cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.45j0r70/42
title: D3_nonengineered_R2.fastq

description: Donor 3 control primary B cells 13 days post nucleofection. Immunoglobulin heavy chain variable regions amplified from cDNA made by RACE with barcoded 5' template switch adapters. NEBnext amplicon sequenced using 400x100 paired end reads on the Illumina MiSeq. This is read 2 (R2).
DOI: 10.5061/dryad.45j0r70/43
title: D3_V374_PG9_engineered_R1.fastq

description: Donor 3, V374-PG9 engineered primary B cells, 13 days post nucleofection. Immunoglobulin heavy chain variable regions amplified from cDNA made by RACE with barcoded 5' template switch adapters. NEBnext amplicon sequenced using 400x100 paired end reads on the Illumina MiSeq. This is read 1 (R1).
DOI: 10.5061/dryad.45j0r70/44
title: D3_V374_PG9_engineered_R2.fastq

description: Donor 3, V374-PG9 engineered primary B cells 13 days post nucleofection. Immunoglobulin heavy chain variable regions amplified from cDNA made by RACE with barcoded 5' template switch adapters. NEBnext amplicon sequenced using 400x100 paired end reads on the Illumina MiSeq. This is read 2 (R2).
DOI: 10.5061/dryad.5mh2450/6
title: Marten & Fisher Harvest Density_Ratio Data

description: Harvest totals and harvest density (total animals trapped [2005-2013]/100 km2) for American martens and fishers, and fisher:marten ratio. Data collected at the scale of New York towns. Data must be joined to town boundary shapefile (also included) using BIOCOTOWN field to display data in GIS.
DOI: 10.5061/dryad.5mh2450/7
title: New York State Town Boundary Shapefile

description: New York State town boundary shapefile for use with the American marten and fisher harvest total, harvest density, and harvest ratio data. These two data sources can be joined using the BIOCOTOWN field.
DOI: 10.5061/dryad.5mh2450/8
title: Post_Hoc_Analysis_Shapefiles

description: Weather station data (30-yr mean climate normal) and American marten southern range boundary used for a post-hoc analysis.
DOI: 10.5061/dryad.7c41q4c/6
title: Figure4  The STDP response of the electronic synapse

description: The stimuli spikes were generated by programming a data acquisition card (NI PCI6259) and recorded. The device was stimulated by spike pairs. The resulting timing-dependent resistance modulation was studied by recording the ∆t(spikTimingDifference) and the device conductance change (SynapticWeightChange(%)).
DOI: 10.5061/dryad.8575jr5/1
title: Transcriptome_Assemblies

description: Transcriptome assemblies of Contradens contradens (UF 507562) and Scabies phaselus (UF 507552).
DOI: 10.5061/dryad.8575jr5/2
title: Unioverse_reference_probe_regions

description: Zipped folder containing the Unioverse reference probe regions.
DOI: 10.5061/dryad.8575jr5/3
title: Unioverse_probes

description: Unioverse probe sequences.
DOI: 10.5061/dryad.8575jr5/4
title: Pipeline_Results

description: Transcriptome and AHE data making through the processing pipeline.
DOI: 10.5061/dryad.8575jr5/5
title: Supermatrices

description: NT_Supermatrix, AA_Supermatrix, and each of the percent variable site supermatrices.
DOI: 10.5061/dryad.8575jr5/6
title: Trees

description: All of the phylogenetic trees relevant to this study.
DOI: 10.5061/dryad.96240sr/1
title: Dracaena coordinates

description: Dracaena species coordinates used in Maxent model. Coordinates for Dracaena afromontana, Dracaena camerooniana, Dracaena surculosa
DOI: 10.5061/dryad.96240sr/11
title: Dracaena_locations_GIS_format

description: GIS layers in shapefile format showing locations of three examined Dracaena species: Dracaena afromontana, Dracaena cameroonaina and Dracaena surculosa
DOI: 10.5061/dryad.d117b3k/2
title: Klaus_Matzke_2019_SysBio_Supplemental_Text

description: supplemental text
DOI: 10.5061/dryad.d82n3f8/1
title: Supplementarydata1
DOI: 10.5061/dryad.dn4676s/1
title: 1. standard WHO susceptibility test results for species complex and subgroup samples
DOI: 10.5061/dryad.dn4676s/2
title: 2. standard WHO susceptibility test results for single species
DOI: 10.5061/dryad.dn4676s/3
title: 3. standard CDC bottle bioassay results for species complex and subgroup samples
DOI: 10.5061/dryad.dn4676s/4
title: 4. paired synergist bioassay results for species complex and subgroup samples
DOI: 10.5061/dryad.dn4676s/5
title: 5. intensity bioassay results for species complex and subgroup samples
DOI: 10.5061/dryad.dn4676s/6
title: 6. Vgsc allele frequencies for species complex and subgroup samples
DOI: 10.5061/dryad.dn4676s/7
title: 7. Vgsc allele frequencies for single species
DOI: 10.5061/dryad.gn8qf6q/1
title: Visual display sequences

description: Sequences of visual display elements of individual displays by male and lek (first data sheet). Column names and element abbreviations are explained in the second data sheet.
DOI: 10.5061/dryad.gn8qf6q/2
title: Acoustic data and metadata

description: This is an R object in the "extended_selection_table" format provided by the R package warbleR. It contains all the acoustic data and associated metadata.  See ?selection_table in R for more information about the  "extended_selection_table" format. The object was saved as an RDS file. The file can be read (after decompression) using the "readRDS" function in R.
DOI: 10.5061/dryad.h517t14.1
title: Data from: The evolution of traits and functions in herbivorous coral reef fishes through space and time
DOI: 10.5061/dryad.h517t14.1/1.1
title: Main data
DOI: 10.5061/dryad.h517t14.1/2.1
title: R Scripts
DOI: 10.5061/dryad.h517t14.1/3.1
title: Phylogenetic trees
DOI: 10.5061/dryad.h517t14.1/4.1
title: Results from the BayesTraits analysis
DOI: 10.5061/dryad.h517t14.2/4.2
title: Results from the BayesTraits analysis
DOI: 10.5061/dryad.m906r59/1
title: Male availability data

description: This dataset contains the complete dataset used for the analysis, describing the social father, the genetic father and the potential sires for each egg of all completely sampled clutches.
DOI: 10.5061/dryad.q7rf263/4
title: Supplementary data

description: This zip file contains (i) the raw data from the carnivoran data set, (ii) the alignment used with morphology-only and molecule-only partitions, (iii) the control file used for the divergence times estimation with the combined data set, (iv) the tree files used to calculate Bayes factors and estimate divergence times, and (v) a README.md file with the details about the data. In addition, each data file contains also a description of its format at the end.
DOI: 10.5061/dryad.rb1bt3j/10
title: FileS10. Gene annotation file for the PacBio-only assembly with extra contigs

description: We transferred gene annotations from Flybase r6.20 to our genome using BLAT and CrossMap v0.2.5.
DOI: 10.5061/dryad.rb1bt3j/11
title: File S11. The sequences of Stellaris probes for Rsp

description: The following Stellaris probes are tagged with Quasar 570 and used to detect Rsp sequences.
DOI: 10.5061/dryad.rb1bt3j/12
title: File S12. The fasta alignment of genomic IGS sequences from D. melanogaster and outgroup species

description: We extracted all IGS elements from the genome using BLAST v2.7.1 with parameters “- task blastn -num_threads 24 -qcov_hsp_perc 90” and custom scripts. We then aligned and manually inspected IGS sequences using Geneious v8.1.6.
DOI: 10.5061/dryad.rb1bt3j/4
title: FileS4. ChIPtigs from the R3 library

description: We created de novo contigs from ChIPseq reads (ChIPtigs) with Spades v3.11.0 (-t 24 -careful –sc;) for the R3 library.
DOI: 10.5061/dryad.rb1bt3j/5
title: FileS5. ChIPtigs from the R4 library

description: We created de novo contigs from ChIPseq reads (ChIPtigs) with Spades v3.11.0 (-t 24 -careful –sc;) for the R4 library.
DOI: 10.5061/dryad.rb1bt3j/6
title: FileS6. ChIPtigs from the S2 library

description: We created de novo contigs from S2 ChIPseq reads (ChIPtigs) with Spades v3.11.0 (-t 24 -careful –sc;) from the S2 library.
DOI: 10.5061/dryad.rb1bt3j/7
title: FileS7. Hybrid PacBio-Nanopore assembly

description: We assembled nanopore (Solare et al. 2018) and PacBio reads (Kim et al. 2014) into a hybrid assembly using Canu v1.7 with default settings. The assembly size is 162,798,260 bp with N50=5,104,646 bp.
DOI: 10.5061/dryad.rb1bt3j/8
title: FileS8. PacBio-only assembly with extra contigs

description: We use the PacBio-only assembly in Chang and Larracuente 2018 and 
added 19 sequences with CENP-A-enriched repeats. Of these 19 sequences, 6 were contigs from the hybrid PacBio-Nanopore assembly (File S7) and the rest were error-corrected PacBio reads.
DOI: 10.5061/dryad.rb1bt3j/9
title: FileS9. Repeat annotation file for the finished PacBio-only assembly with extra contigs

description: We annotated the finished assembly using our custom repeat library (-lib library.fasta -s) and RepeatMasker 4.06.
DOI: 10.5061/dryad.s36hm11/2
title: bronze_annotated sequences

description: The sequences generated from female bronzed cowbirds from Hildago county Texas with annotations
DOI: 10.5061/dryad.s36hm11/3
title: brown_annotated

description: The sequences generated from female brown-headed cowbirds from Hildago county Texas with annotations
DOI: 10.5061/dryad.s36hm11/4
title: red_annotated

description: The sequences generated from female red-winged blackbirds
DOI: 10.5061/dryad.s36hm11/5
title: DE genes only

description: Results of all possible pairwise comparisons
DOI: 10.5061/dryad.s53tm16/1
title: F1 Phenotypes and Parental Genotypes

description: This file contains the phenotypes of the F1 descendants of wild-captured (and wild-mated) parental females from Oahu. Parental females are identified with unique 3-digit numbers. Columns contain count data describing the total number of their male offspring (sons), the number of normal-wing (NW) sons, flatwing (FW) sons, and daughters. The final column contains the genotype of the parental female, if sufficient data existed to infer the parental female’s genotype. We considered a female to be heterozygous if she produced at least one normal-wing and one flatwing son (heterozygous females are coded as “hetero”). We considered a female homozygous only if she produced at least 5 adult sons and all were the same phenotype (homozygous normal-wing was coded “homoNW”; homozygous flatwing was coded “homoFW”). If neither of these conditions were met, we left the “Genotype” blank for that female.
DOI: 10.5061/dryad.s53tm16/2
title: F2 phenotypes

description: This file contains raw phenotype data for the second filial (F2) generation. Each row is a single observation of an individual full-sib family. In the first column, the family is coded using the number of the parental female from which it is descended and a number identifying its F1 mother. For example, the family number “213.F2.3” identifies the full-sib family of F2 crickets whose mother was F1 female #3 descended from parental female #213. Columns contain count data that describe the number of normal-wing males (NWMales), flatwing males (FWMales) and females at each observation. Because the crickets matured at different rates and were phenotyped upon reaching adulthood, we made multiple observations of some families. Count data were therefore aggregated across entries for the same full-sib family prior to analysis.
DOI: 10.5061/dryad.s53tm16/3
title: Field Survey Data - Oahu 2013-2016

description: This file contains data from field surveys of Teleogryllus oceanicus phenotypes; each row is a different observation. See the publication for details of how observations were made. Columns contain count data describing the number of females, flatwing males, and normal-wing males found in each plot, as well as the total number of males and the total number of crickets.
DOI: 10.5061/dryad.s53tm16/4
title: README

description: This file describes the contents of the three spreadsheets containing data published by Tanner, Swanger, and Zuk.
DOI: 10.5061/dryad.t0p2f2c/1
title: Apogon_and_reference_opsins_alignment

description: All cardinalfish opsins identified here aligned with reference opsin sequences and Ccarpio ancestral opsin as outgroup.
DOI: 10.5061/dryad.t0p2f2c/2
title: Apogon_and_reference_opsins_tree

description: Phylogenetic tree of cardinalfish and reference opsin gene sequences.
DOI: 10.5061/dryad.t0p2f2c/3
title: Apogon_genediversity_LWS

description: LWS opsin gene alignment for amino acid by amino acid assessment of sequence diversity.
DOI: 10.5061/dryad.t0p2f2c/4
title: Apogon_genediversity_RH1

description: RH1 opsin gene alignment for amino acid by amino acid assessment of sequence diversity.
DOI: 10.5061/dryad.t3k2t2j/1
title: 15N recovery in two forests at Qingyuan over different time scale
DOI: 10.5061/dryad.tr3dq8c/1
title: patagonia_itv_data3_Sept2018

description: Leaf trait values (LMA, leaf size, leaf N and leaf P concentrations) of saplings of species belonging to the temperate rainforest of southern Chile.
DOI: 10.17632/7ym3nrnskd.2
title: Data for: n-Hexadecane and pyrene biodegradation and metabolization by Rhodococcus sp. T1 isolated from oil contaminated soil

description: Research data
DOI: 10.17632/j8kmdgkvs8.1
title: Data for: Interactive Programs of MC-ICPMS Data Processing for 230Th/U Geochronology

description: Matlab programs for MC-ICPMS U-Th data processing
DOI: 10.17632/j8kmdgkvs8.2
title: Data for: Interactive Programs of MC-ICPMS Data Processing for 230Th/U Geochronology

description: Matlab programs for MC-ICPMS U-Th data processing
DOI: 10.17632/xhh8575ytb.1
title: Data for: The life cycle carbon emissions of China's building and construction industry from 2000-2015: analysis and policy implications

description: This data set includes all indicators which are used in the decomposition analysis. It has four sections, including: section 1, which is related to raw materials consumption and analysis; section 2, which is related to the energy consumption and emissions from construction and construction-related transportation activities; section 3, which is related to the energy consumption and emissions from building operation stage; and section 4 which includes other relevant data.
DOI: 10.5061/dryad.000mn47/1
title: Clinical outcomes

description: This data file describes the clinical data of both control and intervention group. The last columns describe the number and percentage of corresponding measurements in both the data retrieved from the automated EWS system, as well as from the electronic patient records (EMR). This was only applicable for cases in the intervention period since both methods (automated EWS system and EMR) were used.
DOI: 10.5061/dryad.000mn47/2
title: Measurements_control_period

description: This dataset contains every measurement of vital sign(s) recorded in the electronic medical record during the control period.
DOI: 10.5061/dryad.0k2s39c/1
title: Experimental data

description: Meltwater flow and solute concentrations recorded during the experiment. The flow rate can be obtained using the sample volume and the timing of sample collection.
DOI: 10.5061/dryad.11d0f29/1
title: Rhinella_CCSM_Bio1_FINAL

description: Main data to be read by R-script and perform all analyses
DOI: 10.5061/dryad.11d0f29/2
title: R-Script for DRYAD

description: R-script to do all geographical analyses in the paper
DOI: 10.5061/dryad.29p63mb/1
title: Web architecture and site choice data

description: Includes web architecture and site choice data for web-building spiders
DOI: 10.5061/dryad.29p63mb/10
title: Niche analyses

description: Second script to run for spider niche analysis, after running "spiders_calcOverlap.R". Calculates the Tukey HSD tests for each of the web architectural and isotopic variables, and tests for correlation between hypervolume overlaps
DOI: 10.5061/dryad.29p63mb/2
title: Isotope data

description: Master spreadsheet of isotope data for all samples
DOI: 10.5061/dryad.29p63mb/3
title: Gut content data: order level of prey

description: Table showing relative sequence read abundance of different prey orders in spider species, rarefied to 500 reads per spider
DOI: 10.5061/dryad.29p63mb/4
title: Gut content data: OTU level of prey

description: Table showing relative sequence read abundance of different prey OTUs (97% sequence similarity) in spider species, rarefied to 500 reads per spider
DOI: 10.5061/dryad.29p63mb/5
title: Isotope data: controlled for elevation and year

description: Isotope data for samples only collected at higher elevation, and controlled for year (2014 for web-builders, 2016 for Spiny Leg spiders). Used for inter-species comparisons included in Supporting Information
DOI: 10.5061/dryad.29p63mb/6
title: Isotope data: 2014 only

description: Isotope data for samples only collected in 2014. Used to test for isotopic differences between clades (web-building and Spiny Leg) when controlling for year and elevation (used in Supporting Information)
DOI: 10.5061/dryad.29p63mb/7
title: ReadMe

description: Describes raw data files and scripts included in data package
DOI: 10.5061/dryad.29p63mb/8
title: Hypervolume script

description: Script for initial analysis of spider niche data. Performs PCA on web architecture, generates the hypervolume and calculates the hypervolume overlap for web architecture and stable isotopes, and calculates beta diversity of gut contents among species
DOI: 10.5061/dryad.29p63mb/9
title: Hypervolume tools

description: Wrapper functions written by JYL to calculate hypervolume overlap from a dataframe
DOI: 10.5061/dryad.2bm34c2/1
title: Forest bee pollen load diversity

description: Pollen load diversity, bee species, plant species and traits data
DOI: 10.5061/dryad.6039339/1
title: clim

description: climatic variables across all populations used in the study
DOI: 10.5061/dryad.6039339/2
title: competition analysis

description: pair-wise competition experiment conduced in the study
DOI: 10.5061/dryad.6039339/3
title: genetic variation analysis

description: data used for quantitative genetic variation analysis
DOI: 10.5061/dryad.6781kg7/2
title: Data-Frouz et al., 2019

description: Codes and relevant data are described separately in each excel sheet.
DOI: 10.5061/dryad.7jd76kq/1
title: S1_Data.xlsx

description: Unpublished data (nine long-term field studies): All the pairs that have been identified across the nine studies where both pair members have at least one morphological record, including repeated records from different years. This dataset also includes latitude and longitude of the nest site (Lambert azimuthal equal-area projection, units = meters) and year and, if available, the putative date of the first egg.
DOI: 10.5061/dryad.7jd76kq/2
title: S2_Data.xlsx

description: Unpublished data (nine long-term field studies): All available records of morphological traits which covered more than 95% of individuals included in S1_Data.This dataset also includes the location where the individual was caught, the date of catching, and the observer who measured the individual
DOI: 10.5061/dryad.7jd76kq/3
title: S3_Data.xlsx

description: Unpublished data (nine long-term field studies): Data where we combined the information from data S1_Data and S2_Data
DOI: 10.5061/dryad.7vf4004/1
title: Humerus Lengths

description: Humeral lengths used to render humeral cross-sectional traits dimensionless.
DOI: 10.5061/dryad.7vf4004/2
title: Radius Lengths

description: Radial lengths used to render radial cross-sectional traits dimensionless.
DOI: 10.5061/dryad.7vf4004/3
title: Ulna Lengths

description: Ulnar lengths used to render ulnar cross-sectional traits dimensionless.
DOI: 10.5061/dryad.7vf4004/4
title: Mustelid Groupings

description: Locomotor habit of each mustelid species. For source of assigned habit, see Table 1 of article.
DOI: 10.5061/dryad.7vf4004/5
title: Humeral Cross-Sectional Data All Individuals

description: Raw humeral cross-sectional trait data for all individuals. Cross-sectional area (CSA), second moment of area (SMA), and section modulus (MOD) respectively have units of mm^2, mm^4, and mm^3. Column names denote increment of bone length (i.e., P5 indicates 5% of bone length, P10 indicates 10% of bone length, etc.).
DOI: 10.5061/dryad.7vf4004/7
title: Radial Cross-Sectional Data All Individuals

description: Raw radial cross-sectional trait data for all individuals. Cross-sectional area (CSA), second moment of area (SMA), and section modulus (MOD) respectively have units of mm^2, mm^4, and mm^3. Column names denote increment of bone length (i.e., P5 indicates 5% of bone length, P10 indicates 10% of bone length, etc.).
DOI: 10.5061/dryad.9r5bv61/1
title: Data of occurrence records

description: Occurrence records of Nanorana parkeri used for ecological niche models. Occurrences were gathered from the field expeditions, the literature, the Global Biodiversity Information Facility (GBIF), and georeferenced specimen records.
DOI: 10.5061/dryad.9r5bv61/2
title: The accession numbers of COI sequences

description: Partial sequences of cytochrome c oxidase subunit I (COI) were based on Zhou et al. (2014).
DOI: 10.5061/dryad.ck06k75/1
title: Supp data 1_psmdata
DOI: 10.5061/dryad.ck6q52n/1
title: Samples_Dociostaurus_hispanicus

description: Sampling localities for all genotyped individuals and codes used in the different analyses and genomic datasets.
DOI: 10.5061/dryad.d06j48t/1
title: TotalDataGeneRegionAlignments

description: Alignments of total sequence data pre-cleaning. Zip file includes six gene regions (atpB, ITS, matK, ndhF, rbcL, and trnT-F).
DOI: 10.5061/dryad.d06j48t/2
title: sawtooth.totalData.clean.concat.phy

description: Alignment of cleaned total combined dataset (MiSeq and GenBank sequences) used for community phylogeny inference.
DOI: 10.5061/dryad.d06j48t/3
title: speciespersummit_collect.csv

description: Alpine community matrix (rows = plant species collected, columns = summit) and indication if collected from high-alpine meadow (“Meadow” = 1).
DOI: 10.5061/dryad.d06j48t/4
title: sawtooth.totalData

description: Community phylogeny used for estimation of phylogenetic structure within and between nine high-alpine summits.
DOI: 10.5061/dryad.d117b3k/1
title: Supplementary_Material

description: supplemental text, list of taxa, dataset, settings, simmulation test resuls, examples
DOI: 10.5061/dryad.dn4676s/8
title: 8. paired Vgsc allele frequencies from dead and surviving mosquitoes after insecticide exposure
DOI: 10.5061/dryad.fc384rk/1
title: HDY-18-AO311 Microsatellite genotype data

description: Excel spreadsheet file containing genotype scores for eight microsatellite loci used for parentage analysis. Column 1 “ind_code” = code number of individual bird; Column 2 “territory_code” = code of social territory group to which individual bird was a member; Columns 3-18 = allele scores for eight microsatellite loci where the two alleles of each locus appear in separate columns. Locus names in header: 43, 115b, 115a, 112, 67, 201, 206, 208.