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Illinois Data Bank Dataset Search Results
Dataset Search Results
published: 2020-12-31
South, Eric J.; Skinner, Rachel; DeWalt, R. Edward; Kondratieff, Boris; Johnson, Kevin P.; Davis, Mark; Lee, Jonathan; Durfee, Richard (2020): Phylogenomics of the North American Plecoptera. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-6081616_V1
This dataset contains the amino acid and nucleotide alignments corresponding to the phylogenetic analyses of South et al. 2020 in Systematic Entomology. This dataset also includes the gene trees that were used as input for coalescent analysis in ASTRAL.
keywords:
Plecoptera; stoneflies; phylogeny; insects
published: 2020-11-25
Barker, Louise; Gaulke, Sarah M.; Chace, Jordyn Z.; Davis, Mark A.; Niemiller, Matthew L.; Taylor, Steven J.; Schuett, Gordon W. (2020): Video: Agkistrodon contortrix combat behavior. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-9209722_V1
Video recorded by Louise Barker using a Cannon Powershot camera documents late-season combat behavior in Agkistrodon contortrix. Recorded in Beaufort County, North Carolina, 11.1 km SE of downtown Washington on 21 October 2020.
keywords:
Agkistrodon contortrix; combat; mating; reproduction; copperhead; pit viper; Viperidae;
published: 2020-12-15
Khanna, Madhu; Chen, Xiaoguang; Wang, Weiwei; Oliver, Anthony (2020): BEPAM-E Model Code and CABBI Simulation Results for "Repeal of the Clean Power Plan: Social Cost and Distributional Implications". University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-7562109_V1
The dataset consists of results and various input data that are used in the GAMS model for the publication "Repeal of the Clean Power Plan: Social Cost and Distributional Implications". All the data are either excel files or in the .inc format which can be read within GAMS or Notepad. Main data sources include: agriculture, transportation and electricity data. Model details can be found in the paper and the GAMS model package.
keywords:
carbon abatement; welfare cost; electricity sector; partial equilibrium model
published: 2021-01-23
Willson, James; Roddur, Mrinmoy; Warnow, Tandy (2021): Data From: "Comparing Methods for Species Tree Estimation With Gene Duplication and Loss". University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-2418574_V1
Data sets from "Comparing Methods for Species Tree Estimation With Gene Duplication and Loss." It contains data simulated with gene duplication and loss under a variety of different conditions.
keywords:
gene duplication and loss; species-tree inference;
published: 2021-06-16
Warnow , Tandy; Wedell, Eleanor (2021): Fragmentary Sequences for Variable-Sized RNAsim Datasets. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-8788479_V1
Thank you for using these datasets. These RNAsim aligned fragmentary sequences were generated from the query sequences selected by Balaban et al. (2019) in their variable-size datasets (https://doi.org/10.5061/dryad.78nf7dq). They were created for use for phylogenetic placement with the multiple sequence alignments and backbone trees provided by Balaban et al. (2019). The file structures included here also correspond with the data Balaban et al. (2020) provided. This includes: Directories for five varying backbone tree sizes, shown as 5000, 10000, 50000, 100000, and 200000. These directory names are also used by Balaban et al. (2019), and indicate the size of the backbone tree included in their data. Subdirectories for each replicate from the backbone tree size labelled 0 through 4. For the smaller four backbone tree sizes there are five replicates, and for the largest there is one replicate. Each replicate contains 200 text files with one aligned query sequence fragment in fasta format.
keywords:
Fragmentary Sequences; RNAsim
published: 2021-11-19
Shen, Chengze; Park, Minhyuk; Warnow, Tandy (2021): Seven ROSE datasets in high and low fragmentation conditions. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-6128941_V1
This is a general description of the datasets included in this upload; details of each dataset can be found in the individual README.txt in each compressed folder. We have: 1. ROSE-HF.tar.gz 2. ROSE-LF.tar.gz HF (high fragmentary): 50% of the sequences are made fragmentary, which have average lengths of 25% of the original lengths with a standard deviation of 60 bp. LF (low fragmentary): 25% of the sequences are made fragmentary, which have average lengths of 50% of the original lengths with a standard deviation of 60 bp. The seven ROSE datasets made fragmentary are: 1000L1, 1000L3, 1000L4, 1000M3, 1000S1, 1000S2 and 1000S4. "ROSE-HF.tar.gz" contains HF versions of the seven ROSE datasets. "ROSE-LF.tar.gz" contains LF versions of the seven ROSE datasets.
keywords:
ROSE; simulation; fragmentary
published: 2020-09-18
Clark, Lindsay; Njuguna, Joyce; Jin, Xiaoli; Petersen, Karen; 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 (2020): RAD-seq genotypes for a Miscanthus sacchariflorus diversity panel. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-8170405_V1
Restriction site-associated DNA sequencing (RAD-seq) data from 643 Miscanthus accessions from a diversity panel, including 613 Miscanthus sacchariflorus, three M. sinensis, and 27 M. xgiganteus. DNA was digested with PstI and MspI, and single-end Illumina sequencing was performed adjacent to the PstI site. Variant and genotype calling was performed with TASSEL-GBSv2, using the Miscanthus sinensis v7.1 reference genome from Phytozome 12 (https://phytozome.jgi.doe.gov). Additional ploidy-aware genotype calling was performed by polyRAD v1.1.
keywords:
variant call format (VCF); genotyping-by-sequencing (GBS); single nucleotide polymorphism (SNP); grass; genetic diversity; biomass
published: 2020-08-01
Xu, Ye; Dietrich, Christopher H.; Zhang, Yalin; Dmitriev, Dmitry; Zhang, Li; Wang, Yi-Mei; Lu, Si-Han; Qin, Dao-Zheng (2020): NEXUS morphological data file for phylogenetic analysis of Empoascini. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-4470290_V1
The Empoascini_morph_data.nex text file contains the original data used in the phylogenetic analyses of Xu et al. (Systematic Entomology, in review). 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 nine lines of the file indicate the file type (Nexus), that 110 taxa were analyzed, that a total of 99 characters were analyzed, the format of the data, and specification for symbols used in the dataset to indicate different character states. For species that have more than one state for a particular character, the states are enclosed in square brackets. Question marks represent missing data.The pdf file, Appendix1.pdf, is available here and describes the morphological characters and character states that were scored in the dataset. The data analyses are described in the cited original paper.
keywords:
Hemiptera; Cicadellidae; morphology; biogeography; evolution
published: 2020-09-25
Androwski, Rebecca; Asad, Nadeem; Wood, Janet; Hofer, Allison; Locke, Steven; Smith, Cassandra; Rose, Becky; Schroeder, Nathan (2020): Data From: Mutually exclusive dendritic arbors in C. elegans neurons share a common architecture and convergent molecular cues. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-0818023_V1
This dataset includes neuronal development of the Caenorhabditis elegans dauer and adult.
keywords:
Nematode; Dendrite; Stress
published: 2021-03-08
Jaikumar, Nikhil S.; Fernandes, Samuel B.; Leakey, Andrew D.B.; Brown, Patrick J.; Stutz, Samantha S.; Bernacchi, Carl; Long, Stephen P. (2021): Photosynethic Performance Measurements in Biomass Sorghum Varietals in Central Illinois during Four Growing Seasons.. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-4580996_V2
In a set of field studies across four years, the effect of self-shading on photosynthetic performance in lower canopy sorghum leaves was studied at sites in Champaign County, IL. Photosynthetic parameters in upper and lower canopy leaves, carbon assimilation, electron transport, stomatal conductance, and activity of three C4-specific photosynthetic enzymes, were compared within a genetically diverse range of accessions varying widely in canopy architecture and thereby in the degree of self-shading. Accessions with erect leaves and high light transmission through the canopy are henceforth referred to as ‘erectophile’ and those with low leaf erectness, ‘planophile’. In the final year of the study, bundle sheath leakiness in erectophile and planophile accessions was also compared.
keywords:
Sorghum; Photosynethic Performance; Leaf Inclination
published: 2020-07-15
Legried, Brandon; Molloy, Erin K.; Warnow, Tandy; Roch, Sebastien (2020): Data from: Polynomial-Time Statistical Estimation of Species Trees under Gene Duplication and Loss. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-2626814_V3
This repository includes scripts and datasets for the paper, "Polynomial-Time Statistical Estimation of Species Trees under Gene Duplication and Loss."
keywords:
Species tree estimation; gene duplication and loss; identifiability; statistical consistency; quartets; ASTRAL
published: 2020-05-31
Zhang, Chuanyi; El-Kebir, Mohammed; Ochoa, Idoia (2020): Simulated multi-sample tumor bulk sequencing data. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-9059263_V1
This repository includes a simulated dataset and related scripts used for the paper "Moss: Accurate Single-Nucleotide Variant Calling from Multiple Bulk DNA Tumor Samples".
keywords:
Somatic Mutations; Bulk DNA Sequencing; Cancer Genomics
published: 2020-04-20
Ferrer, Astrid (2020): Data for: Contribution of fungal and invertebrate communities to mass loss and wood depolymerization in tropical terrestrial and aquatic habitats. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-1530066_V1
Supplemental data sets for the Manuscript entitled "Contribution of fungal and invertebrate communities to mass loss and wood depolymerization in tropical terrestrial and aquatic habitats"
keywords:
Coiba Island; wood decomposition; cellulose; hemicellulose; lignin breakdown; aquatic fungi
published: 2020-01-31
Bradshaw, Therin M.; Blake-Bradshaw, Abigail G.; Fournier, Auriel M.V.; Lancaster, Joseph D. ; O'Connell, John; Jacques, Christopher N.; Eicholtz, Michael W.; Hagy, Heath M (2020): Marsh bird occupancy of wetlands managed for waterfowl in the Midwestern USA - Analysis Inputs. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-5152821_V1
Data inputs, and scripts for the analysis detailed in Bradshaw et al, published in PlosONE 2020.
keywords:
Marsh birds; wetlands
published: 2022-08-31
Seyfried, Georgia; Midgley, Meghan; Phillips, Richard; Yang, Wendy (2022): Data for Refining the role of nitrogen mineralization in mycorrhizal nutrient syndromes. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-5586647_V2
This dataset includes data on soil properties, soil N pools, and soil N fluxes presented in the manuscript, "Refining the role of nitrogen mineralization in mycorrhizal nutrient syndromes". Please refer to that publication for details about methodologies used to generate these data and for the experimental design. For this verison 2, we added specific gross nitrogen mineralization rates (ugN/gOM/d), microbial biomass carbon (ugC/gdw), microbial biomass nitrogen (ugN/gdw) and microbial biomass C:N ratios to the newest version of the data set. Additionally, we updated values for gross nitrogen mineralization, microbial NO3 assimilation and microbial NH4 assimilation to reflect slight changes in data processing. Those changes are reflected in "220829_All data_repository.csv". "220829_nitrogen_mineralization_readme.txt " is updated readme for the new file. The other 2 files begin with “220426_” are older version and same as in V1.
keywords:
Nitrogen cycling; Ectomycorrhizal fungi; Arbuscular mycorrhizal fungi; Nitrogen fertilization; Gross mineralization
published: 2023-07-01
Tonks, Adam; Hwang, Jeongwoo (2023): Data for the paper "Assessment of spatiotemporal flood risk due to compound precipitation extremes across the contiguous United States". University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-6626437_V1
This is the data used in the paper "Assessment of spatiotemporal flood risk due to compound precipitation extremes across the contiguous United States". Code from the Github repository https://github.com/adtonks/precip_extremes can be used with the data here to reproduce the paper's results. v1.0.0 of the code is also archived at https://doi.org/10.5281/zenodo.8104252 This dataset is derived from NOAA-CIRES-DOE 20th Century Reanalysis V3. The NOAA-CIRES-DOE Twentieth Century Reanalysis Project version 3 used resources of the National Energy Research Scientific Computing Center managed by Lawrence Berkeley National Laboratory which is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231 and used resources of NOAA's Remotely Deployed High Performance Computing Systems.
keywords:
spatiotemporal; CONUS; United States; precipitation; extremes; flooding
published: 2022-05-20
Haselhorst, Derek; Moreno, J. Enrique; Tcheng, David K.; Punyasena, Surangi W. (2022): Images and annotated counts for aerial pollen samples from the Barro Colorado Island megaplot, Panama (1994 – 2010). University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-2176715_V1
This dataset includes images and annotated counts for 150 airborne pollen samples from the Center for Tropical Forest Science 50 ha forest dynamics plot on Barro Colorado Island, Panama. Samples were collected once a year from April 1994 to June 2010.
keywords:
aerial pollen traps; automated pollen identification; Barro Colorado Island; convolutional neural networks; Neotropics; palynology; phenology
published: 2019-12-20
Wang, Yu; Burgess, Steven J. ; de Becker, Elsa ; Long, Stephen P. (2019): Data and code for: Photosynthesis in the fleeting shadows: An overlooked opportunity for increasing crop productivity?. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-9453481_V1
This dynamic photosynthesis model of soybean canopy is developed by Yu Wang (yuwangcn@illinois.edu), IGB, University of Illinois. If you want to know more details, please check the following publication Yu Wang, Steven J. Burgess, Elsa de Becker, Stephen P. Long. Photosynthesis in the fleeting shadows: An overlooked opportunity for increasing crop productivity? The Plant Journal.
keywords:
Matlab; Soybean canopy; photosynthesis model
published: 2020-03-13
Sweet, Andrew; Johnson, Kevin; Cameron, Stephen (2020): Data from: Mitochondrial genomes of Columbicola feather lice are highly fragmented, indicating repeated evolution of minicircle-type genomes in parasitic lice . University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-2211060_V2
Data files associated with the assembly of mitochondrial minicircles from five species of parasitic lice. This includes data from four species in the genus Columbicola and from the human louse (Pediculus humanus). The files include FASTA sequences for all five species, reference sequences for read mapping approaches, resulting contigs produced by various assembly approaches, and alignments of human louse minicircles mapped to published sequences of the same species.
keywords:
mitochondria; FASTA; nucleotide sequences; alignment; Columbicola; Pediculus
published: 2021-10-15
Jianhao, Peng; Idoia, Ochoa (2021): Synthetic datasets for SimiC . University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-4996748_V1
This is the 5 states 5000 cells synthetic expression file we used for validation of SimiC, a single cell gene regulatory network inference method with similarity constraints. Ground truth GRNs are stored in Numpy array format, and expression profiles of all states combined are stored in Pandas DataFrame in format of Pickle files.
keywords:
Numpy array; GRNs; Pandas DataFrame;
published: 2016-05-16
Imker, Heidi (2016): Phylogenetic Analysis of the NRPS AmbE Condensation Domains for the L-2-amino-4-methoxy-trans-3-butenoic acid (AMB) Biosynthetic Pathway in Pseudomonas aeruginosa. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-4602893_V1
This dataset contains the protein sequences and trees used to compare Non-Ribosomal Peptide Synthetase (NRPS) condensation domains in the AMB gene cluster and was used to create figure S1 in Rojas et al. 2015. Instead of having to collect representative sequences independently, this set of condensation domain sequences may serve as a quick reference set for coarse classification of condensation domains.
keywords:
NRPS; biosynthetic gene cluster; antimetabolite; Pseudomonas; oxyvinylglycine; secondary metabolite; thiotemplate; toxin
published: 2020-08-25
Allan, Brian; Fredericks, Lisa (2020): AllanLab fluidigm pipeline test dataset. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-0095812_V1
The Allan Lab has published a Fluidigm pipeline online. This is the url: https://github.com/HPCBio/allan-fluidigm-pipeline. This url includes a tutorial for running the pipeline. However it does not have test datasets yet. This tarball hosted at the Illinois Data Bank is the dataset that completes the github tutorial. It includes inputs (custom database of tick pathogens and fluidigm raw reads) and output files (tables of samples with taxonomic classifications).
keywords:
custom database of tick pathogens; fluidigm pipeline; fluidigm paired reads; fluidigm tutorial
published: 2019-09-17
Fraebel, David T.; Kuehn, Seppe (2019): Sequencing data for migration rate selection experiments (0.2% agar, 1mM sugar). University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-2128477_V1
BAM files for evolved strains from migration rate selection experiments conducted in low viscosity (0.2% w/v) agar plates containing M63 minimal medium with 1mM of mannose, melibiose, N-acetylglucosamine or galactose
published: 2019-07-04
Sashittal, Palash; El-Kebir, Mohammed (2019): SharpTNI Results. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-9734610_V1
Results generated using SharpTNI on data collected from the 2014 Ebola outbreak in Sierra Leone.
published: 2019-08-05
Skinner, Rachel; Dietrich, Christopher; Walden, Kimberly; Gordon, Eric; Sweet, Andrew; Podsiadlowski, Lars; Petersen, Malte; Simon, Chris; Takiya, Daniela; Johnson, Kevin (2019): Data for Phylogenomics of Auchenorrhyncha (Insecta: Hemiptera) using Transcriptomes: Examining Controversial Relationships via Degeneracy Coding and Interrogation of Gene Conflict. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-1461292_V1
The data in this directory corresponds to: Skinner, R.K., Dietrich, C.H., Walden, K.K.O., Gordon, E., Sweet, A.D., Podsiadlowski, L., Petersen, M., Simon, C., Takiya, D.M., and Johnson, K.P. Phylogenomics of Auchenorrhyncha (Insecta: Hemiptera) using Transcriptomes: Examining Controversial Relationships via Degeneracy Coding and Interrogation of Gene Conflict. Systematic Entomology. Correspondance should be directed to: Rachel K. Skinner, rskinn2@illinois.edu If you use these data, please cite our paper in Systematic Entomology. The following files can be found in this dataset: Amino_acid_concatenated_alignment.phy: the amino acid alignment used in this analysis in phylip format. Amino_acid_raxml_partitions.txt (for reference only): the partitions for the amino acid alignment, but a partitioned amino acid analysis was not performed in this study. Amino_acid_concatenated_tree.newick: the best maximum likelihood tree with bootstrap values in newick format. ASTRAL_input_gene_trees.tre: the concatenated gene tree input file for ASTRAL README_pie_charts.md: explains the the scripts and data needed to recreate the pie charts figure from our paper. There is also another Corresponds to the following files: ASTRAL_species_tree_EN_only.newick: the species tree with only effective number (EN) annotation ASTRAL_species_tree_pp1_only.newick: the species tree with only the posterior probability 1 (main topology) annotation ASTRAL_species_tree_q1_only.newick: the species tree with only the quartet scores for the main topology (q1) ASTRAL_species_tree_q2_only.newick: the species tree with only the quartet scores for the first alternative topology (q2) ASTRAL_species_tree_q3_only.newick: the species tree with only the quartet scores for the second alternative topology (q3) print_node_key_files.py: script needed to create the following files: node_keys.key: text file with node IDs and topologies complete_q_scores.key: text file with node IDs multiplied q scores EN_node_vals.key: text file with node IDs and EN values create_pie_charts_tree.py: script needed to visualize the tree with pie charts, pp1, and EN values plotted at nodes ASTRAL_species_tree_full_annotation.newick: the species tree with full annotation from the ASTRAL analysis. NOTE: It may be more useful to examine individual value files if you want to visualize the tree, e.g., in figtree, since the full annotations are extensive and can make viewing difficult. Complete_NT_concatenated_alignment.phy: the nucleotide alignment that includes unmodified third codon positions. The alignment is in phylip format. Complete_NT_raxml_partitions.txt: the raxml-style partition file of the nucleotide partitions Complete_NT_concatenated_tree.newick: the best maximum likelihood tree from the concatenated complete analysis NT with bootstrap values in newick format Complete_NT_partitioned_tree.newick: the best maximum likelihood tree from the partitioned complete NT analysis with bootstrap values in newick format Degeneracy_coded_nt_concatenated_alignment.phy: the degeneracy coded nucleotide alignment in phylip format Degeneracy_coded_nt_raxml_partitions.txt: the raxml-style partition file for the degeneracy coded nucleotide alignment Degeneracy_coded_nt_concatenated_tree.newick: the best maximum likelihood tree from the degeneracy-coded concatenated analysis with bootstrap values in newick format Degeneracy_coded_nt_partitioned_tree.newick: the best maximum likelihood tree from the degeneracy-coded partitioned analysis with bootstrap values in newick format count_ingroup_taxa.py: script that counts the number of ingroup and/or outgroup taxa present in an alignment
keywords:
Auchenorrhyncha; Hemiptera; alignment; trees