Dataset Search

This page contains the data for the manuscript "Autophagy suppression in DNA damaged cells occurs through a newly identified p53-proteasome-LC3 axis" currently available in preprint on bioRxiv

Data includes carbon mineralization rates, potential denitrification rates, net nitrous oxide fluxes, and soil chemical properties from a laboratory incubation of soil samples collected from 20 locations across an Illinois maize field.

This repository contains the the data and code to recreate the simulations in "High Costs of GHG Abatement with Electrifying the Light-Duty Vehicle Fleet with Heterogeneous Preferences of Vehicle Consumers." The model can be run by calling the bash file in the SLURM environment with parameters set for different scenarios. BEPEAM-E model details: (1) the "Main.gms" file in GAMS format that contains the initiating stage settings with input and main optimization model (2) the "output.gms" file in GAMS format that prepare the output file from BEPAM model. (3) the rest are the intermediate input files for model to generate the input and output files for the model. (4) Four bash files are the script file that call the GAMS model on the HPC that includes both HPC environment and the scenario settings. Four bash files are uploaded corresponding to 4 scenarios

This dataset contains weather data taken at the University of Illinois Urbana-Champaign Energy Farm using automatic sensors and averaged every 15 minutes. Measurements include average air temperature, average relative humidity, average wind speed, maximum wind speed, average wind direction, average photosynthetically active radiation, total precipitation, and average air pressure.

Data are provided that are relevant to the rare plant Phlox pilosa ssp. sangamonensis, or Sangamon phlox, and other members of the genus that occur in its native range. Sangamon phlox is a state-endangered subspecies that is only known to occur in two Illinois counties. Data provided come from all known Sangamon phlox populations, which we estimate as 10 separate populations. Data include genetic data from DNA microsatellite loci (allele sizes and basic summaries), flowering population size estimates, rates of fruit set, and rates of seed set. Additionally, genetic data (from microsatellites) are provided for Phlox divaricata ssp. laphamii (three populations), Phlox pilosa ssp. pilosa (two populations), and Phlox pilosa ssp. fulgida (two populations).

Data: Variation in pesticide toxicity in the western honey bee (Apis mellifera) associated with consuming phytochemically different monofloral honeys Includes: Identification and quantification of phenolic components of honeys: Raw_data_JOCE.xlsx – sheet: “HoneyPhytochemicals” Effects of honey phytochemicals on acute pesticide toxicity: Raw_data_JOCE.xlsx – sheet: “raw_LD50 Raw_data_JOCE.xlsx – sheet: “raw_LD50_hive_based”

This dataset contains BEPAM model code and input data to the replicate the results for "Assessing the Returns to Land and Greenhouse Gas Savings from Producing Energy Crops on Conservation Reserve Program Land." The dataset consists of: (1) The replication codes and data for the BEPAM model. The code file is named as output_0213-2020_Complete_daycent-agversion-[rental payment level]%_[biomass price].gms. (BEPAM-CRP model-Sep2020.zip) (2) Simulation results from the BEPAM model (BEPAM_Simulation_Results.csv) * Item (1) is in GAMS format. Item (2) is in text format.

Datasets that accompany Beilke, Blakey, and O'Keefe 2021 publication (Title: Bats partition activity in space and time in a large, heterogeneous landscape; Journal: Ecology and Evolution).

Data files and R code to replicate the econometric analysis in the journal article: B Chen, BM Gramig and SD Yun. “Conservation Tillage Mitigates Drought Induced Soybean Yield Losses in the US Corn Belt.” Q Open. https://doi.org/10.1093/qopen/qoab007

This dataset includes five files developed using the procedures described in the article 'Developing County-level Data of Nitrogen Fertilizer and Manure Inputs for Corn Production in the United States' and Supplemental Information published in the Journal of Cleaner Production in 2021. Citation: Xia, Yushu, Hoyoung Kwon, and Michelle Wander. "Developing county-level data of nitrogen fertilizer and manure inputs for corn production in the United States." Journal of Cleaner Production 309 (2021): e126957. Brief method: The fertilizer and manure inputs for corn were generated with a top-down approach by assigning county-level total N inputs reported by USGS to different crops using state- and county-level survey data. The corn N needs were estimated using empirical extension-based equations coupled with soil and environmental covariates. The estimates of fertilizer N inputs were further refined for corn grain and silage production at the county level and gap-filling (using state-level averages) was carried out to generate final files for U.S. county-level N inputs. The dataset is provided in an alternative format in Google Earth Engine: https://code.earthengine.google.com/13a0078e7ee727bc001e045ad0e8c6fc

Survey questions and data collected from Illinois land managers on practices and knowledge relating to impacts to wildlife. 0s indicated non-selection, 1s indicate selection of answer.

The data provided in this submission are the gene annotations for the Illinois EBP pilot project samples, as well as the predicted proteins for each sample in FASTA format.

Photographs and video of two Lesser Chameleons (Furcifer minor) nesting together at the same time near Itremo, Madagascar.

Photographs and video of the snake Compsophis infralineatus predating upon the chameleons Calumma crypticum and Calumma gastrotaenia near Mandraka, Madagascar.

These data are the result of analyses of the metagenome of North American bats, including 18s and 16s barcode genes designed to target microorganisms of the gut. These files are Phyloseq import files created by the DADA2 program. Each barcode gene is uploaded separately as the four files required to build a phyloseq object. For each barcode gene, the files include amplicon sequence variant (ASV) sequences, sequence tables (seqtab) which connect individual samples to the ASVs, tax tables (taxtab) which identify the taxa present as determined by a Bayesian RDP classifier, and rooted phylogenetic trees for the ASVs. Additionally, we have included a "sample_data" file which is necessary for sorting of samples across all four sequence analysis data sets by study and species. Some sample information which could identify the location of endangered species has been restricted. Multiple studies are represented in the data which can be accessed using standard methods in the Phyloseq program (e.g. For a study of bats, parasites, and gut microbiome dysregulation by Bennett, Suski, and OKeefe 2024 [in prep March 2024], study specific data can be accessed using the Study variable "DYSBIOMICS." File names include reference to the primer set used to generate them (18s primer sets: G3, G4, G6; 16s primer set: 341F3_806R5).

This file contains the delta 15N values for leaf material collected from Cyathea rojasiana tree ferns before and after fertilization using ammonium -15N chloride solution to determine whether 15N update is possible from senescent leaves. Details of the experiment are provided in the online supplement to the published paper. Briefly, In February 2022 we selected three mature C. rojasiana individuals 1-1.5m in height that had leaves rooted in the soil and one new developing (but unexpanded) leaf. For each fern, two plastic pots (10 x 10 x 12 cm) were filled with a 50:50 mixture of washed river sand and soil from the Chorro watershed. For each pot, one senescent leaf that was rooted in the soil was carefully excavated and its roots transplanted into the pot. Pots were then fertilized by adding 30 ml of a 0.02 M 15N solution of ammonium-15N chloride (98% 15N; Sigma-Aldrich 299251; St Louis, MO) to yield a target concentration of 2 µg15N cm-3 of soil. After fertilization pots were carefully enclosed within thick plastic bags, and sealed around the senescent leaf rachis to prevent leaching any of 15N from the pot to the surrounding soil. At the time of N fertilization, pinnae of the youngest fully expanded leaf were collected from each fern. One pinna was collected from the base of the leaf and one from the distal end of the leaf. In March 2022, after 28 days the roots were removed from pots and two additional leaf pinnae sampled from each fern: one from the base and one from the distal end of the youngest (now fully expanded) leaf. Leaf samples were dried for 72 hours at 60 C and then leaf lamina tissue finely ground with a bead beater. The delta 15N for each leaf sample determined at the University of Illinois, Urbana-Champaign using a Thermo Delta V Advantage IRMS run in combination with a Costech 4010 Elemental Analyzer. Samples were run in continuous flow relative to laboratory standards that were calibrated with USGS 40, 41, and NBS 19 reference materials.

This accompanying study is published under the title "Estimating soil N2O emissions induced by organic and inorganic fertilizer inputs using a Tier-2, regression-based meta-analytic approach for U.S. agricultural lands" at Science of the Total Environment. The study is authored by Dr. Yushu Xia, Dr. Hoyoung Kwon, and Dr. Michelle Wander. The DOI for this study is <a href="https://doi.org/10.1016/j.scitotenv.2024.171930">https://doi.org/10.1016/j.scitotenv.2024.171930</a>.

This data publication provides example video clips related to research on association among flight ability of juvenile songbirds at fledging and juvenile morphological traits (wing emergence, wing length, body condition, mass, and tarsus length. File names reflect the species dropped in each video. These videos are supplemental material for scientific publications by the authors and reflect an example subset of all videos collected form 2017-2018 as part of a larger study on the post-fledging ecology of grassland and shrubland birds in east-Central Illinois, USA. No birds were harmed/injured in the production of these videos and procedures were approved by the Illinois Institutional Animal Care and Use Committee (IACUC), protocol no. 18221. Individuals depicted in the videos have given consent for the videos to be shared (talent/model release form; <a href="https://publicaffairs.illinois.edu/resources/release/">https://publicaffairs.illinois.edu/resources/release/</a>)

Bee movement between habitat patches in a naturally fragmented ecosystem depended on species, patch, and matrix variables. Using a mark-recapture methodology in the naturally fragmented Ozark glade ecosystem, we assessed the importance of bee size, nesting biology, the distance between patches (e.g., isolation), and nesting and floral resources in habitat patches and the surrounding matrix on bee movement. This dataset includes seven data files, three R code files, and a QGIS tool. Three of the data files include information collected at the study sites with regard to bees and matrix and patch characteristics. The other four data files are spatial files used to quantify the characteristics of the forest canopy between the study sites and the edge-to-edge distances between the study sites. R code in the R Markdown file recreates the analysis and data presentation for the associated publication. R script files contain processes for calculating some of the explanatory variables used in the analysis. The QGIS tool can be used as the first step to obtaining average values from a raster file where the cells are large relative to the areas of interest (AOI) that you would like to characterize. The second step is contained in one of the aforementioned R scripts. Detected effects included: Larger bees were more likely to move between patches. Bee movement was less likely as the distance between patches increased. However, relatively short distances (~50 m) inhibited movement more than our a priori expectations. Bees were unlikely to move away from home patches with abundant and diverse floral and below-ground nesting resources. When home patches were less resource-rich, bee movement depended on the characteristics of the away patch or the matrix. In these cases, bees were more likely to move to away patches with greater below-ground nesting and floral resources. Matrix habitats with more available floral and below-ground nesting resources appear to impede movement to neighboring patches, potentially because they already provide supplemental resources for bees.

This repository includes scripts and datasets for the paper, "Statistically consistent divide-and-conquer pipelines for phylogeny estimation using NJMerge." All data files in this repository are for analyses using the logdet distance matrix computed on the concatenated alignment. Data files for analyses using the average gene-tree internode distance matrix can be downloaded from the Illinois Data Bank (https://doi.org/10.13012/B2IDB-1424746_V1). The latest version of NJMerge can be downloaded from Github (https://github.com/ekmolloy/njmerge).<br /> <strong>List of Changes:</strong> &bull; Updated timings for NJMerge pipelines to include the time required to estimate distance matrices; this impacted files in the following folder: <strong>data.zip</strong> &bull; Replaced "Robinson-Foulds" distance with "Symmetric Difference"; this impacted files in the following folders: <strong> tools.zip; data.zip; scripts.zip</strong> &bull; Added some additional information about the java command used to run ASTRAL-III; this impacted files in the following folders: <strong>data.zip; astral64-trees.tar.gz (new)</strong>

Data associated with the manuscript "Niche conservatism and spread explain hybridization and introgression between native and invasive fish" by Jordan H. Hartman, Joel B. Corush, Eric R. Larson, Jeremy S. Tiemann, Philip Willink, and Mark A. Davis. For this project, we combined results of ecological niche models (ENMs) and next-generation restriction site-associated DNA sequencing (RADseq) to test theories of niche conservatism and biotic resistance on the success of invasion, hybridization, and extent of introgression between native Western Banded Killifish and non-native Eastern Banded Killifish. This dataset provides the sampling locations and number of Banded Killifish in each population, accession numbers for RADseq from the National Center for Biotechnology Information Sequence Read Archive and the assignment of each Banded Killifish, the habitat associations of each population from the ENMs, and the occurrence points used to build the ENMs.

This is the dataset for the manuscript titled, "Differing physiological performance of coexisting cool- and warmwater fish species under heatwaves in the Midwestern United States"

This data set is related to a SoyFACE experiment conducted in 2004, 2006, 2007, and 2008 with the soybean cultivars Loda and HS93-4118. The experiment looked at how seed elements were affected by elevated CO2 and yield. In this V2, 2 new files were added per journal requirement. Total there are 5 data files in text format within the digrado_et_al_gcb_data_V2 and 1 readme file. The name of files are listed below. Details about headers are explained in the readme.txt file. <b>1. ionomic_data.txt file</b> contains the ionomic data (mg/kg) for the two cultivars. The file contains all six technical replicates for each plot. The cultivar, year, treatment, and the plot from which the samples were collected are given for each entry. <b>2. yield_data.txt file</b> contains the yield data for the two cultivars (seed yield in kg/ha, seed yield in bu/a, Protein (%), Oil (%)). The file contains yield data for every plot. The cultivar, year, treatment, and the plot from which the samples were collected are given for each entry. <b>3. mineral_pro_oil_yield.txt file</b> contains the yield per hectare for each mineral (g/ha) along with the yield per hectare for protein and oil (t/ha). This was obtained by multiplying the seed content of each element (minerals, protein, and oil) by the total seed yield. The file contains yield data for every plots. The cultivar, year, treatment, and the plot from which the samples were collected are given for each entry. <b>4. economic_assessment.txt file</b> contains data used to assess the financial impact of altered seed oil content on soybean oil production. <b>5. meteorological_data.txt file</b> contains the meteorological data recorded by a weather station located ~ 3km from the experimental site (Willard Airport Champaign). Data covering the period between May 28 and September 24 were used for 2004; between May 25 and September 24 were used in 2006; between May 23 and September 17 in 2007; and between June 16 and October 24 in 2008.

BAM files for founding strain (MG1655-motile) as well as evolved strains from replicate motility selection experiments in low-viscosity agar plates containing either rich medium (LB) or minimal medium (M63+0.18mM galactose)

This deposit contains all raw data and analysis from the paper "In-cell titration of small solutes controls protein stability and aggregation". Data is collected into several types: 1) analysis*.tar.gz are the analysis scripts and the resulting data for each cell. The numbers correspond to the numbers shown in Fig.S1. (in publication) 2) scripts.tar.gz contains helper scripts to create the dataset in bash format. 3) input.tar.gz contains headers and other information that is fed into bash scripts to create the dataset. 4) All rawData*.tar.gz are tarballs of the data of cells in different solutes in .mat files readable by matlab, as follows: - Each experiment included in the publication is represented by two matlab files: (1) a calibration jump under amber illumination (_calib.mat suffix) (2) a full jump under blue illumination (FRET data) - Each file contains the following fields: &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;coordleft - coordinates of cropped and aligned acceptor channel on the original image &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;coordright - coordinates of cropped and aligned donor channel on the original image] &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;dataleft - a 3d 12-bit integer matrix containing acceptor channel flourescence for each pixel and time step. Not available in _calib files &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;dataright - a 3d 12-bit integer matrix containing donor channel flourescence for each pixel and time step. This will be mCherry in _calib files and AcGFP in data files. &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;frame1 - original image size &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;imgstd - cropped dimensions &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;numFrames - number of frames in dataleft and dataright &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;videos - a structure file containing camera data. Specifically, videos.TimeStamp includes the time from each frame.