Illinois Data Bank
Deposit Dataset
Find Data
Policies
Guides
Contact Us
Log in with NetID
Toggle navigation
Illinois Data Bank
Deposit Dataset
Find Data
Policies
Guides
Contact Us
Log in with NetID
Displaying 226 - 250 of 382 in total
<
1
2
…
6
7
8
9
10
11
12
13
14
15
16
>
25 per page
50 per page
Show All
Go
Clear Filters
Generate Report from Search Results
Subject Area
Life Sciences (382)
Social Sciences (0)
Physical Sciences (0)
Technology and Engineering (0)
Uncategorized
Arts and Humanities (0)
Funder
Other (140)
U.S. National Science Foundation (NSF) (92)
U.S. Department of Energy (DOE) (45)
U.S. Department of Agriculture (USDA) (44)
U.S. National Institutes of Health (NIH) (31)
Illinois Department of Natural Resources (IDNR) (19)
U.S. Geological Survey (USGS) (5)
Illinois Department of Transportation (IDOT) (3)
U.S. National Aeronautics and Space Administration (NASA) (2)
U.S. Army (2)
Publication Year
2021 (66)
2024 (61)
2020 (60)
2022 (55)
2019 (42)
2023 (40)
2018 (24)
2017 (19)
2016 (12)
2025 (3)
2009 (0)
2011 (0)
2012 (0)
2014 (0)
2015 (0)
License
CC0 (229)
CC BY (140)
custom (13)
Illinois Data Bank Dataset Search Results
Dataset Search Results
published: 2019-12-03
de Moya, Robert (2019): Heteroptera Transcriptome Set. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-7784896_V1
These are the alignments of transcriptome data used for the analysis of members of Heteroptera. This dataset is analyzed in "Deep instability in the phylogenetic backbone of Heteroptera is only partly overcome by transcriptome-based phylogenomics" published in Insect Systematics and Diversity.
keywords:
Heteroptera; Hemiptera; Phylogenomics; transcriptome
published: 2020-11-05
Miller, Andrew; Raudabaugh, Daniel (2020): Data from Species Distribution, Phylogenetic Structure, and Functional Roles of Detritius Inhabiting Fungi Across Contrasting Aquatic Environments.. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-6862941_V2
This version 2 dataset contains 34 files in total with one (1) additional file, called "Culture-dependent Isolate table with taxonomic determination and sequence data.csv". The remaining files (33) are identical to version 1. The following is the information about the new file and its variables: <b>Culture-dependent Isolate table with taxonomic determination and sequence data.csv</b>: Culture table with assigned taxonomy from NCBI. Single direction sequence for each isolate is include if one could be obtained. Sequence is derived from ITS1F-ITS4 PCR amplicons, with Sanger sequencing in one direction using ITS5. The files contains 20 variables with explanation as below: IsolateNumber : unique number identify each isolate cultured Time: season in which the sample was collected Location: the specific name of the location Habitat: type of habitat : either stream or peatland State: state in the USA in which the specific location is located Incubation_pH ID: pH of the medium during isolation of fungal cultures Genus: phylogenetic genus of the fungal isolates (determined by sequence similarity) Sequence_quality: base call quality of the entire sequence used for blast analysis, if known %_coverage: sequence coverage reported from GenBank %_ID: sequence similarity reported from GenBank Life_style : ecological life style if known Phylum: phylogenetic phylum as indicated by Index Fungorum Subphylum: phylogenetic subphylum as indicated by Index Fungorum Class: phylogenetic class as indicated by Index Fungorum Subclass: phylogenetic subclass as indicated by Index Fungorum Order: phylogenetic order as indicated by Index Fungorum Family: phylogenetic Family as indicated by Index Fungorum ITS5_Sequence: single direction sequence used for sequence similarity match using blastn. Primer ITS5 Fasta: sequence with nomenclature in a fasta format for easy cut and paste into phylogenetic software Note: blank cells mean no data is available or unknown.
keywords:
ITS1 forward reads; Illumina; peatlands; streams; bogs; fens
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: 2019-12-03
de Moya, Robert (2019): Feather Louse Orthology set. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-0440388_V1
This is the data set associated with the manuscript titled "Extensive host-switching of avian feather lice following the Cretaceous-Paleogene mass extinction event." Included are the gene alignments used for phylogenetic analyses and the cophylogenetic input files.
keywords:
phylogenomics, cophylogenetics, feather lice, birds
published: 2019-06-12
Miller, Andrew; Raudabaugh, Daniel (2019): Supplemental data sets for Raudabaugh et al., Where are they hiding? Testing the body snatchers hypothesis in pyrophilous fungi. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-1530363_V1
The data set contains Supplemental data sets for the Manuscript entitled "Where are they hiding? Testing the body snatchers hypothesis in pyrophilous fungi." Environmental sampling: Amplification of nuclear DNA regions (ITS1 and ITS2) were completed using the Fluidigm Access Array and the resulting amplicons were sequenced on an Illumina MiSeq v2 platform runs using rapid 2 × 250 nt paired-end reads. Illumina sequencing run amplicons that were size selected into <500nt and >500nt sub-pools, then remixed together <500nt: >500nt by nM concentration in a 1x:3x proportion. All amplification and sequencing steps were performed at the Roy J. Carver Biotechnology Center at the University of Illinois Urbana-Champaign. ITS1 region primers consisted of ITS1F (5'-CTTGGTCATTTAGAGGAAGTAA-'3) and ITS2 (5'-GCTGCGTTCTTCATCGATGC-'3). ITS2 region primers consisted of fITS7 (5'-GTGARTCATCGAATCTTTG-'3) and ITS4 (5'-TCCTCCGCTTATTGATATGC-'3). Supplemental files 1 through 5 contain the raw data files. Supplemental 1 is the ITS1 Illumina MiSeq forward reads and Supplemental 2 is the corresponding index files. Supplemental 3 is the ITS2 Illumina MiSeq forward reads and Supplemental 4 is the corresponding index files. Supplemental 5 is the map file needed to process the forward reads and index files in QIIME. Supplemental 6 and 7 contain the resulting QIIME 1.9.1. OTU tables along with UNITE, NCBI, and CONSTAX taxonomic assignments in addition to the representative OTU sequence. Numeric samples within the OTU tables correspond to the following: 1 Brachythecium sp. 2 Usnea cornuta 3 Dicranum sp. 4 Leucodon julaceus 5 Lobaria quercizans 6 Rhizomnium sp. 7 Dicranum sp. 8 Thuidium delicatulum 9 Myelochroa aurulenta 10 Atrichum angustatum 11 Dicranum sp. 12 Hypnum sp. 13 Atrichum angustatum 14 Hypnum sp. 15 Thuidium delicatulum 16 Leucobryum sp. 17 Polytrichum commune 18 Atrichum angustatum 19 Atrichum angustatum 20 Atrichum crispulum 21 Bryaceae 22 Leucobryum sp. 23 Conocephalum conicum 24 Climacium americanum 25 Atrichum angustatum 26 Huperzia serrata 27 Polytrichum commune 28 Diphasiastrum sp. 29 Anomodon attenuatus 30 Bryoandersonia sp. 31 Polytrichum commune 32 Thuidium delicatulum 33 Brachythecium sp. 34 Leucobryum glaucum 35 Bryoandersonia sp. 36 Anomodon attenuatus 37 Pohlia sp. 38 Cinclidium sp. 39 Hylocomium splendens 40 Polytrichum commune 41 negative control 42 Soil 43 Soil 44 Soil 45 Soil 46 Soil 47 Soil If a sample number is not present within the OTU table; either no sequences were obtained or no sequences passed the quality filtering step in QIIME. Supplemental 8 contains the Summary of unique species per location.
published: 2019-07-29
Christensen, Sarah; Molloy, Erin K.; Vachaspati, Pranjal; Warnow, Tandy (2019): Data from TRACTION: Fast non-parametric improvement of estimated gene trees. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-1747658_V1
Datasets used in the study, "TRACTION: Fast non-parametric improvement of estimated gene trees," accepted at the Workshop on Algorithms in Bioinformatics (WABI) 2019.
keywords:
Gene tree correction; horizontal gene transfer; incomplete lineage sorting
published: 2019-08-30
Allen, Maximilian (2019): Wisconsin Bobcat Harvest Data. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-2501832_V1
This dataset includes the data from an analysis of bobcat harvest data with particular focus on the relationship between catch-per-unit-effort and population size. The data relate to bobcat trapper and hunter harvest metrics from Wisconsin and include two RDS files which can be open in the software R using the readRDS() function.
keywords:
bobcat; catch-per-unit-effort; CPUE; harvest; Lynx rufus; wildlife management; trapper; hunter
published: 2017-12-22
Scheidler, Andrew; Kinnett-Hopkins, Dominique; Learmonth, Yvonne; Motl, Robert; Lopez-Ortiz, Citlali (2017): Targeted ballet program mitigates ataxia and improves agility in moderate-to-advanced multiple sclerosis. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-6858418_V2
TBP assessment raw data files of pre- and post- motion capture velocity and center of pressure force plate data. Labels are self-explanatory. The .mat files refer to data exported from the force plate for the time-to-stabilization assessments while the .txt files are the data collected for smoothness of gait assessments. These files do not relate to one another and are from separate assessments. Version2's files are the result from using Python code Data_Bank_Cleaner.py on version1's. Please find more information in READ_ME_databank.txt.
keywords:
Multiple Sclerosis; Rehabilitation; Balance; Ataxia; Ballet; Dance; Targeted Ballet Program
published: 2019-08-29
de Moya, Robert (2019): Bemisia tabaci ortholog set. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-5333299_V1
This is the published ortholog set derived from whole genome data used for the analysis of members of the B. tabaci complex of whiteflies. It includes the concatenated alignment and individual gene alignments used for analyses (Link to publication: https://www.mdpi.com/1424-2818/11/9/151).
published: 2020-10-01
Strickland, Lynette (2020): No choice mating trials and two choice mating trials in the polymorphic tortoise beetle, Chelymorpha alternans. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-8972634_V1
These datasets were performed to assess whether color pattern phenotypes of the polymorphic tortoise beetle, Chelymorpha alternans, mate randomly with one another, and whether there are any reproductive differences between assortative and disassortative pairings.
keywords:
mate choice, color polymorphisms, random mating
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: 2019-01-27
Le, Thien; Sy, Aaron; Molloy, Erin K.; Zhang, Qiuyi; Rao, Satish; Warnow, Tandy (2019): Using INC within Divide-and-Conquer Phylogeny Estimation - Datasets. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-8518809_V1
This repository include datasets that are studied with INC/INC-ML/INC-NJ in the paper `Using INC within Divide-and-Conquer Phylogeny Estimation' that was submitted to AICoB 2019. Each dataset has its own readme.txt that further describes the creation process and other parameters/softwares used in making these datasets. The latest implementation of INC/INC-ML/INC-NJ can be found on https://github.com/steven-le-thien/constraint_inc. Note: there may be files with DS_STORE as extension in the datasets; please ignore these files.
keywords:
phylogenetics; gene tree estimation; divide-and-conquer; absolute fast converging
published: 2023-02-10
Emmet, Robert L.; Benson, Thomas J.; Allen, Maximilian L.; Stodola, Kirk W. (2023): Integrating multiple data sources improves prediction and inference for upland game occupancy models. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-0477888_V1
Data and documentation for Ornithological Applications manuscript “Integrating multiple data sources improves prediction and inference for upland game bird occupancy models” by Robert L. Emmet, Thomas J. Benson, Maximilian L. Allen, and Kirk W. Stodola We combined data from the North American Breeding Bird Survey and eBird with a targeted survey (IDNR upland game) to estimate habitat use of northern bobwhite and ring-necked pheasant in Illinois and to document the efficiency and overlap among the various data sources. Data include, eBird, USGS Breeding Bird Survey, National Land Cover Database, Upland game bird surveys, stream data)
keywords:
data integration; occupancy; avian population modelling; northern bobwhite;Colinus virginianus; ring-necked pheasant; Phasianus colchicus
published: 2021-04-11
Park, Minhyuk; Zaharias, Paul; Warnow, Tandy (2021): Disjoint Tree Mergers for Large-Scale Maximum LikelihoodTree Estimation. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-7008049_V1
This dataset contains RNASim1000, Cox1-Het datasets as well as analyses of RNASim1000, Cox1-Het, and 1000M1(HF).
keywords:
phylogeny estimation; maximum likelihood; RAxML; IQ-TREE; FastTree; cox1; heterotachy; disjoint tree mergers; Tree of Life
published: 2021-09-03
Clark, Lindsay V.; Mays, Wittney; Lipka, Alexander E.; Sacks, Erik J. (2021): Dataset for evaluating the Hind/He statistic in polyRAD. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-4814898_V1
All of the files in this dataset pertain to the evaluation of a novel statistic, Hind/He, for distinguishing Mendelian loci from paralogs. They are derived from a RAD-seq genotyping dataset of diploid and tetraploid Miscanthus sacchariflorus.
published: 2021-03-15
Stodola, Alison P.; Lydeard, Charles; Lamer, James T.; Douglass, Sarah A.; Cummings, Kevin; Campbell, David (2021): Data and Images for "Hiding in plain sight: genetic confirmation of putative Louisiana Fatmucket Lampsilis hydiana in Illinois". University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-5609050_V1
Dataset associated with "Hiding in plain sight: genetic confirmation of putative Louisiana Fatmucket Lampsilis hydiana in Illinois" as submitted to Freshwater Mollusk Biology and Conservation by Stodola et al. Images are from cataloged specimens from the Illinois Natural History Survey (INHS) Mollusk Collection in Champaign, Illinois that were used for genetic research. File names indicate the species as confirmed in Stodola et al. (i.e., Lampsilis siliquoidea or Lampsilis hydiana) followed by the INHS Mollusk Collection catalog number, followed by the individual specimen number, followed by shell view (interior or exterior). If no specimen number is noted in the file name, there is only one specimen for that catalog number. For example: Lsiliquoidea_46515_1_2_3_exterior. Images were created by photographing specimens on a metric grid in an OrTech Photo-e-Box Plus with a Nikon D610 single lens reflex camera using a 60mm lens. Post-processing of images (cropping, image rotation, and auto contrast) occurred in Adobe Photoshop and saved as TIFF files using no image compression, interleaved pixel order, and IBM PC Byte Order. One additional partial lot, INHS Mollusk Catalog No. 37059 (shown with both interior and exterior view in one image), is included for reference but was not genetically sequenced. A .csv file contains an index of all specimens photographed. SPECIES: species confirmed using genetic analyses GENE: cox1 or nad1 mitochondrial gene ACCESSION: GenBank accession number INHS CATALOG NO: Illinois Natural History Survey Mollusk Collection Catalog number WATERBODY: waterbody where specimen was collected PUTATIVE SPECIES: species determination based on morphological characters prior to genetic analysis Phylogenetic sequence data (.nex files) were aligned using BioEdit (Hall, T.A. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series 41:95-98.). Pertinent methodology for the analysis are contained within the manuscript submittal for Stodola et al. to Freshwater Mollusk Biology and Conservation. In these files, "N" is a standard symbol for an unknown base.
keywords:
Lampsilis hydiana; Lampsilis siliquoidea; unionid; Louisiana Fatmucket; Fatmucket; genetic confirmation
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: 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: 2020-12-07
Tian, Yuan; Smith-Bolton, Rachel (2020): Data for Regulation of growth and cell fate during tissue regeneration by the two SWI/SNF chromatin-remodeling complexes of Drosophila. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-1681718_V1
This page contains the data for the publication "Regulation of growth and cell fate during tissue regeneration by the two SWI/SNF chromatin-remodeling complexes of Drosophila" published in Genetics, 2020
published: 2017-03-08
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.
keywords:
Soybean cyst nematode; Embryogenesis; Post-embryonic development
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: 2017-03-07
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
published: 2016-12-14
Brown, Patrick (2016): 14IL008,16IL003,16IL007. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-6648634_V1
published: 2017-09-19
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
published: 2023-07-27
Feng, Ling; Takiya, Daniela; Krishnankutty, Sindhu; Dietrich, Christopher; Zhang, Yalin (2023): NEXUS file for Phylogeny and Biogeography of the Sharpshooters (Hemiptera: Cicadellidae: Cicadellinae). University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-0855589_V1
The text file contains the original aligned DNA nucleotide sequence data used in the phylogenetic analyses of Feng et al. (in review), comprising the 3 protein-coding genes (histone H3, cytochrome oxidase I and 2) and 2 ribosomal genes (28S D8 and 16S). The text file is marked up according to the standard NEXUS format commonly used by various phylogenetic analysis software packages. The file will be parsed automatically by a variety of programs that recognize NEXUS as a standard bioinformatics file format. The first six lines of the file identify the file as NEXUS, indicate that the file contains data for 257 taxa (species) and 2995 characters (nucleotide positions), indicate that the characters are DNA sequence, that gaps inserted into the DNA sequence alignment are indicated by a dash, and that missing data are indicated by a question mark. The remainder of the file contains the aligned nucleotide sequence data for the five genes. Data partitions, representing the individual genes and different codon positions of the protein-coding genes, are indicated by the lines beginning "charset" near the end of the file. Two supplementary tables in the provided PDF file provide additional information on the species in the dataset, including the GenBank accession numbers for the sequence data (Table S1) and the DNA substitution models used for each of the data partitions used for analyses in the phylogenetic analysis program IQ-Tree (version 1.6.8) (Table S3), as described in the Methods section of the paper. The supplemental tables will also be linked to the article upon publication at the journal website.
keywords:
Insect; leafhopper; dispersal; vicariance; evolution