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Datasets
published: 2024-04-18
Liao, Ling-Hsiu; Wu, Wen-Yen; Berenbaum, May (2024): Data: Variation in pesticide toxicity in the western honey bee (Apis mellifera) associated with consuming phytochemically different monofloral honeys. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-6733018_V1
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”
keywords:
Honey; honey bee; phenolic acid; flavonoids; bifenthrin; LD50
published: 2024-04-15
Belmont, Andrew; Gholamalamdari, Omid; Kumar, Pradeep (2024): Nuclear locale immunofluorescence imaging and segmentation in four human cell lines. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-9792611_V1
The immunofluorescence and segmented images of three nuclear locales, (nuclear periphery, nuclear speckles, and nucleolus) in four human cells lines (H1-hESC, HCT116, HFFc6, and K562). For each of the cell lines, this dataset includes original, cropped, and binary 4D images (3D + antibody) in addition to max projected thumbnails of cell nuclei.
keywords:
microscopy; immunostaining; segmentation; human nuclei
published: 2024-04-05
Sinaiko, Guy; Cao, Yanghui; Dietrich, Christopher H. (2024): Datasets for phylogenomics of the leafhopper genus Neoaliturus Distant. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-8336414_V2
The following files include specimen information, DNA sequence data, and additional information on the analyses used to reconstruct the phylogeny of the leafhopper genus Neoaliturus as described in the Methods section of the original paper: 1. Taxon_sampling.csv: contains data on the individual specimens from which DNA was extracted, including sample code, taxon name, collection data (locality, date and name of collector) and museum unique identifier. 2. Alignments.zip: a ZIP archive containing 432 separate FASTA files representing the aligned nucleotide sequences of individual gene loci used in the analysis. 3. Concatenated_Matrix.fa: is a FASTA file containing the concatenated individual gene alignments used for the maximum likelihood analysis in IQ-TREE. 4. Genes_and_Loci.rtf: identifies the individual genes and loci used in the analysis. The partition name is the same as the name of the individual alignment file in the zipped Alignments folder. 5. Partitions_best_scheme.nex: is a text file in the standard NEXUS format that indicates the names of the individual data partitions and their locations in the concatenated matrix, and also indicates the substitution model for each partition. 6. (New in this version 2) Scripts & Description.zip includes 8 custom shell or perl scripts used to assemble the DNA sequence data by perform reciprocal blast searches between the reference sequences and assemblies for each sample, extract the best sequences based on the blast searches, screen the hits for each locus and keep only the best result, and generate the nucleotide sequence dataset for the predicted orthologues (see the file description.txt for details). 7. (New in this version 2) Full_genetic_distances_matrix.csv shows the genetic distances between pairs of samples in the datset (proportion of nucleotides that differ between samples).
keywords:
leafhopper; phylogeny; anchored-hybrid-enrichment; DNA sequence; insect
planned publication date: 2024-08-24
Jones, Todd; Llamas, Alfredo; Phillips, Jennifer (2024): Data for Jones et al. GCB-23-1273.R1. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-6010827_V1
Dataset associated with Jones et al. GCB-23-1273.R1 submission: Phenotypic signatures of urbanization? Resident, but not migratory, songbird eye size varies with urban-associated light pollution levels. Excel CSV file with all of the data used in analyses and file with descriptions of each column.
keywords:
body size; demographics; eye size; phenotypic divergence; songbirds; sensory pollution; urbanization
planned publication date: 2024-10-16
Smith, Rebecca; Huang, Conghui (2024): Data for A modeling study on SARS-CoV-2 transmission in primary and middle schools in Illinois. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-3705306_V1
School testing data were provided by Shield Illinois (ShieldIL), which conducted weekly in-school testing on behalf of the Illinois Department of Public Health (IDPH) for all participating schools in the state excluding Chicago Public Schools. The populations and proportions of students and employees in the studied school districts are reported by Elementary/Secondary Information System (ElSi) database.
keywords:
COVID-19; school testing
published: 2024-03-25
Xia, Yushu; Kwon, Hoyoung; Wander, Michelle (2024): Soil Nitrous Oxide Emissions Data for 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". University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-9808669_V1
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 (TBD). Please refer to the study for detailed data extraction and processing methods.
keywords:
soil; nitrous oxide; agriculture; fertilizers; meta-analysis
published: 2024-03-25
Suski, Cory; Dai, Qihong (2024): Data for "Differing physiological performance of coexisting cool- and warmwater fish species under heatwaves in the Midwestern United States". University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-1022017_V1
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"
keywords:
climate change; heat wave; metabolic rate; swimming; predator-prey interaction; thermal tolerance; Sander vitreus; walleye; largemouth bass; species distributions
published: 2024-01-31
Wang, Xiudan; Dietrich, Christopher; Zhang, Yalin (2024): Datasets for Phylogeny and historical biogeography of leafhopper subfamily Coelidiinae (Hemiptera: Cicadellidae) based on morphological and molecular data . University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-5847605_V1
The included files were used to reconstruct the phylogeny of Coelidiinae using combined morphological and molecular data, estimate divergence times and reconstruct ancestral biogeographic areas as described in the manuscript submitted for publication. The file “Coelidiinae_dna_morph_combined.nex” is a text file in standard NEXUS format used by various phylogenetic analysis programs. This file includes the aligned and concatenated nucleotide sequences or five gene regions (mitochondrial COI and 16S, and nuclear 28S D-2, histone H3, histone H2A and wingless) indicated by standard “ACGT” nucleotide symbols with missing data indicated by “?”, and morphological character data as defined in Table S3 used in the analyses. The data partitions are indicated toward the end of the file by ranges of numbers (“charset Subset 1 – 4” for the DNA data and “charset morph” for the morphological characters) followed by commands for the phylogenetic analysis program MrBayes that specify the model settings for each data partition. Detailed data on species included (as rows) in the dataset, including collection localities and GenBank accession numbers are provided in the Table_S1_Specimen_information.csv file. The file "TablesS2-S4.pdf" lists the primers used for polymerase chain reaction amplification, the list of morphological character definitions, and the morphological character matrix. The file “RASP_Distribution.csv” contains a list of the species included in the phylogenetic dataset (first column) and a code (second column) indicating their distributions as follows: (A) Oriental, (B) Palaearctic, (C) Australian, (D) Afrotropical, (E) Neotropical, and (F) Nearctic. More than one letter indicates that the species occurs in more than one region. The file "infile_for_BEAST.txt" is the input file in XML format used for the molecular divergence time analysis using the program BEAST (Bayesian Evolutionary Analysis by Sampling Trees) as described in the Methods section of the manuscript. This file includes comments that document the steps of the analysis.
keywords:
leafhopper; phylogeny; DNA sequence; insect; timetree; biogeography
published: 2024-02-25
Coshic, Kush; Maffeo, Christopher; Winogradoff, David; Aksimentiev, Aleksei (2024): Select trajectories, simulation setup, and analysis for "The structure and physical properties of a packaged bacteriophage particle". University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-4930709_V1
Simulation trajectory data and scripts for Nature manuscript "The structure and physical properties of a packaged bacteriophage particle" that reports the all-atom structure of a complete HK97 virion, including its entire 39,732 base pair genome, obtained through multi-resolution simulations.
keywords:
Virus capsid; Bacteriophage packaging; Multiresolution simulations; all-atom MD simulation
published: 2023-12-19
Bush, Daniel; Calla, Bernarda; Berenbaum, May (2023): Data for "An Aspergillus Strain from Bee Bread of the Western Honey Bee (Apis mellifera) Displays Adaptations to Distinctive Features of the Hive Environment". University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-7212497_V1
Data for the Appendices of Bush et al. article published in Ecology and Evolution. Contains genomic analysis information for a strain of Aspergillus flavus isolated from bee bread in East Central Illinois.
keywords:
Excel; UIUC; Evolution and Ecology; Aspergillus flavus; genome
published: 2024-02-15
Hoggatt, Meredith; Starbuck, Clarissa; O'Keefe, Joy (2024): Data for "Acoustic monitoring yields informative bat population density estimates". University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-7001459_V1
Dataset includes the dataset for estimating bat density from acoustic data and the R code. The data support a publication by Meredith L. Hoggatt, Clarissa A. Starbuck, and Joy M. O'Keefe entitled Acoustic monitoring yields informative bat population density estimates.
keywords:
acoustics; bats; monitoring; population density; random encounter model
published: 2024-02-21
Hartman, Jordan H; Corush, Joel B; Larson, Eric R; Tiemann, Jeremy S; Willink, Philip; Davis, Mark A (2024): Data for "Niche conservatism and spread explain hybridization and introgression between native and invasive fish". University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-6979965_V1
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.
keywords:
Banded Killifish; ecological niche model; Fundulus diaphanus; hybrid swarm; invasive species; Laurentian Great Lakes
published: 2024-01-19
Digrado, Anthony; Montes, Christopher; Baxter, Ivan; Ainsworth, Elizabeth (2024): Soybean seed quality response to eCO2 data files. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-6453957_V2
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.
keywords:
protein; oil; mineral; SoyFACE; nutrient; Glycine max; soybean; yield; CO2; agriculture; climate change
published: 2023-12-01
Hohoff, Tara; Deppe, Jill (2023): Data for little brown occupancy and associated landcover data from McHenry County, Illinois. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-0365076_V1
Mist netting data for little brown bats (Myotis lucifugus) in McHenry County, Illinois and output of acoustic data processed using Kaleidoscope (Version 5.1.9, Bats of North America 5.1.0; Wildlife Acoustics) auto-identification software. Associated survey metadata and landcover metrics calculated using Fragstats included.
keywords:
little brown bats; mist netting; acoustics
published: 2024-02-08
Martinez, Carlos; Pena, Gisselle; Wells, Kaylee K. (2024): "Prairie Directory of North America" (2013) Entries for the Tallgrass, Mixed Grass, and Shortgrass Prairie Regions of the United States. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-0421892_V1
This dataset contains transcribed entries from the "Prairie Directory of North America" (Adelman and Schwartz 2013) for the Tallgrass, Mixed Grass, and Shortgrass prairie regions of the united states. We identified the historical spatial extent of the Tallgrass, Mixed Grass, and Shortgrass prairie regions using Ricketts et al. (1999), Olson et al. (2001), and Dixon et al. (2014) and selected the counties entirely or partially within these boundaries from the USDA Forest Service (2022) file. The resulting lists of counties are included as separate files. The dataset contains information on publicly accessible grasslands and prairies in these regions including acreage and amenities like hunting access, restrooms, parking, and trails.
keywords:
grasslands; prairies; prairie directory of north america; site amenities; site attributes
published: 2019-02-07
Nute, Michael; Yarlagadda, Karthik; Stumpf, Rebecca (2019): PICAN-PI Public Data. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-1678505_V1
This dataset contains all data used in the two studies included in "PICAN-PI..." by Nute, et al, other than the original raw sequences. That includes: 1) Supplementary information for the Manuscript, including all the graphics that were created, 2) 16S Reference Alignment, Phylogeny and Taxonomic Annotation used by SEPP, and 3) Data used in the manuscript as input for the graphics generation (namely, SEPP outputs and sequence multiplicities).
keywords:
microbiome; data visualization; graphics; phylogenetics; 16S
published: 2019-03-06
Makhnenko, Roman; Tarokh, Ali (2019): Experimental data on bulk and unjacketed moduli of porous rocks. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-7478121_V2
This dataset is provided to support the statements in Tarokh, A., and R.Y. Makhnenko. 2019. Remarks on the solid and bulk responses of fluid-filled porous rock, Geophysics. The unjacketed bulk modulus is a poroelastic parameter that can be directly measured in a laboratory test under a loading that preserves the difference between the mean stress and pore pressure constant. For a monomineralic rock, the measurement of the unjacketed bulk modulus is ignored because it is assumed to be equal to the bulk modulus of the solid phase. To examine this assumption, we tested porous sandstones (Berea and Dunnville) and limestones (Apulian and Indiana) mainly composed of quartz and calcite, respectively, under the unjacketed condition. The presence of microscale inhomogeneities, in the form of non-connected (occluded) pores, was shown to cause a considerable difference between the unjacketed bulk modulus and the bulk modulus of the solid phase. Furthermore, we found the unjacketed bulk modulus to be independent of the unjacketed pressure and Terzaghi effective pressure and therefore a constant.
keywords:
Poroelasticity; anisotropic solid skeleton; unjacketed bulk modulus; non-connected porosity
published: 2019-03-13
Ando, Amy; Fraterrigo, Jennifer; Guntenspergen, Glenn; Howlader, Aparna; Mallory, Mindy; Olker, Jennifer; Stickley, Samuel (2019): Spatial Conservation and Investment Portfolios to Manage Climate-Related Risk. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-2887291_V1
keywords:
climate change; conservation; diversification; environmental investments; MPT; porftfolio; risk; uncertainty
published: 2019-03-22
Jones, Todd M.; Benson, Thomas J.; Ward, Michael P. (2019): Flight Ability of Juvenile Songbirds at Fledgling: Examples of Fledgling Drop Tests. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-2044905_V1
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>)
keywords:
songbirds; flight ability; wing development; wing length; wing emergence; nestling development; post-fledging
published: 2019-03-19
Molloy, Erin K.; Warnow, Tandy (2019): Data from: TreeMerge: A new method for improving the scalability of species tree estimation methods. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-9570561_V1
This repository includes scripts and datasets for the paper, "TreeMerge: A new method for improving the scalability of species tree estimation methods." The latest version of TreeMerge can be downloaded from Github (https://github.com/ekmolloy/treemerge).
keywords:
divide-and-conquer; statistical consistency; species trees; incomplete lineage sorting; phylogenomics
published: 2019-05-16
Molloy, Erin K.; Warnow, Tandy (2019): Data from: Statistically consistent divide-and-conquer pipelines for phylogeny estimation using NJMerge. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-0569467_V2
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> • 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> • Replaced "Robinson-Foulds" distance with "Symmetric Difference"; this impacted files in the following folders: <strong> tools.zip; data.zip; scripts.zip</strong> • 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>
keywords:
divide-and-conquer; statistical consistency; species trees; incomplete lineage sorting; phylogenomics
published: 2019-05-10
Pradhan, Dikshant; Jensen, Paul (2019): Pradhan 2019 Data. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-3352362_V1
Data necessary for production of figures presented in "Efficient enzyme coupling algorithms identify functional pathways in genome-scale metabolic models" by Pradhan et al.
keywords:
Efficient enzyme coupling algorithms identify functional pathways in genome-scale metabolic models;
published: 2019-05-31
Krichels, Alexander (2019): Data for Dynamic controls on field-scale soil nitrous oxide hot spots and hot moments across a microtopographic gradient. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-9733959_V1
This dataset includes all data presented in the manuscript entitled: "Dynamic controls on field-scale soil nitrous oxide hot spots and hot moments across a microtopographic gradient"
keywords:
denitrification; depressions; microtopography; nitrous oxide; soil oxygen; soil temperature
published: 2019-06-03
Rando, Halie; Wadlington, William; Johnson, Jennifer; Stutchman, Jeremy; Trut, Lyudmila; Farré, Marta; Kukekova, Anna (2019): Red Fox (Vulpes vulpes) Y-Chromosome Sequence. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-4447017_V1
This dataset contains raw data associated with the red fox Y-chromosome assembly (see https://doi.org/10.3390/genes10060409). It includes a fasta file of the 171 scaffolds from the red fox reference genome assembly identified as likely to contain Y-chromosome sequence, the raw BLAST results, and the ABySS assemblies described in the manuscript.
keywords:
Y-chromosome; carnivore; Vulpes vulpes; sex chromosomes; MSY; Y-chromosome genes; copy-number variation; BCORY2; UBE1Y; next-generation sequencing
published: 2019-06-22
MacDonald, Sean; Ward, Michael; Sperry, Jinelle (2019): Manipulating social information to promote frugivory by birds on a Hawaiian Island. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-9223847_V1
keywords:
conspecific attraction; fruit-eating bird; Hawaiian flora; playback experiment; seed dispersal; social information; Zosterops japonicas