cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.8h8q5/1
title: dHNF4_RNAseq_DiffExpr_1.5fold

description: Total RNA was extracted from dHNF4 mutants and genetically-matched control adult males (8 days old) using TriPure isolation reagent (Roche) followed by further purification/cleanup by RNeasy kit (QIAGEN). RNA from 4 biological replicates (n=40 flies per sample) per genotype was polyA-selected and assembled into barcoded libraries and pooled into a single-flow cell lane for Illumina HighSeq2000 50-cycle single-read sequencing, which produced ≥ 21.9 million reads per sample. Standard replicate RNAseq analysis was performed using USeq and DESeq analysis packages with alignment to the Drosophila melanogaster dm3 genome assembly. Transcripts meeting a cutoff of ≥1.5 fold difference in mRNA abundance (~Log2 ≥ +/- 0.6) and FDR ≤ 1% were considered as differentially expressed genes. RNA quality control, library preparation, sequencing, and data analysis were performed at the University of Utah High Throughput Genomics and Bioinformatics Core Facilities.
DOI: 10.5061/dryad.9jh6m/1
title: Fibronectin_Modulation_Dataset

description: The associated .csv files constitute quantitative datasets underpinning the manuscript "Heterogeneity in mesenchymal motility reflects adaptive switching between two distinct migration modes", by Shafqat-Abbasi et al. Three datasets are presented with equivalent structures, reflecting data derived from multiscale, high resolution imaging of randomly migrating H1299-PL cells. These datasets focus on comparison of cells: attached on different concentrations of fibronectin (extracellular-matrix ligand, Fibronectin_Modulation_Dataset); following inhibition of Rho-associated kinase (ROCK, Y27632 inhibitor) or a control treatment (DMSO, ROCK_Modulation_Dataset); or following siRNA-mediated depletion of talin 1 protein levels compared to control siRNA treatment (Talin_Modulation_Dataset). Accordingly, each data set is divided into two conditions (denoted “1” or “2”), between which feature values are quantitatively compared throughout the manuscript. In each case, the values 1 and 2 in the “condition” column refer to: Fibronectin_Modulation_Dataset: 1 = 2.5 µg/ml FN (2580 observations), 2 = 10 µg/ml FN (7000 observations); ROCK_Modulation_Dataset: 1 = DMSO (2666 observations), 2 = 6 µM ROCK Inh (985 observations); Talin_Modulation_Dataset: 1 = Control siRNA (3154 observations), 2 = talin 1 siRNA (6263 observations). Column structure within the files is as follows. The first 6 columns are indexing columns, wherein the: experimental condition is defined (1 vs 2, as above); experimental date is define; individual cell identities are defined; the mesenchymal cell migration mode is defined (0 = undetermined, e.g. dead cells or cells in contact; 1 = Discontinuous migration mode; 2 = Continuous migration mode); cell centre of area (row), and; cell centre of area (column) are defined. The following 60 columns define quantitative features extracted based on image analyses. These include 5 Behavioral features and 55 Organizational features, as defined in Figure 3 – figure supplement 1.
DOI: 10.5061/dryad.9jh6m/2
title: Cell Adhesion and Migration Analysis Toolbox

description: This zip file contains code, data and documentation associated with the Cell Adhesion and Migration Analysis Toolbox. This Toolbox provides data analysis and organization tools for cell adhesion and migration data. To this end, this Toolbox provides a set of analysis features that can be combined to gain a coherent and comprehensive picture of the cell adhesion and migration systems. Some of the provided features may also be used in isolation to address alternate questions (i.e. complex processes other than cell adhesion/migration). The code is tailored to handle microscopy-derived multi-scale, multivariate time series data that can be image based or constitute extracted quantitative feature datasets from cell adhesion and migration experiments. This document describes the features listed in the table of contents and how the Cell adhesion and migration analysis Toolbox allows their implementation.
DOI: 10.5061/dryad.bh215/1
title: Asymmetric_interaction

description: Matlab code to model translocations of competitive and mutualistic systems with asymmetric interaction.
DOI: 10.5061/dryad.bn410/1
title: CSV files of all paper data

description: The data provided below should be enough to reproduce the primary data figures in the paper. They are organized in the order in which they appear in the  paper. Each CSV file contains 11 columns:- Algorithm: The name of the algorithm being tested- Number: Stimulus ID- SNR: Input SNR (dB) of the stimulus- Composite Signal: Composite estimate of speech distortion- Composite Background: Composite estimate of background intrusiveness- Composite Overall: Composite estimate of overall quality- STOI: Short-time objective intelligibility- LLR: Log-likelihood ratio- Segmental SNR: Output segmental SNR (dB)- PESQ: Perceptual estimate of sound quality- WSS: Weighted spectral slopeFigure 5- 1_speakers_speech_shaped_noise.csv- 16_speakers_speech_shaped_noise.csvFigure 7- 1_speakers_babble.csv- 16_speakers_babble.csvFigure 8- delays_babble.csv- delays_speech_shaped_noise.csvSupplementary Figure 2- 16_speakers_cafe.csv- 16_speakers_car.csv- 16_speakers_home.csv- 16_speakers_largetrain_babble.csv- 16_speakers_largetrain_speech_shaped_noise.csv- 16_speakers_reverberant.csv- 16_speakers_street.csvSupplementary Figure 3- all_speakers_airport.csv- all_speakers_birds.csv- all_speakers_machine.csv- all_speakers_ocean.csv- all_speakers_pinknoise.csv- all_speakers_rain.csv- all_speakers_rainforest.csv- all_speakers_station.csv- all_speakers_theater.csv- all_speakers_train.csv- all_speakers_whitenoise.csv- all_speakers_wind.csv
DOI: 10.5061/dryad.cp3d8/1
title: The sequencing data of porB, tbpB, 23S rRNA, mtrR and penA genes

description: The sequencing data of porB, tbpB, 23S rRNA, mtrR and penA genes in Neisseria gonorrhoeae
DOI: 10.5061/dryad.d449r/1
title: Results of the online Turing test

description: The data files contain players' scores for experts and general public. See filenames for description.
DOI: 10.5061/dryad.d449r/2
title: Positional data 1

description: Data files containing coordinates of fish in experiments
DOI: 10.5061/dryad.d449r/3
title: Positional data 2

description: Data files containing coordinates of fish
DOI: 10.5061/dryad.d449r/4
title: Positional data 3

description: Data files containing coordinates of fish
DOI: 10.5061/dryad.gh18c/1
title: Asplenium_trnLF_rps4_trnS_trnGR_rbcL

description: The nexus file used to generate the phylogeny tree.
DOI: 10.5061/dryad.gk1s2/2
title: Brontotheriidae phylogenetic data

description: Phylogenetic character matrix for Brontotheriidae
DOI: 10.5061/dryad.gk1s2/3
title: Brontotheriidae characters

description: Character states and descriptions for Brontotheriidae phylogenetic data
DOI: 10.5061/dryad.j5f51/1
title: 20 simulated datasets for 3,000 individuals over different heritability (h2)  and dominance ratio (d2) conditions
DOI: 10.5061/dryad.nh8ph.2
title: Data from: Diversity and population structure of northern switchgrass as revealed through exome capture sequencing
DOI: 10.5061/dryad.nh8ph.2/1.2
title: dendogram.tree
DOI: 10.5061/dryad.nq8h7/4
title: ranging behaviour_laying to dependent juv

description: group movement data relative to the reproductive period, from egg laying to offspring independence
DOI: 10.5061/dryad.nq8h7/5
title: ranging behaviour_ nesting

description: group movement data relative to the active nest
DOI: 10.5061/dryad.nq8h7/6
title: condition, survival data-breeders and nonbreeders

description: body mass and survival data, including potential predictors (e.g  sex, breeder vs non-breeder status, group size)
DOI: 10.5061/dryad.rd25r/1
title: Size-corrected Procrustes coordinates of the mammalian braincase

description: Mammalian braincase shape (7 landmarks and 4 semi-landmarks) based on a compilation of 467 2D images from open online resources. Species nomenclature followed Wilson and Reeder's Mammals Species of the World, which was also used for constructing the supertree (Bininda-Emonds  et al 2007). The file is a tab-delimited text.
DOI: 10.5061/dryad.rd25r/2
title: Size-corrected Procrustes coordinates of the mammalian face

description: Mammalian face shape (6 landmarks and 2 semi-landmarks) based on a compilation of 467 2D images from open online resources. Species nomenclature followed Wilson and Reeder's Mammals Species of the World, which was also used for constructing the supertree (Bininda-Emonds  et al 2007). The file is a tab-delimited text.
DOI: 10.5061/dryad.rd25r/3
title: Size-corrected Procrustes coordinates of the mammalian cranium

description: Mammalian cranium shape (13 landmarks and 6 semi-landmarks) based on a compilation of 207 2D images from open online resources. Species nomenclature followed Wilson and Reeder's Mammals Species of the World, which was also used for constructing the supertree (Bininda-Emonds  et al 2007). The file is a tab-delimited text.
DOI: 10.5061/dryad.rd25r/4
title: Size-corrected Procrustes coordinates of the mammalian mandible

description: Mammalian mandible shape (4 landmarks and 6 semi-landmarks) based on a compilation of 207 2D images from open online resources. Species nomenclature followed Wilson and Reeder's Mammals Species of the World, which was also used for constructing the supertree (Bininda-Emonds  et al 2007). The file is a tab-delimited text.
DOI: 10.5061/dryad.v1ff0/1
title: Demultiplexed sequence reads

description: 16S rRNA sequences in fastq format. The paired-end reads have been merged and assigned to sample IDs using sample-specific barcodes.
DOI: 10.5061/dryad.v1ff0/2
title: Metadata for sequenced samples

description: Indicates flu (+/ -) and group (wt versus IL28R) for sequenced samples included in the study.
DOI: 10.5061/dryad.vb766/1
title: Com_psbA__NexusAlignment

description: This nexus file contains our alignment for sequences from the psbA-trnH chloroplast spacer.
DOI: 10.5061/dryad.vb766/2
title: Com_ETS_NexusAlignment

description: This nexus file is an alignment containing all sequences for the nrETS marker using in this study.
DOI: 10.5061/dryad.vb766/3
title: ITS_ARAFY

description: This nexus file is an alignment containing all sequences for the nrITS marker for the Arafy clade, used in this study.
DOI: 10.5061/dryad.vb766/4
title: Com_ITS_Rhyncho_NexusAlignment

description: This nexus file is an alignment containing all sequences for the nrITS marker for the Rhynchocarpa clade, used in this study.
DOI: 10.5061/dryad.vb766/5
title: Com_trnDT_NexusAlignment

description: This nexus file is an alignment containing all sequences for the trnD-trnT chloroplast spacer used in this study.
DOI: 10.5061/dryad.vq2s1/1
title: plan_reccomendations_PONE_D_15_42499R1_no_demographics

description: This is a Stata data file (version 12).  The data are labeled. At the request of Dryad and to limit the potential for indirect identification of study participants, demographic variables on age, race/ethnicity, income, marital status, and education are omitted from this data set.  However, the estimates of interest for this paper are consistent across model specifications that do and do not include these demographic variables.
DOI: 10.5061/dryad.0n205/1
title: Korean cattle 50K SNP data

description: This compressed data contains our original 50K SNP data of three Korean cattle breeds and 13 cattle breeds compiled from Bovine Hapmap data (Gautier et al., 2010).
DOI: 10.5061/dryad.1bm8c/1
title: All data files by all participants in all experiments

description: E* describes the experiment number, S* describes the participant number. Each file is a trial, except of the file with the name "stimlist" in which there is information about which condition was presented in each trial. More detailed information about what exactly is contained in the data and stimlist files is provided in the "readme" file.
DOI: 10.5061/dryad.2p1t8/1
title: Metabarcoding samples details (mapping file)

description: Metabarcoding samples´ details including library tags and sample correspondence.
DOI: 10.5061/dryad.2p1t8/2
title: FASTA file (metabarcoding data; zipped)

description: Metabarcoding data (quality filtered chimera-free merged reads) from the two MiSeq runs needed to generate the paper dataset.
DOI: 10.5061/dryad.541g6/1
title: Perl script that maps SAM reads to known Acropora genes

description: This perl script parse the output of TopHat alignment software (Trapnell et al., Bioinformatics, 2009), which is given in the Sequence Alignment/Map (SAM) format (http://samtools.sourceforge.net/), and convert it into the raw number of reads aligned to each Acropora gene
DOI: 10.5061/dryad.7s8h6/1
title: CecropieaeMorphology

description: Description of morphological characters used in phylogenetic reconstruction of Cecropieae tribe (Urticaceae)
DOI: 10.5061/dryad.7s8h6/2
title: Cecropieae morphological matrix

description: Matrix used for tree analysis of Cecropieae based on characters outlined in Cecropieae morphology.
DOI: 10.5061/dryad.80jh7.2
title: Data from: Epigenetic divergence as a potential first step in darter speciation
DOI: 10.5061/dryad.80jh7.2/1.2
title: Patuxent MSAP Matrices

description: Methylation susceptible (MS) and unmethylated (UM) matrices from five sampling locations in the Patuxent River.
DOI: 10.5061/dryad.80jh7.2/3.2
title: Interspecific MSAP Matrices

description: Methylation susceptible (MS) and unmethylated (UM) matrices for eight species pairs used in the interspecific analyses.
DOI: 10.5061/dryad.88nd5/1
title: Raw time-series data

description: 75 high quality mammalian population time series, representing 33 species, spanning six orders, drawn from the Living Planet Index vertebrate population abundance data base. The first column represents the years over which monitoring took place, and all subsequent columns represent the abundance of different population IDs.
DOI: 10.5061/dryad.88nd5/2
title: Kalman-filtered time-series

description: The first column represents the years over which monitoring took place, and all subsequent columns represent the abundance of different population IDs, following the application of the Kalman filter (to account for potential sources of uncertainty arising from count errors).
DOI: 10.5061/dryad.88nd5/3
title: Decline-curve data set for comparative analyses

description: Dataset used for generalized linear mixed modelling of decline curve-type. Please see the ReadMe file for further descriptions of each column title.
DOI: 10.5061/dryad.8d6k1/1
title: Pinus pinaster 6100 SNP data for 509 individuals

description: The excel file contains genotype data (6100 SNPs) for 509 Pinus pinaster trees, from 34 populations sampled along the species' natural distribution range.
DOI: 10.5061/dryad.8g531/1
title: Parental age and identity

description: Age and identity of mother and father of chicks
DOI: 10.5061/dryad.8h8q5/2
title: dHNF4_ChIPseq_NearestNeighbor

description: dHNF4-DNA bound complexes were immunoprecipitated using polyclonal antibody against endogenous dHNF4 protein. Barcoded libraries for dHNF4-IP and input control samples were generated by the University of Utah High Throughput Genomics core facility and sequenced in a single lane Illumina HiSeq 5-cycle single-read sequencing. Data analysis was performed by the Bioinformatics Core at the University of Utah School of Medicine using USeq and Model-based Analysis for ChIP-seq (MACS2) run with a peak shift of 100 bp. Enrichment peaks were identified with an FDR cutoff of 1% and nearest neighboring genes were compiled using USeq FindNeighboringGenes and UCSC dm3 EnsGenes gene tables. Nearest neighbor genes were compared to our RNA-seq dataset to identify neighbors that are also misexpressed in dHNF4 mutants, highlighting these as direct targets of dHNF4.
DOI: 10.5061/dryad.9f1p2/1
title: 24B Sdc RNAi Sdc and FasII

description: Raw image of muscle expressed Sdc RNAi, stained with Sdc and Fasciclin II
DOI: 10.5061/dryad.9f1p2/2
title: Elav Sdc RNAi Sdc and FasII

description: Raw image of neural expressed Sdc RNAi, stained with Sdc and Fasciclin II
DOI: 10.5061/dryad.9f1p2/3
title: Sdc and FasII in wt

description: Raw image of wild type 3rd instar larvum, stained with Sdc and Fasciclin II
DOI: 10.5061/dryad.9f1p2/4
title: 24BUASFLsdcmyc1

description: Raw image of muscle expressed Sdc-FL, stained with HRP and anti-Myc
DOI: 10.5061/dryad.9f1p2/5
title: Elav x UAS-Sdc myc

description: Raw image of neural expressed Sdc-FL, stained with HRP and anti-Myc
DOI: 10.5061/dryad.9f1p2/6
title: CS for overexpression

description: Raw image of wild type larvum stained with HRP and anti-Myc
DOI: 10.5061/dryad.9f1p2/7
title: Normalized Bouton Counts

description: Raw data and analyzed data on bouton counts used to generate bar graphs in Figure 2
DOI: 10.5061/dryad.bh215/2
title: Sensitivity_InteractionStrength

description: Matlab code to check the sensitivity of the models to different interaction strengths in translocations of species in consumer-resource, competitive and mutualistic systems.
DOI: 10.5061/dryad.bh215/3
title: Sensivity_delay

description: Matlab code to check the sensitivity of the models to different delay times for translocations of species consumer-resource, competitive and mutualistic systems.
DOI: 10.5061/dryad.bh215/4
title: Simultaneous_VS_Sequential_Translocation

description: Matlab code to model simultaneous and sequential translocations in consumer-resource, competitive and mutualistic systems.
DOI: 10.5061/dryad.bj546/1
title: GPS_PhiST_DeBiasse_et_al_Journal_of_Biogeography

description: This file contains the sampling site GPS coordinates and PhiST values for Callyspongia vaginalis, Leucothoe ashelyae, Leucothoe kensleyi, and Ophiothrix suensonii required for the Barrier analyses associated with the Journal of Biogeography manuscript "Shared phylogeographical breaks in a Caribbean coral reef sponge and its invertebrate commensals" by Melissa B. DeBiasse, Vincent P. Richards, Mahmood S. Shivji, and Michael E. Hellberg.
DOI: 10.5061/dryad.c128h/1
title: phylogenetic methods and sensitivity tests

description: Complete data used in Wang and Graeme's paper, including following files: data matrix of Mesozoic birds, age of the terminal taxa, most parsimonious trees, code in R analysis, and the complete results of the sensitive tests.
DOI: 10.5061/dryad.ds6gc/1
title: Mitochondrial 16s ribosomal gene fragment sequences from killer whale feces

description: There are 15 fasta files containing DNA sequences from a ~330bp fragment of the mitochondrial 16s ribosomal RNA gene.  These sequences were amplified from 175 killer whale feces collected from the wild.  The samples are pooled into 13 experimental groups; the numbers in the file names correspond to the sample pools described in Table S1 of the associated publication which contains sampling information (time, location, whale ID if known).  Samples 23 and 24 are controls, as described in the publication.  Methodological details including primers and sequencing methods are described in the associated publication.
DOI: 10.5061/dryad.f1170/1
title: Monnin_2016_Supporting_Data

description: Survival data, Wolbachia density data, lipid peroxidation data (tbars), antioxidant capacity data (trolox) and expression data.
DOI: 10.5061/dryad.f2b52/1
title: Ploton et al. 2016 - Pantropical tree biomass database
DOI: 10.5061/dryad.ft70n/1
title: Holman and Bro-Jorgensen - R script for analyses and figures

description: R script used for analyses and figure-making. Has lots of annotation to explain what it does.
DOI: 10.5061/dryad.ft70n/2
title: Reply to Raia et al - Dryad data

description: This is our raw data, for use with the attached R file.
DOI: 10.5061/dryad.gh4k7/1
title: Crowdsourced morphometrics data

description: This zip file contains geometric morphometric landmark data collected by Mechanical Turk workers, as well as BAMM input and output files.
DOI: 10.5061/dryad.gt2m0/1
title: All data from manuscript

description: Dry weights, root length colonized, and leaf nitrogen and phosphorus concentrations for inoculated and non-inoculated Andropogon gerardii and Elymus canadensis.
DOI: 10.5061/dryad.h30g3/1
title: theoretical_models

description: R code used for the graphical models in figure 3.
DOI: 10.5061/dryad.h30g3/2
title: defence_offence_correlation

description: data used to check correlation between sperm defence and sperm offence.
DOI: 10.5061/dryad.j82k4/1
title: Egocentric_File_RSOS

description: The file Egocentric_File_RSOS.csv contains data corresponding to egocentric networks of 3,106,293 individuals derived from anonymized call detail records for a single month in the year 2007 from a mobile phone service provider in a European country.
DOI: 10.5061/dryad.jm2m1/1
title: Hansson et al. Plates count data

description: This file includes the raw data from the study 'Lateral plate number in low-plated threespine stickleback: a study of plasticity and heritability' by Truls H. Hansson, Barbara Fischer, Anna B. Mazzarella, Kjetil L. Voje and Leif Asbjørn Vøllestad published 2016 in Ecology and Evolution. For 739 threespine stickleback offspring individuals, which were either raised in saltwater or freshwater, lateral plates were counted. For each of these individuals (in rows), the file has the following information (in columns): FishID (individual fish ID), FamilyID (ID for the 16 Crosses), Treatment (F for freshwater, S for saltwater), Plates left (no of lateral plates on the left side of the fish), Plates right (no of lateral plates on right side of the fish), Density (no of individuals per tank, in which they were raised) and Size  (body length, in mm).
DOI: 10.5061/dryad.mf133/1
title: data used for Age at First Reproduction

description: this file contains ages at first reproduction and weight at first reproduction
DOI: 10.5061/dryad.mf133/2
title: male function

description: This file contains data for number of offspring by male function and paternity success
DOI: 10.5061/dryad.mf133/3
title: female function DRYAD

description: this file contains female fecundity and juvenile survival for adult inbreeding depression
DOI: 10.5061/dryad.mf133/4
title: Inbreeding Depression first experiment DRYAD
DOI: 10.5061/dryad.mf133/5
title: Inbreeding Depression second experiment DRYAD
DOI: 10.5061/dryad.mf133/6
title: comportment observations data DRYAD

description: this file contains all data from observations of sexual comportment: time spent on copulation male and female, number of partners, number of copulations...
DOI: 10.5061/dryad.nh8ph.2/10.2
title: SNIPE_all_plates_matrix_biallelic_only_nomissing.txt
DOI: 10.5061/dryad.nh8ph.2/2.2
title: Pvirgatum_v1.1_273_gene_exons_updated_ChrUn_representative.gff3
DOI: 10.5061/dryad.nh8ph.2/3.2
title: Pvirgatum_v1.1_273_hardmasked_ChrUn.coord
DOI: 10.5061/dryad.nh8ph.2/4.2
title: Pvirgatum_v1.1_273_hardmasked_ChrUn.fasta
DOI: 10.5061/dryad.nh8ph.2/6.2
title: SNIPE_all_plates_matrix_biallelic_only_nomissing.exonic_variant_function
DOI: 10.5061/dryad.nh8ph.2/7.2
title: SNIPE_all_plates_matrix_biallelic_only_nomissing.variant_function
DOI: 10.5061/dryad.nh8ph.2/8.2
title: switchgrass_upland_panel_down_cnv_list.txt
DOI: 10.5061/dryad.nh8ph.2/9.2
title: switchgrass_upland_panel_up_cnv_list.txt
DOI: 10.5061/dryad.p9f07/1
title: Food web data

description: Food webs used for the ERGM analysis.
DOI: 10.5061/dryad.pk462/1
title: Characteristics and prediction data

description: Excel file with subject characteristics and prediction data
DOI: 10.5061/dryad.pp72j/1
title: All_Amb_CoordEnv_26July2012

description: All Ambrosia occurrences in the French Alps
DOI: 10.5061/dryad.pp72j/2
title: Pop Info 6Sept2012

description: Description of the sampled populations
DOI: 10.5061/dryad.pp72j/3
title: AllDataCG_29Oct12

description: All trait measured in the common garden
DOI: 10.5061/dryad.pp72j/4
title: CleanAllAFLP

description: All sampled population AFLP
DOI: 10.5061/dryad.q60vk/1
title: Nitrogen and carbon data

description: File includes data on DOC and DTN concentrations in the different predator treatments and the control (no-predation) after 48h of incubation.