropic factors inferred by our method and tSVD as comparison. Please see README for detailed breakdown.