cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.2j27b/14
title: i2_barcodes_July2016_MEC-17-0128

description: Barcodes associated with ZBCi2-V1T-1_S43_L006_R1_001.fastq.gz.
DOI: 10.5061/dryad.2j27b/15
title: i1_barcodes_July2016_MEC-17-0128

description: Barcodes associated with ZBCi1-V1T-1_S42_L006_R1_001.fastq.gz.
DOI: 10.5061/dryad.2j27b/16
title: ZBCi8-V1T-1_S49_L006_R1_001.fastq
DOI: 10.5061/dryad.2j27b/17
title: ZBCi2-V1T-1_S43_L006_R1_001.fastq
DOI: 10.5061/dryad.2j27b/18
title: ZBCi1-V1T-1_S42_L006_R1_001.fastq
DOI: 10.5061/dryad.2j27b/8
title: i5_barcodes_July2016_MEC-17-0128

description: Barcodes associated with ZBCi5-V1T-1_S46_L006_R1_001.fastq.gz.
DOI: 10.5061/dryad.2j27b/9
title: i6_barcodes_July2016_MEC-17-0128

description: Barcodes associated with ZBCi6-V1T-1_S47_L006_R1_001.fastq.gz.
DOI: 10.5061/dryad.2qk88/5
title: Fossil-calibrated penalized likelihood tree, 4 calibrations: trs.calib.jackknife.4.annotated

description: Tree calibrated using the discrete clock model, penalized likelihood, as implemented in the chronos function of ape (https://cran.r-project.org/web/packages/ape/index.html), 4 calibration points. File generated using Treeannotator (https://www.beast2.org/treeannotator/); uncertainty at nodes estimated by calibrating trees 500x, drawing dates from distributions as described in paper, on delete-half jackknife trees (as described in paper).
DOI: 10.5061/dryad.2qk88/6
title: Table S01: samples included in study.

description: Metadata for all samples sequenced, including samples excluded from study as described in paper.
DOI: 10.5061/dryad.2qk88/7
title: TableS02.specimenRecords

description: Specimens utilized in estimating soils and climatic niche, including information on which records were excluded from analysis and why.
DOI: 10.5061/dryad.2qk88/8
title: Soils and bioclim variables: all.eco.data.exportedFromR.2016-02-03

description: Soil and bioclim variables utilized in niche diversification analyses.
DOI: 10.5061/dryad.2qk88/9
title: Tab-delimited soils.metadata.2016-02-03

description: Description of soils variables and indication of which were used in niche diversification analyses.
DOI: 10.5061/dryad.32152/1
title: Total Tn-seq read counts for all annotated S. meliloti genes

description: Table shows the total number of Illumina reads obtained for each S. meliloti gene for all tested conditions. The raw results are shown as observed and then the normalized read counts per gene are also included.
DOI: 10.5061/dryad.32152/2
title: All S. meliloti genes Tn-seq results highlighting all Tn insertions

description: The table shows all Tn insertions that have been observed by Illumina sequencing and their corresponding read counts for each condition. The dataset includes raw read counts for each Tn insertion as well as the normalized read counts. The dataset also includes the location of each transposon in each corresponding gene.
DOI: 10.5061/dryad.33th5/1
title: environmental data and location information

description: Climatic and edaphic descriptors of individual samples
DOI: 10.5061/dryad.33th5/2
title: mapping file associated with the sequences
DOI: 10.5061/dryad.35q4h/1
title: ASTRAL-II input (protein-coding data set) with Liolaemus tenuis tenuis.

description: File containing gene trees estimated by RaxML (which are the input for ASTRAL-II). Protein-coding genes data set, including Liolaemus tenuis tenuis.
DOI: 10.5061/dryad.35q4h/2
title: ASTRAL-II input (UCEs data set) with Liolaemus tenuis tenuis.

description: File containing gene trees estimated by RaxML (which are the input for ASTRAL-II). Ultraconserved elements (UCEs) data set, including Liolaemus tenuis tenuis.
DOI: 10.5061/dryad.35q4h/3
title: ASTRAL-II input (full data set) with Liolaemus tenuis tenuis.

description: File containing gene trees estimated by RaxML (which are the input for ASTRAL-II). Protein-coding genes + ultraconserved elements data set (full data set), including Liolaemus tenuis tenuis.
DOI: 10.5061/dryad.35q4h/4
title: ASTRAL-II input (full data set) without Liolaemus tenuis tenuis.

description: File containing gene trees estimated by RaxML (which are the input for ASTRAL-II). Full data set, excluding Liolaemus tenuis tenuis.
DOI: 10.5061/dryad.35q4h/5
title: ASTRAL-II inferred tree using the protein-coding data set with Liolaemus tenuis tenuis.

description: Results of ASTRAL-II: inferred tree using the protein-coding data set with Liolaemus tenuis tenuis.
DOI: 10.5061/dryad.35q4h/6
title: ASTRAL-II inferred tree using the UCEs data set with Liolaemus tenuis tenuis.

description: Results of ASTRAL-II: inferred tree using the ultraconserved elements (UCEs) data set with Liolaemus tenuis tenuis.
DOI: 10.5061/dryad.35q4h/7
title: ASTRAL-II inferred tree using the full data set with Liolaemus tenuis tenuis.

description: Results of ASTRAL-II: inferred tree using the full data set with Liolaemus tenuis tenuis.
DOI: 10.5061/dryad.36f3q/1
title: deposit_data_WHS

description: The folder contains data for behavior, maximum allele frequencies, and SNPs.
DOI: 10.5061/dryad.3cf36/1
title: Data files for the paper
DOI: 10.5061/dryad.45g3s/1
title: AustraliaTbData

description: Body temperature data for lizards from Western Australia. area = site name, number = field tag number, species name, BT = body temperature (°C), time and date, microhabitat, and family. for general methods, see E. R. Pianka, Ecology and Natural History of Desert Lizards.  (Princeton University Press, Princeton, N.J., 1986).
DOI: 10.5061/dryad.45g3s/2
title: KalahariTbData

description: Body temperature data for lizards from Western Australia. area = site name, number = field tag number, species name, BT = body temperature (°C), time and date, microhabitat, and family. for general methods, see E. R. Pianka, Ecology and Natural History of Desert Lizards.  (Princeton University Press, Princeton, N.J., 1986) and R. B. Huey, E. R. Pianka, J. Hoffmann, Seasonal variation in thermoregulatory behavior and body temperatures of diurnal Kalahari lizards. Ecology 58, 1066-1075 (1977).
DOI: 10.5061/dryad.45g3s/3
title: NorthAmericanTbData

description: Body temperature data for lizards from Western Australia. area = site name, number = field tag number, species name, BT = body temperature (°C), time and date, microhabitat, and family. for general methods, see E. R. Pianka, Ecology and Natural History of Desert Lizards.  (Princeton University Press, Princeton, N.J., 1986).
DOI: 10.5061/dryad.474mm/1
title: Microsatellite genotypes for sturgeon parentage assignment

description: Empirical genotypes from microsatellite (SSR) loci collected from sturgeon spawners and offspring sampled in hatchery setting.
DOI: 10.5061/dryad.6gh7b/1
title: Nannoperca australis liver transcriptome

description: Nannoperca australis liver transcriptome assembled using Trinity based on RNAseq data from five individuals. Assembly contains 201,037 Trinity transcripts clustered into 96,717 Trinity "genes".
DOI: 10.5061/dryad.6gh7b/2
title: ORF_counts

description: Raw counts data for 27,425 longest open reading frames
DOI: 10.5061/dryad.6gh7b/3
title: TMM_ORF_counts

description: cross sample normalized counts for 27,425 ORFs
DOI: 10.5061/dryad.6gh7b/4
title: SPP_trinotate_annotation_report

description: annotation information for Trinity.fasta assembly
DOI: 10.5061/dryad.9k6g8/1
title: Data for analyses reported in article

description: This Excel file contains one page for each of the four SAS analyses performed. The Codebook page describes the meaning of the headings. Please consult the Methods section of the article for further information about analyses and data.
DOI: 10.5061/dryad.db561/2
title: Snake Tree Files
DOI: 10.5061/dryad.hb8r0/1
title: biomass_1.2

description: biomass per mesocosm and harvest and species (or community if no species-specific values available)
DOI: 10.5061/dryad.hb8r0/2
title: NDVI

description: NDVI data per mesocosm and date
DOI: 10.5061/dryad.hc321/1
title: Mapping_file_Longomoleco

description: Mapping file for 16S V4 rRNA amplicon analysis
DOI: 10.5061/dryad.hc321/2
title: Longo_otu_table

description: Raw OTU table produced by Qiime 1.9.
DOI: 10.5061/dryad.hc321/3
title: Longorep_set

description: Tree file produced by Qiime
DOI: 10.5061/dryad.k46r2/27
title: TCB_Scen6.2b_map

description: Landscape map portraying restoration Scenario 6.2
DOI: 10.5061/dryad.k46r2/28
title: TCB_Scen6.3b_map

description: Landscape map portraying restoration Scenario 6.3
DOI: 10.5061/dryad.k46r2/29
title: TCB_Scen6.4b_map

description: Landscape map portraying restoration Scenario 6.4
DOI: 10.5061/dryad.k46r2/31
title: TCB_Scen7.1b_map

description: Landscape map portraying restoration Scenario 7.1
DOI: 10.5061/dryad.k46r2/32
title: TCB_Scen7.2b_map

description: Landscape map portraying restoration Scenario 7.2
DOI: 10.5061/dryad.k46r2/33
title: TCB_Scen7.3b_map

description: Landscape map portraying restoration Scenario 7.3
DOI: 10.5061/dryad.nd4dp/1
title: STACKS output

description: Output of the STACKS ref_map.pl pipeline run for mapped reads of 78 samples (reads archived at ENA, accession PRJEB20958). Details about the analysis can be found at https://github.com/hdetering/orycun.
DOI: 10.5061/dryad.nd4dp/2
title: PLINK output

description: Output files generated by PLINK association test for 78 samples in two groups (36 dead, 42 survivors). Details about the analysis are at https://github.org/hdetering/orycun.
DOI: 10.5061/dryad.q1f65.2
title: Data from: Declines in low-elevation subalpine tree populations outpace growth in high-elevation populations with warming
DOI: 10.5061/dryad.rc1p0/1
title: S1 Appendix

description: Raw data from the laboratory experiment.
DOI: 10.5061/dryad.rc1p0/2
title: S2 Appendix

description: Raw data from the field experiment.
DOI: 10.5061/dryad.s4f13/1
title: Reflectance confocal microscopy features of BRAF V600E mutated thin melanomas detected by immunohistochemistry data

description: Data in excel sheet used in the article: Reflectance confocal microscopy features of BRAF V600E mutated thin melanomas detected by immunohistochemistry
DOI: 10.5061/dryad.s4f13/2
title: UAC_Tables 1 to 7_PONE-D-17-07514_RCM of BRAF V600E mutated thin melanomas detected IHQ

description: All tables (1 to 7) in the article Reflectance confocal microscopy features of BRAF V600E mutated thin melanomas detected by immunohistochemistry
DOI: 10.5061/dryad.s4f13/3
title: UAC_PONE-D-17-07514_RCM of BRAF V600E mutated thin melanomas detected IHQ statistical analyses

description: Statistical analysis of data presented in the paper Reflectance confocal microscopy features of BRAF V600E mutated thin melanomas detected by immunohistochemistry
DOI: 10.5061/dryad.12751/58
title: Appendix Figure 50

description: The Data (an Origin file) used for Appendix Figure 50
DOI: 10.5061/dryad.12751/59
title: Appendix Figure 51

description: The Data (an Origin file) used for Appendix Figure 51
DOI: 10.5061/dryad.164m0/1
title: analysis_script

description: R script containing code for all analyses contained in paper
DOI: 10.5061/dryad.164m0/2
title: aviary_data

description: data from competitive mating experiment
DOI: 10.5061/dryad.164m0/3
title: devel_data

description: data from non-competitive mating experiment
DOI: 10.5061/dryad.164m0/4
title: testis_data

description: male morphology data
DOI: 10.5061/dryad.164m0/5
title: README

description: Description of column names in data files
DOI: 10.5061/dryad.20864/1
title: Port-Jackson shark social network data

description: The DataZip file contains the following objects 1) “Data1_Proxi2012.csv” is the data from the proximity logger deployed in 2012 in which the location “outside” and within Orion Beach receiver detection’s range “JB4” are indicated; 2) “Data2_2012MiniSUR-10m.csv” is the data from the MiniSUR receivers deployed in 2012 (the MiniSUR identification number is provided in column “MiniSUR”); 3) “Data3_2012-VR2W-Orion.csv” is the data from the VR2W acoustic receiver from Orion Beach only in 2012; 4) “Data4_2012-AllVR2W.csv” is the data from all VR2W acoustic receivers from Jervis Bay in 2012 provided with “Station_name”; 5) “Data5_2013MiniSUR-10m.csv” is the data provided by the MiniSUR receivers deployed in 2013 restricted to 10m detection range; 6) “Data6_2013MiniSUR-60m.csv” is the data provided by the the MiniSUR receivers deployed in 2013 recorded with 60m range; 7) “Data7_2013-VR2W-Orion.csv” is the data provided by the VR2W deployed at Orion Beach in 2013; 8) “Data8_2013-AllVR2W.csv” is the data from all VR2W acoustic receivers from Jervis Bay in 2013.
In all data files above are indicated the shark tag number “TagID”, the group number “Group”, the date and time of the sighting “Timestamp” and the hourly sampling period “SP”.
DOI: 10.5061/dryad.25743/2
title: Calibrated species trees based on trnK-matK, rbcL, and ndhF omitting Psathyrostachys.

description: Calibrated multispecies coalescent derived from three chloroplast loci trnK-matK, rbcL and ndhF considering all genomic Triticeae groups covered in the study but omitting Psathyrostachys and polyploid wheats. Sequences of Brachypodium distachyon, Oryza sativa and Zea mays were included as outgroups. Posterior probability values are given for all nodes. Divergence time estimates were inferred using the secondary calibration points from Marcussen et al. [20] for the Brachypodium-Triticeae split (mean 44.44 million years ago). Node bars indicate the age range with 95% interval of the highest probability density. For the analysis Triticum monococcum and T. boeoticum, Secale cereale and S. vavilovii, Pseudoroegneria tauri and Ps. libanotica, Taeniatherum caput-medusae and Tae. crinitum, Agropyron cristatum and Agr. cimmericum were each subsumed under a single species name (Additional file 1: Table S1).
DOI: 10.5061/dryad.25743/3
title: Full representation of the Bayesian phylogenetic tree based on whole chloroplast genome sequences.

description: Phylogenetic tree derived from an alignment of whole genome chloroplast sequences via Bayesian phylogenetic inference (BI). The multiple sequence alignment comprised 183 genomes assembled in the present study and 39 genomes that were downloaded from GenBank. Brachypodium distachyon was used as outgroup taxon. The tree shown corresponds to an analysis based on the complete alignment of 123,531 base pairs (bp). Posterior probabilities (pp) for the main clades are depicted next to the nodes if they were higher then 0.75. Support values of a second BI analysis based on 114,788 bp of whole chloroplast genomes were alignment positions with more than 50% of missing data were masked are shown below the values of the corresponding nodes in the complete chloroplast analysis if the values differed between analyses. For clades comprising multiple taxa, the taxon affiliation of single accession is indicated by the same symbols behind accession and taxon name (e.g. ‘;“, *). The ploidy level is provided in brackets after the taxon label. Single accessions grouping apart from other accessions of their taxon are shown in bold. To the right the genomic groups are indicated. The red circle represents the secondary calibration point from Marcussen et al. [20] used for node calibrations in multispecies coalescent analyses (MSC). Major nodes are shown in blue and their estimated ages in million years are given in the box. Two age values for the same node correspond to the analysis with (first value) and without the inclusion of Psathyrostachys (second value). For more information on the results of the MSC analyses see Additional file 5: Fig. S2 and Additional file 6: Fig. S3. For the full representation of the tree showing the grouping of all single accessions see Additional file 4: Fig. S1. For species synonyms see Additional file 1: Table S1. Arrows with support values indicate the nodes they refer to.
DOI: 10.5061/dryad.25743/4
title: Marginal likelihoods and Bayes factor evaluation of Triticeae chloroplast relationships.

description: Stepping-stone estimates of marginal likelihoods calculated with MRBAYES 3.2.6 on the ndhF dataset and Bayes factor estimated as 2(H1-H2), where H1 enforces monophyly and H2 enforces polyphyly of Triticeae chloroplasts. BF12
DOI: 10.5061/dryad.25743/5
title: Read numbers mapping to the complete chloroplast sequences and ndhF.

description: Number of reads mapping and mean coverage for the entire chloroplast genome and ndhF after the removal of duplicated reads. Also the proportions of all reads mapping to the chloroplast that mapped to ndhF are given.
DOI: 10.5061/dryad.25743/6
title: Accessions considered in the study.

description: Overview of the material considered in this study. For all materials, the GenBank identifier, the accession and species name as used in this study (Species) as well as their species synonyms used in the donor seed banks or in the NCBI GenBank (Material source/Reference) are provided. The genome symbol, and the country of origin, where the material was originally collected are given. The ploidy level measured in the scope of this study and the information if a herbarium voucher could be deposited in the herbarium of IPK Gatersleben (GAT) is given. Genomic formulas of tetraploids and hexploids are given as "female x male parent". The genomes of Aegilops taxa follow Kilian et al. [74] and Li et al. [84]. Genome denominations for Hordeum follow Blattner [107] and Bernhardt [12] for the remaining taxa.
DOI: 10.5061/dryad.2j27b/19
title: ZBCi3-V1T-1_S44_L006_R1_001.fastq
DOI: 10.5061/dryad.2j27b/20
title: ZBCi4-V1T-1_S45_L006_R1_001.fastq
DOI: 10.5061/dryad.2j27b/21
title: ZBCi5-V1T-1_S46_L006_R1_001.fastq
DOI: 10.5061/dryad.2j27b/22
title: ZBCi6-V1T-1_S47_L006_R1_001.fastq
DOI: 10.5061/dryad.2j27b/23
title: ZBCi7-V1T-1_S48_L006_R1_001.fastq
DOI: 10.5061/dryad.2j27b/24
title: Grp1_i06_Nov2015.fastq
DOI: 10.5061/dryad.2j27b/25
title: Grp2_i03_Mar2016.fastq
DOI: 10.5061/dryad.2j27b/26
title: Grp1_i12_Mar2016.fastq
DOI: 10.5061/dryad.2j27b/27
title: Grp5_i06_Mar2016.fastq
DOI: 10.5061/dryad.2j27b/28
title: Grp3_i04_Mar2016.fastq
DOI: 10.5061/dryad.35q4h/10
title: Input for SVDquartets, full dataset, without Liolaemus tenuis tenuis.

description: ​Input sequences in nexus format for SVDquartets, full dataset, excluding Liolaemus tenuis tenuis.
DOI: 10.5061/dryad.35q4h/11
title: Input for SVDquartets, protein-coding dataset, with Liolaemus tenuis tenuis.​

description: ​Input sequences in nexus format for SVDquartets, protein-coding dataset, with Liolaemus tenuis tenuis.
DOI: 10.5061/dryad.35q4h/12
title: Input for SVDquartets, ultraconserved elements dataset, with Liolaemus tenuis tenuis.​

description: ​Input sequences in nexus format for SVDquartets, ultraconserved elements (UCEs) dataset, with Liolaemus tenuis tenuis.
DOI: 10.5061/dryad.35q4h/13
title: SVDquartets output for the full data set with Liolaemus tenuis tenuis.

description: SVDquartets output (phylogenetic tree) for the full data set with Liolaemus tenuis tenuis.
DOI: 10.5061/dryad.35q4h/14
title: SVDquartets output for the full data set without Liolaemus tenuis tenuis.

description: SVDquartets output (phylogenetic tree) for the full data set excluding Liolaemus tenuis tenuis.
DOI: 10.5061/dryad.35q4h/15
title: SVDquartets output for the protein-coding data set with Liolaemus tenuis tenuis.

description: SVDquartets output (phylogenetic tree) for the protein-coding data set with Liolaemus tenuis tenuis.
DOI: 10.5061/dryad.35q4h/17
title: IQTREE Partitions for the full data set with Liolaemus tenuis tenuis

description: IQTREE Partitions (input) in nexus format for the full data set with Liolaemus tenuis tenuis.
DOI: 10.5061/dryad.35q4h/8
title: ASTRAL-II inferred tree using the full data set without Liolaemus tenuis tenuis.

description: Results of ASTRAL-II: inferred tree using the full data set excluding Liolaemus tenuis tenuis.
DOI: 10.5061/dryad.35q4h/9
title: Input for SVDquartets, full dataset, with Liolaemus tenuis tenuis.

description: Input sequences in nexus format for SVDquartets, full dataset, with Liolaemus tenuis tenuis.
DOI: 10.5061/dryad.4r05g/1
title: RNAseq of uPA (PLAU) knockdown in human corneal fibroblasts

description: Scarring and fibrotic disease result from the persistence of myofibroblasts characterized by high surface expression of αv integrins and subsequent activation of TGFβ, however the mechanism controlling their surface abundance is unknown. We previously found that knockdown of uPA (urokinase plasminogen activator) in primary human corneal fibroblasts generated myofibroblasts with cell surface accumulation of integrin αvβ5 (Wang et al., 2012, 
PMID: 22470492). Genetic screening of these myofibroblasts was pursued to test for changes in the gene expression of degradation machinery (ligases or deubiquitinases) that could effect cell surface expression of integrins. We found that a subset of human deubiquitinases were increased in these myofibroblasts. Secondary screening revealed that the deubiquitinase USP10 regulates alpha v integrin protein expression.
DOI: 10.5061/dryad.5gd04/1
title: PLOS ONE RAW DATA

description: Raw data set used  in the manuscript.
DOI: 10.5061/dryad.5tj50/1
title: DRE Disease Data

description: This file includes data used to asses parasite richness and abundance responses to experimental host resource supply and host diversity treatments. The columns from left to right are: the unique plot ID, the experimental block, the plot planting treatment, the host diversity treatment, the resource supply treatment, community load for all parasites, rarefied parasite richness, microbial parasite load, insect parasite load, microbial rarefied richness, and insect rarefied richness.
DOI: 10.5061/dryad.5tj50/2
title: DRE Disease Analysis

description: This file contains the r code used to assess the impacts of experimental host diversity and resource supply to hosts on parasite abundance and parasite richness.
DOI: 10.5061/dryad.65h9g/1
title: Zhang et al 2017 SUSD2 ENCa Data files

description: FACS histograms, Western blot, qPCR and cell death prism files, photographs of cell senescence.
DOI: 10.5061/dryad.743p5/1
title: DTEno-matchBLASTnSequences

description: This markdown file includes the BLASTnSequencing results for the DTE analysis (the sequences without matches)
DOI: 10.5061/dryad.743p5/2
title: NEWESTFinalMUS

description: Gene ID by Transcript ID matrix
DOI: 10.5061/dryad.743p5/3
title: NEWmergedcounts

description: Salmon merged quant file
DOI: 10.5061/dryad.96ng4/1
title: rawdata for all experiments

description: This file includes rawdata for all phenotypes described within this study.
DOI: 10.5061/dryad.d5m8f/1
title: Production potential of non-timber forest products

description: Dry weight biomass of berry producing dwarf shrubs (V. myrtillus and V. vitis-idaea) and ground living lichens (utilized by reindeers during winter) in five treatments. Lichen data are from sites located in the counties currently utilized as winter grazing areas (site 895 and sites located north of site 895). Treatments were: Thinning (Th), No thinning (NoTh), Nitrogen fertilization (N), thinning+ nitrogen fertilization (Th+N), and Thiining + N and P fertilization (Th+N+P).