Illinois Data Bank
Log in with NetID
University Library, University of Illinois at Urbana-Champaign
Illinois Data Bank
Log in with NetID
25 per page
50 per page
Displaying datasets 151 - 175 of 186 in total
Generate Report from Search Results
Life Sciences (186)
Social Sciences (0)
Physical Sciences (0)
Technology and Engineering (0)
Arts and Humanities (0)
U.S. National Science Foundation (NSF) (52)
U.S. Department of Energy (DOE) (19)
U.S. National Institutes of Health (NIH) (17)
U.S. Department of Agriculture (USDA) (16)
Illinois Department of Natural Resources (IDNR) (8)
U.S. National Aeronautics and Space Administration (NASA) (2)
U.S. Geological Survey (USGS) (2)
U.S. Army (1)
CC BY (54)
Clark, Lindsay V.; Jin, Xiaoli; Petersen, Karen K.; Anzoua, Kossanou G.; Bagmet, Larissa; Chebukin, Pavel; Deuter, Martin; Dzyubenko, Elena; Dzyubenko, Nicolay; Heo, Kweon; Johnson, Douglas A.; Jørgensen, Uffe; Kjeldsen, Jens B.; Nagano, Hironori; Peng, Junhua; Sabitov, Andrey; Yamada, Toshihiko; Yoo, Ji Hye; Yu, Chang Yeon; Long, Stephen P.; Sacks, Erik J. (2018): Population genetic structure of Miscanthus sacchariflorus. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-0170190_V3
This repository contains datasets and R scripts that were used in a study of the population structure of Miscanthus sacchariflorus in its native range across East Asia. Notably, genotypes of 764 individuals at 34,605 SNPs, called from reduced-representation DNA sequencing using a non-reference bioinformatics pipeline, are provided. Two similar SNP datasets, used for identifying clonal duplicates and for determining the ancestry of ornamental and hybrid Miscanthus plants identified in previous studies respectively, are also provided. There is also a spreadsheet listing the provenance and ploidy of all individuals along with their plastid (chloroplast) haplotypes. Software output for Structure, Treemix, and DIYABC is also included. See README.txt for more information about individual files. Results of this study are described in a manuscript in revision in Annals of Botany by the same authors, "Population structure of Miscanthus sacchariflorus reveals two major polyploidization events, tetraploid-mediated unidirectional introgression from diploid Miscanthus sinensis, and diversity centered around the Yellow Sea."
Miscanthus; restriction site-associated DNA sequencing (RAD-seq); single nucleotide polymorphism (SNP); population genetics; Miscanthus xgiganteus; Miscanthus sacchariflorus; R scripts; germplasm; plastid haplotype
Brown, Patrick (2018): Glycine tomentella GBS. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-9154233_V1
GBS data from soybean lines carrying introgressions from Glycine tomentella. This project is led by Dr. Randy Nelson, USDA scientist at the University of Illinois. Fastq files contain raw Illumina data. Txt files are keyfiles containing barcodes for each genetic entity.
Brown, Patrick (2018): Phaseolus GBS. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-6255617_V1
GBS data from Phaseolus accessions, for a study led by Dr. Glen Hartman, UIUC. <br />The (zipped) fastq file can be processed with the TASSEL GBS pipeline or other pipelines for SNP calling. The related article has been submitted and the methods section describes the data processing in detail.
Brown, Patrick (2018): Glycine soja GBS. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-6967733_V1
GBS data for G. max x G. soja crosses, a project led by Dr. Randy Nelson.
Sukenik, Shahar; Salam, Mohammed; Wang, Yuhan; Gruebele, Martin (2018): Dataset for: In-cell titration of small solutes controls protein stability and aggregation. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-4308433_V1
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: coordleft - coordinates of cropped and aligned acceptor channel on the original image coordright - coordinates of cropped and aligned donor channel on the original image] dataleft - a 3d 12-bit integer matrix containing acceptor channel flourescence for each pixel and time step. Not available in _calib files 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. frame1 - original image size imgstd - cropped dimensions numFrames - number of frames in dataleft and dataright videos - a structure file containing camera data. Specifically, videos.TimeStamp includes the time from each frame.
Live cell; FRET microscopy; osmotic challenge; intracellular titrations; protein dynamics
Zaya, David N.; Leicht-Young, Stacey A.; Pavlovic, Noel; Hetrea, Christopher S.; Ashley, Mary V. (2017): Data for "Mislabeling of an Invasive Vine (Celastrus orbiculatus) as a Native Congener (C. scandens) in Horticulture" . University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-3661776_V2
Data used for Zaya et al. (2018), published in Invasive Plant Science and Management DOI 10.1017/inp.2017.37, are made available here. There are three spreadsheet files (CSV) available, as well as a text file that has detailed descriptions for each file ("readme.txt"). One spreadsheet file ("prices.csv") gives pricing information, associated with Figure 3 in Zaya et al. (2018). The other two spreadsheet files are associated with the genetic analysis, where one file contains raw data for biallelic microsatellite loci ("genotypes.csv") and the other ("structureResults.csv") contains the results of Bayesian clustering analysis with the program STRUCTURE. The genetic data may be especially useful for future researchers. The genetic data contain the genotypes of the horticultural samples that were the focus of the published article, and also genotypes of nearly 400 wild plants. More information on the location of the wild plant collections can be found in the Supplemental information for Zaya et al. (2015) Biological Invasions 17:2975–2988 DOI 10.1007/s10530-015-0926-z. See "readme.txt" for more information.
Horticultural industry; invasive species; microsatellite DNA; mislabeling; molecular testing
Smith, Rebecca (2017): DairyCoinfection. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-1513733_V2
These are the results of an 8 month cohort study in two commercial dairy herds in Northwest Illinois. From each herd, 50 cows were selected at random, stratified over lactations 1 to 3. Serum from these animals was collected every two months and tested for antibodies to Bovine Leukosis Virus, Neospora caninum, and Mycobacterium avium subsp. paratuberculosis. Animals that left the herd during the study were replaced by another animal in the same herd and lactation. At the last sampling, serum neutralization assays were performed for Bovine Herpesvirus type 1 and Bovine Viral Diarrhea virus type 1 and 2. Production data before and after sampling was collected for the entire herd from PCdart.
Sweet, Andrew; Bush, Sarah; Gustafsson, Daniel; Allen, Julie; DiBlasi, Emily; Skeen, Heather; Weckstein, Jason; Johnson, Kevin (2018): Data from: host and parasite morphology influence congruence between host and parasite phylogenies. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-2011663_V1
Concatenated sequence alignment, phylogenetic analysis files, and relevant software parameter files from a cophylogenetic study of Brueelia-complex lice and their avian hosts. The sequence alignment file includes a list of character blocks for each gene alignment and the parameters used for the MrBayes phylogenetic analysis. 1) Files from the MrBayes analyses: a) a file with 100 random post-burnin trees (50% burnin) used in the cophylogenetic analysis - analysisrandom100_trees_brueelia.tre b) a majority rule consensus tree - treeconsensus_tree_brueelia.tre c) a maximum clade credibility tree - mcc_tree_brueelia.tre The tree tips are labeled with louse voucher names, and can be referenced in Supplementary Table 1 of the associated publication. 2) Files related to a BEAST analysis with COI data: a) the XML file used as input for the BEAST run, including model parameters, MCMC chain length, and priors - beast_parameters_coi_brueelia.xml b) a file with 100 random post-burnin trees (10% burnin) from the BEAST posterior distribution of trees; used in OTU analysis - beast_100random_trees_brueelia.tre c) an ultrametric maximum clade credibility tree - mcc_tree_beast_brueelia.tre 3) A maximum clade credibility tree of Brueelia-complex host species generated from a distribution of trees downloaded from https://birdtree.org/subsets/ - mcc_tree_brueelia_hosts.tre 4) Concatenated sequence alignment - concatenated_alignment_brueelia.nex
bird lice; Brueelia-complex; passerines; multiple sequence alignment; phylogenetic tree; Bayesian phylogenetic analysis; MrBayes; BEAST
Miao, Guofang; Guan, Kaiyu (2018): Data from: Sun-Induced chlorophyll fluorescence, photosynthesis, and light use efficiency of a soybean field. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-1329706_V1
This dataset provides the time series (Aug. - Sep. 2016) data of sun-induced chlorophyll fluorescence, photosynthesis, photosynthetically active radiation, and associated vegetation indices that were collected in a soybean field in the farm of University of Illinois at Urbana and Champaign. Data contain 255 records and 6 variables (PPFD-IN: Photosynthetically active radiation; GPP-Gross Primary Production; SIF: Sun-Induced Fluorescence; NDVI: Normalized Difference Vegetation Index; Rededge: Rededge Index; Redege_NDVI: Rededge Normalized Difference Vegetation Index). The timestamp uses the standard time. Data are available from 8 am to 4 pm (corresponding to 9 am to 5 pm local time) every day.
sun-induced chlorophyll fluorescence; photosynthesis; soybean
Christensen, Sarah; Molloy, Erin K; Vachaspati, Pranjal; Warnow, Tandy (2018): Datasets from the study "OCTAL: Optimal Completion of Gene Trees in Polynomial Time". University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-1616387_V1
Datasets used in the study, "OCTAL: Optimal Completion of Gene Trees in Polynomial Time," under review at Algorithms for Molecular Biology. Note: DS_STORE file in 25gen-10M folder can be disregarded.
phylogenomics; missing data; coalescent-based species tree estimation; gene trees
Haselhorst, Derek S; Tcheng, David K. ; Moreno, J. Enrique ; Punyasena, Surangi W. (2017): Pollen types from Haselhorst et al. (2017) Ecological Informatics: Table S1. Pollen types identified in the BCI and PNSL pollen rain data sets. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-2059727_V1
Table S1. Pollen types identified in the BCI and PNSL pollen rain data sets. Pollen types were identified to species when possible and assigned a life form based on descriptions provided in Croat, T.B. (1978). Taxa from BCI and PNSL were assigned a 1 if present in forest census data or a 0 if absent. The relative representation of each taxon has been provided for each extended record and by dry and wet season representation respectively. CA loadings are provided for axes 1 and 2 (Fig. 1).
pollen; identifications; abundance; data; BCI; PNSL; Panama
McEntee, Kenneth B. (2017): International Registry of Reproductive Pathology Database. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-3175716_V1
The International Registry of Reproductive Pathology Database is part of pioneering work done by Dr. Kenneth McEntee to comprehensively document thousands of disease cases studies. His large and comprehensive collection of case reports and physical samples was complimented by development of the International Registry of Reproductive Pathology Database in the 1980s. The original FoxPro Database files and a migrated access version were completed by the College of Veterinary Medicine in 2016. Access CSV files were completed by the University of Illinois Library in 2017.
Animal Pathology; Databases; Veterinary Medicine
Price, Edward P. F.; Spyreas, Greg; Matthews, Jeffrey (2017): Biotic homogenization of regional wetland plant communities within short timescales in the presence of an aggressive invader. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-0478588_V2
This is the dataset used in the Journal of Ecology publication of the same name. It is a site by species matrix of species relative abundances. The file BH.veg.data.csv contains a site by species matrix of species relative abundance (percent cover across all sampling quadrats within site). Data under the heading Year refers to sampling periods. Year 1 refers to the first set of samples taken between 1997 and 2000, Year 2 refers to the second set taken between 2002 and 2005, Year 3 refers to the third set taken between 2007 and 2010, and Year 4 refers to the fourth set taken between 2012 and 2015. All sites met Critical Trends Assessment Program (CTAP) size criteria of being at least 2 ha in size with a minimum of 500 m2 of suitable sampling area. The data in file BH.site.location.csv contains Public Land Survey System ranges and townships in which specific sites were located. All sites were located within the U.S. state of Illinois. More information about this dataset: Interested parties can request data from the Critical Trends Assessment Program, which was the source for the data on the wetlands in this study. More information on the program and data requests can be obtained by visiting the program webpage. Critical Trends Assessment Program, Illinois Natural History Survey. http://wwx.inhs.illinois.edu/research/ctap/
biodiversity; biotic homogenization; invasive species; Phalaris arundinacea; plant population and community dynamics; similarity index; wetlands
Nute, Michael; Jed, Chou; Molloy, Erin K.; Warnow, Tandy (2017): Data from: The Performance of Coalescent-Based Species Tree Estimation Methods under Models of Missing Data. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-7735354_V1
Kozuch, Laura; Walker, Karen; Marquardt, William (2017): Modern sinistral whelk spire angles, genus Busycon . University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-2031816_V2
Spire angle data for sinistral whelks of the family Busyconidae. Data focuses on spire angles, with some data on total shell length. Locality information is present for all modern specimens.
lightning whelk; sinistral whelk; spire angle; sourcing; Busycon; Cahokia; Spiro
Haselhorst, Derek S.; Tcheng, David K.; Moreno, J. Enrique ; Punyasena, Surangi W. (2017): Pollen and climate data from Haselhorst et al. (2017) Ecological Informatics: Table S2. Raw pollen counts and climatic data for each seasonal sampling period. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-8658584_V1
Table S2. Raw pollen counts and climatic data for each seasonal sampling period. Climatic data reflects the average daily conditions observed over the duration samples were collected (˚C/day, mm/day, MJ/m2/day). Lycopodium counts and counts for each pollen taxon reflect the aggregated pollen sum from four sampling heights.
pollen; count; climate; data; BCI; PNSL; Panama
Haselhorst, Derek S.; Tcheng, David K.; Moreno, J. Enrique ; Punyasena, Surangi W. (2017): Model results from Haselhorst et al. (2017) Ecological Informatics: Table S3. Mean slope response for each predictive model used in the ecoinformatic analysis. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-7821127_V1
Table S3. Mean slope response for each predictive model used in the ecoinformatic analysis. Mean responses are provided for each seasonal and annual pollen data set analyzed from BCI and PNSL and are summarized by life form. Calculated p-values are provided for each model.
pollen; response; climate; ecoinformatics; BCI; PNSL; Panama
Christensen, Sarah; Molloy, Erin K.; Vachaspati, Pranjal; Warnow, Tandy (2017): Datasets from the study: Optimal completion of incomplete gene trees in polynomial time using OCTAL. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-8402610_V1
Datasets used in the study, "Optimal completion of incomplete gene trees in polynomial time using OCTAL," presented at WABI 2017.
phylogenomics; missing data; coalescent-based species tree estimation; gene trees
Merrill, Loren; Naylor, Madeleine; Dalimonte, Merria; McLaughlin, Shaun; Stewart, Tara; Grindstaff, Jennifer (2017): Dataset: early-life immune activation impacts sexual signals and their associations. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-4021048_V1
Dataset includes maternal antigen treatment and early-life antigen treatment for male zebra finches. Also includes data on beak coloration, measures of song complexity for each male, and female responses to treated males. Male beak color and song metadata: * MATID= Maternal Identity * MATTRT=Maternal antigen treatment prior to egg laying (KLH=keyhole limpet hemocyanin, LPS= lipopolysaccharide, PBS=phosphate buffered saline) * YGTRT= Young antigen treatment post-hatch (KLH=keyhole limpet hemocyanin, LPS= lipopolysaccharide, PBS=phosphate buffered saline)) * NESTBANDNUM= Nestling band number * Haptoglobin=haptoglobin levels at day 28 (mg/ml) * Mean TE= Mean number of total elements in that male's song * TE (z)= Z-transformed total elements * Mean UE=Mean number of unique elements in the song * UE (z)= z-transformed unique elements * mean phrases= Mean number of song phrases * Phrases (z)= z-transformed song phrases * Mean D= Mean song duration in seconds * D (z)=z-transformed song duration * B2 standard=beak brightness standardized so that lower values reflect less bright beaks * B2 (z)=z-transformed brightness * S1R standard= beak saturation at high wavelengths standardized so that lower values reflect less red beaks * S1R (z)=z-transformed S1R * S1U standard= beak saturation at low wavelengths standardized so that lower values reflect less red beaks * S1U (z)=z-transformed S1U * H4B standard= beak hue standardized so that lower values reflect less red beaks * H4B (z)=z-transformed H4B Female choice metadata: * Control Bird=PBS denotes that all control males received phosphate buffered saline * Treatment Bird= Treatment the male received (keyhole limpet hemocyanin (KLH) or lipopolysaccharide (LPS)) * Beak Wipes Control=# of beak wipes the female performed when on the control male side * Beak Wipes Treatment=# of beak wipes the female performed when on the "treatment male" side * Hops Control=# of hops female performed when on the control male side * Hops Treatment=# of hops female performed when on the treatment male side * Time Spent Near Control=amount of time (sec) female spent on the control male side * Time Spent Near Treatment=amount of time (sec) the female spent on the treatment male side
early-life; stress; immune response; phenotypic correlation; sexual signal; zebra finch;birdsongs; acoustic signals; beak coloration; mate selection
Nelson, Kirsten; Collins, Scott; Sass, Greg; Wahl, David (2017): Data from: A response-surface examination of competition and facilitation between native and invasive fishes. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-9706842_V1
Data (fish growth, prey responses) from a series of experiments examining interspecific interactions between native and invasive juvenile fishes.
Thapa, Sita; Schroeder, Nathan; Patel, Jayna; Reuter-Carlson, Ursula (2017): Data from: Embryogenesis in the plant parasitic nematode Heterodera glycines is independent of host-derived stimulation. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-6946735_V2
This dataset includes early embryogenesis and post-embryonic development of Soybean cyst nematode.
Soybean cyst nematode; Embryogenesis; Post-embryonic development
Mickalide, Harry; Fraebel, David T.; Kuehn, Seppe (2017): Sample video and supplementary code for cell tracking. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-4912922_V2
This is a sample 5 minute video of an E coli bacterium swimming in a microfluidic chamber as well as some supplementary code files to be used with the Matlab code available at https://github.com/dfraebel/CellTracking
Reiley, Bryan (2017): Does flooding affect the apparent survival and body condition of a ground foraging migrant passerine?. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-0341890_V1
This data was collected between 2004 and 2010 at White River National Wildlife Refuge (WRNWR) and Saint Francis National Forest (SF). It was collected as part of two master’s and one PhD project at Arkansas State University USA studying Swainson’s Warbler habitat use, survival, and body condition.
Swainson’s Warbler; Limnothlypis swainsonii; flooding; natural disturbance; apparent survival; body condition
Brown, Patrick (2017): Sorghum bicolor GBS: diversity study II. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-7570206_V1
GBS data from diverse sorghum lines. Project funded by DOE, ARPA-E, and startup funds to PJ Brown.
Brown, Patrick (2017): Sorghum bicolor GBS: recombination study. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-6534803_V1
GBS data from biparental sorghum populations provided by Dr. Bill Rooney, TAMU. Data produced and analyzed by Pradeep Hirannaiah to study recombination in sorghum. Funding for this study was provided by the Sorghum Checkoff.