cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.6s5vv/1
title: Raw Data for "Impulsivity in Toxoplasma infected rats"

description: Entire raw data
DOI: 10.5061/dryad.77bv0/1
title: Lujan_et_al_data

description: Producers and non-producers growth rates and non-producer´s relative fitness in soil microcosms. Data from the Electronic Supplementary Material is also included
DOI: 10.5061/dryad.7kp78/1
title: Bythotrephes Morphological Measurements Lake Michigan

description: See ReadMe file
DOI: 10.5061/dryad.905sq/1
title: Alignments and evolutionary rate estimates

description: Both pairwise and multiple sequence alignments, with exon/intron junction trimming (tab-separated text files), and associated evolutionary rate estimates (Excel spreadsheets).
DOI: 10.5061/dryad.b8d21/1
title: Environmental data for manuscript mec-14-1145

description: Excel-file containing environmental data from the sampling site OF-2 (59.186668N, 10.691667E), Oslofjorden, Norway, in the study period September 2009-June 2011.
DOI: 10.5061/dryad.b8d21/2
title: Table_S2_Egge_et_al_2015_jeukmic

description: Table containing information about the haptophyte V4 SSU rRNA OTUs recorded in Skagerrak in the period September 2009 – June 2011. First published in Egge ES, Eikrem W, Edvardsen B (2015) “Deep-branching Novel Lineages and High Diversity of Haptophytes in the Skagerrak (Norway) Uncovered by 454 Pyrosequencing”, Journal of Eukaryotic Microbiology 62, 121-140. DOI: 10.1111/jeu.12157
DOI: 10.5061/dryad.b8d21/3
title: Haptophyte_ref_alignment_284tax

description: Reference alignment comprising 281 haptophyte 18S rDNA sequences representing all cultured haptophyte species, environmental sequences forming novel clades, and the best BLAST hits in NCBI-nr to the Oslofjorden OTUs. Three outgroup sequences are included (AJ564771 Telonema subtilis, AY919672 Kathablepharis remigera, L28811 Chilomonas paramecium). The sequences from cultured species and environmental sequences that formed novel clades were aligned in MAFFT v.6 with the Q-INS-i strategy (Katoh and Toh 2008). BLAST hits in NCBI-nr that were not already present in the alignment were inserted into the existing alignment using the add-in function in MAFFT for full-length sequences, with method L-INS-1 (Katoh and Frith 2012).
DOI: 10.5061/dryad.b8d21/5
title: MEC-14-1145-OTUtab_piconanopool_notsubsamp

description: OTU table, read number not subsampled to even sampling depth.
DOI: 10.5061/dryad.b8d21/6
title: Table of OTU read abundance per sample, subsampled to even sampling depth.

description: OTU table, read number subsampled to even sampling depth (5553 reads).
DOI: 10.5061/dryad.b8d21/7
title: RAxML reference tre of 281 haptophyte taxa + 3 outgroups

description: Maximum likelihood phylogenetic trees of 281 reference haptophyte sequences (all cultured species  + selected environmental sequences) + 3 outgroups (L28811 Chilomonas paramecium, AY919672 Kathablepharis remigera, AJ564771 Telonema subtilis), constructed using RAxML v. 7.3.2 (Stamatakis 2006, Bioinformatics 22:2688-2690), with substitution model GTRCAT and 100 bootstrap runs. RAxML was run on the Lifeportal on the University of Oslo computer cluster (www.lifeportal.uio.no).
DOI: 10.5061/dryad.b8d21/8
title: Fasta-file of 156 haptophyte OTUs.

description: Fasta file of 156 haptophyte OTUs, aligned (using MAFFT add-in) to the reference alignment with 281 haptophyte reference sequences.
DOI: 10.5061/dryad.d3k37/1
title: Microarray raw data
DOI: 10.5061/dryad.d3k37/2
title: Plant volatile analysis
DOI: 10.5061/dryad.jt2sm/1
title: Inlet-to-outlet area ratio study data
DOI: 10.5061/dryad.k4g78/1
title: DNA sequences

description: Compressed zip file containing the alignments of DNA sequences used in the study in FASTA format
DOI: 10.5061/dryad.p3b61/1
title: Borrelia Sequences Associated with Birds and Ticks

description: Sequence data from various Borrelia genospecies prepared in FASTA format.
DOI: 10.5061/dryad.p3b61/2
title: Bird and Tick Infection and Infestation data

description: These data represent all birds, Ixodes pacificus nymphs, and Ixodes pacificus larvae sampled in the associated study, and what Borrelia genospecies were found in each sample.
DOI: 10.5061/dryad.vn872/1
title: TRANSCRIPTOMES.tar

description: TRANSCRIPTOMES folder includes: (1) The transcriptome assembly for each of the 18 reptile individuals sequenced (e.g. file name: SM1_centroids_nucleotides.fasta), see list below. These contain the longest open reading frames (ORFs) produced by Trinity, which were then clustered by UCLUST into centroids to reduce redundancy within a single species' transcriptome. A centroid may have collapsed multiple isoforms, truncated transcripts, and alleles from a gene, but it may also have collapsed very recent paralogs. Files are named by sequence identifier (e.g. SM) listed below.(2) The Trinotate annotation databases for each transcriptome (e.g. file name: trinotate_annotation_report_SM1.xls). The prot_id corresponds to the centroid sequence in the transcriptome .fasta file.(3) An ortholog key file (Ortholog_Key_3_20_2014.xlsx) that contains a list of each putative ortholog clustered by OrthoMCL, the best blast hit to uniprot, the number of species that were included in the ortholog, and the centroid IDs of those species (corresponding the the transcriptome assembly .fasta files).  OrthoMCL was ran on 74 total species, and we excluded form our alignments 8 species with very poor representation (for a maximum of 66 species contained within the alignments analysed for the paper).		Sequence ID, Common Name, Species IDSM1, Snapping turtle, Cheyldra serpentina SM2, Anolis lizard, Anolis sagrei 	SM3, California alligator lizard, Elgaria multicarinata SM4, African House, Lamprophis fuliginosus SM5, Cottonmouth, Agkistrodon piscivorus SM6, Sunbeam snake, Xenopeltis unicolor SM7, Alligator, Alligator mississippiensis SM8, Fence Lizard, Sceloporus undulatus 	SM9, Bearded dragon, Pogona vitticeps  	SM10, Stinkpot turtle, Sternotherus odoratus SM11, Sideneck turtle, Pelusios castaneusSM12, Skink, Scincella lateralis SM13, Box turtle, Terrapene ornata SM14, Viper Boa, Candoia aspera SM15, Gecko, Eublepharis macularius 	TC, Western aquatic garter snake, Thamnophis couchii HS08, Western terrestrial garter snake –lakeshore (fast-living) ecotype, Thamnophis elegans HS11, Western terrestrial garter snake –meadow (slow-living) ecotype, Thamnophis elegans
DOI: 10.5061/dryad.vn872/2
title: ALIGNED_BEST_FIRST_1500_ORTHOLOGS.tar

description: ALIGNED_BEST_FIRST_15000_ORTHOLOGS folder: “Best” ortholog amino acid and nucleotide alignments. The 104,235 putative orthologs described in ALIGNED_ALL-ORTHOLOGS often contained more than two representative sequences per species. For the first 15,000 putative orthologs (those with the most species included in the alignments) we used UCLUST to find the best representative per species per ortholog by taking the sequence that was closest to the centroid for that ortholog. Alignments contain one representative per species per alignment (found by centroid clustering explained in the methods) are given for Orthologs 1-15,000, regardless of how many species are contained in the centroid. After designating one representative sequence per species, alignments were performed as described in the methods (e.g. MSAProbs followed by TranslatorX). Amino acid and nucleotides are given in their respective folders.- Also included in each folder is an ortholog key file (Ortholog_Key_3_20_2014.xlsx) that contains a list of each putative ortholog clustered by OrthoMCL, the best blast hit to uniprot, the number of species that were included in the ortholog, and the centroid IDs of those species (corresponding the the transcriptome assembly .fasta file).  OrthoMCL was ran on 74 total species, and we excluded form our alignments 8 species with very poor representation (for a maximum of 66 species contained within the alignments analyzed for the paper).
DOI: 10.5061/dryad.vn872/3
title: ALIGNED_ALL_ORTHOLOGS.tar

description: ALIGNED_ALL_ORTHOLOGS folder: We used OrthoMCL to cluster ORF-centroids from all species into putative orthologs from all the species included in this study. This folder contains the putative ortholog amino acid alignments and corresponding nucleotide alignments for which there were two or more species present in the ortholog clustered by OrthoMCL (104,235 total alignments). These are available as separate files for each ortholog (104,235 total orthologs with two or more species). Amino acid and nucleotides are given in their respective folders.- Also included is an ortholog key file (Ortholog_Key_3_20_2014.xlsx) that contains a list of each putative ortholog clustered by OrthoMCL, the best blast hit to uniprot, the number of species that were included in the ortholog, and the centroid IDs of those species (corresponding the the transcriptome assembly .fasta file).  OrthoMCL was ran on 74 total species, and we excluded form our alignments 8 species with very poor representation (for a maximum of 66 species contained within the alignments analyzed for the paper).
DOI: 10.5061/dryad.vn872/4
title: IIS-TOR_TEST_GENES.tar

description: IIS-TOR_TEST_GENES folder: The hand-curated nucleotide and amino acid alignments for 61 IIS/TOR network genes. The supplementary text in the PNAS paper explains the quality controls. These were the final alignments used in the PAML and Ka/Ks analyses. This folder also contains an excel file with the annotation for the IIS/TOR test genes.
DOI: 10.5061/dryad.vn872/5
title: Species.Identifier

description: Species.Identifiers file. For the species included in this study this file contains the (i) Sequence Identifier (for the transcriptomes we developed) or the Ensemble identifier (for the genomes and transcriptomes we downloaded); (2)  the species name; (3) the common name; (4) any "nicknames" that were used during the analysis, and (5) the identifiers used in the alignments. Further details on these individuals used in this study can be found in Supplementary Table 2 of the PNAS paper (McGaugh et al. 2015 PNAS).
DOI: 10.5061/dryad.vn872/6
title: Ortholog_Key

description: An ortholog key file (Ortholog_Key_3_20_2014.xlsx) that contains a list of each putative ortholog clustered by OrthoMCL, the best blast hit to uniprot, the number of species that were included in the ortholog, and the centroid IDs of those species (corresponding the the transcriptome assembly .fasta file).  OrthoMCL was ran on 74 total species, and we excluded form our alignments 8 species with very poor representation (for a maximum of 66 species contained within the alignments analyzed for the paper).
DOI: 10.5061/dryad.vn872/7
title: CONTROL_GENES.tar

description: CONTROL_GENES folder: The final nucleotide and amino acid alignments for the 1417 "control genes". This folder also contains an excel file with the annotation for the control genes.
DOI: 10.5061/dryad.vn872/8
title: Readme

description: The Readme file explaining the contents of this Dryad submission.
DOI: 10.7267/n9np22cf
title: GLiMR toolset (ArcGIS geoprocessing tools), instruction manual, and 3D data used in support of the manuscript "GLiMR: A GIS-Based Method for the Geometric Morphometric Analysis of Artifacts"

description: Here, we describe and demonstrate a geographic information systems-based lithic morphometric research (GLiMR) software approach. GLiMR accurately and rapidly handles a sequence of ArcGIS procedures to extract geometric morphometric data from 2D and 3D scan files of lithic artifacts. GLiMR generates three main types of geometric properties: shape data, topographic data and domain aggregate data. These data can be extracted in ways that support other analyses of artifact form, including Generalized Procrustes Analysis, Principal Components Analysis and Cluster Analyses. We illustrate the use of GLiMR by presenting a basic case study that compares the geometric morphometry of Western Stemmed Tradition projectile points found in two cache features at Idaho’s Cooper’s Ferry site and from other sites in the Columbia River Plateau region of the Pacific Northwest. This collection also includes the XYZ scan files for artifacts used for case study analysis.
DOI: 10.5061/dryad.123qg/11
title: Tpi

description: Alleles of intron of the Tpi locus from Helicoverpa armigera
DOI: 10.5061/dryad.16qc5/1
title: Data from echolocation convergence study

description: The data in this folder accompany the publication:Thomas GWC and Hahn MW. 2015 Determining the null model for detecting adaptive convergence from genomic data: a case study using echolocating mammals. Molecular Biology and Evolution.The files in this repository are:1.	alignments:		The 6,400 amino acid alignments (in fasta format) of the 9 mammals used in this study along with the ancestral states as inferred by PAML.2.	species_tree.nwk	The newick formatted species tree inferred from the original alignments with RAxML and average consensus. Internal nodes have been labeled to correspond with the labels of the ancestral state sequences from the alignments.
DOI: 10.5061/dryad.1c1d4/1
title: Diniz-Filho_etal_Theropoda35

description: There are two txt in the rar file. One is the phylogeny of 35 Theropoda genera in newick format (Theropoda_35_phy.txt"). The other file (Theropoda35_geomPC.txt") contains the two "traits" analyzed in the paper (geom1 and geom2), which are principal warps of morphometric data representing variation in skull shape. For details of morphometric analyses, see Brusatte et al. (Journal of Evolutionary BIology 35: 365-377, 2012). With these two files, all analyses in the paper can be reproduced using the R script found in the online supporting information.
DOI: 10.5061/dryad.1pj04/1
title: CEL file for isolate IC899

description: aCGH raw data submitted to Gene Expression Omnibus
DOI: 10.5061/dryad.1pj04/2
title: CEL file for isolate IC904

description: aCGH raw data submitted to Gene Expression Omnibus
DOI: 10.5061/dryad.21517/1
title: Reproductive, incubation, micro-climate, and phenology data

description: This Microsoft Excel file contains 10 tabs, 5 of which contain data and 5 a description of variables. These include: all data associated with components of reproduction (Table 1), measures of incubation behaviour (Table 2), plant phenology and insect abundance (Results), and cell-specific micro-climate (Table 3, Fig S3).
DOI: 10.5061/dryad.3vc83/10
title: Fig5

description: (A) Quantitative real-time PCR analysis of Nox2 mRNA expression in Rad9+/+ and Rad9-/- MES cells exposed to 1G or SMG condition for 1 or 5days. The expression levels of Nox2 were normalized to the endogenous control GAPDH expression. (B) Quantitative real-time PCR analysis of Nox4 mRNA expression in Rad9+/+ and Rad9-/- MES cells exposed to 1G or SMG condition for 1 or 5days. The expression levels of Nox4 were normalized to the endogenous control GAPDH expression. (D) Quantitative comparison of Nox2 expression. Data were derived from three independent experiments . The expression levels of Nox2 protein were normalized to the endogenous control GAPDH protein expression.
DOI: 10.5061/dryad.3vc83/11
title: Fig6-A

description: Histograms of superoxide dismutase enzyme activity
DOI: 10.5061/dryad.3vc83/12
title: Fig6-B

description: Histograms of catalase enzyme activity
DOI: 10.5061/dryad.3vc83/13
title: Fig6-C

description: Histogram of Glutahione peroxidase
DOI: 10.5061/dryad.3vc83/14
title: Fig7

description: Quantitative comparison of Nox2 expression. Data were derived from three independent experiments The expression levels of Nox2 were normalized to the endogenous control GAPDH expression
DOI: 10.5061/dryad.3vc83/15
title: Fig8A

description: (A) The initial MES cells seeding number was 3×104. The doubling generation curve was generated by dividing the cell number with 104 and then transferring the quotient to the logarithm to the base2.
DOI: 10.5061/dryad.3vc83/7
title: Fig3 a,b,c

description: (A) Flow cytometric analysis of ROS activity in Rad9+/+ and Rad9-/- MES cells exposed to 1G or SMG condition for 1 or 5days.  (B) Flow cytometric analysis of ROS activity in Rad9-/-+Rad9 MES cells exposed to 1G or SMG condition for 1 or 5days.  (C) N-acetylcysteine inhibited SMG-induced increase of ROS formation in Rad9-/- MES cells.  Rad9-/- MES cells were mock-treated or treated with 0.05, 0.1 or 0.5 mM N-acetylcysteine under SMG for 1 day.
DOI: 10.5061/dryad.3vc83/8
title: Fig3 d e

description: (D) Evaluation of DNA damage by alkaline comet assay in Rad9-/- MES cells mock-treated or treated with 0.5 mM N-acetylcysteine under 1G of SMG condition for 1 day.  (E) Evaluation of DNA damage by neutral comet assay in Rad9-/- MES cells mock-treated or treated with 0.5 mM N-acetylcysteine under 1G of SMG condition for 1 day.
DOI: 10.5061/dryad.3vc83/9
title: Fig4

description: (A) Flow cytometric analysis of ROS activity in Mdc1+/+ and Mdc1-/- MEF cells exposed to 1G or SMG condition for 1 or 5days.(B) N-acetylcysteine inhibited SMG-induced increase of ROS formation in Mdc1-/- MEF cells. Mdc1-/- MEF cells were mock-treated or treated with 0.05, 0.1 or 0.5 mM N-acetylcysteine under SMG for 1 day. (C) Evaluation of DNA damage by neutral comet assay in Mdc1-/- MEF cells mock-treated or treated with 0.5 mM N-acetylcysteine under 1G of SMG condition for 1 day.
DOI: 10.5061/dryad.4nh84/1
title: Historical and projected climate and land-use for New South Wales, Australia
DOI: 10.5061/dryad.4nh84/2
title: Estimated land value for NSW, Australia
DOI: 10.5061/dryad.5g1k6/1
title: 2V1K_horse_deoxy
DOI: 10.5061/dryad.5g1k6/2
title: horse_oxy
DOI: 10.5061/dryad.5g1k6/3
title: horse_oxy_10ns
DOI: 10.5061/dryad.5g1k6/4
title: horse_oxy_only_wbi_10ns
DOI: 10.5061/dryad.5g1k6/5
title: horse_oxy-OLE_wbi_100ns
DOI: 10.5061/dryad.5g1k6/6
title: horse_oxy-PLM_wbi_100ns
DOI: 10.5061/dryad.5g1k6/7
title: mutant_complex_wbi
DOI: 10.5061/dryad.5g1k6/8
title: par_all27
DOI: 10.5061/dryad.65pm3/1
title: Mitochondrial DNA sequences

description: File may be viewed using ProSeq software at http://dps.plants.ox.ac.uk/sequencing/proseq.htm [Filatov DA (2009) Processing and population genetic analysis of multigenic datasets with ProSeq3 software. Bioinformatics 25: 3189-3190].
DOI: 10.5061/dryad.7625d/1
title: Nuclear alignment Figure 3.

description: Nuclear alignment used for constructing MrBayes phylogeny in Figure 3.
DOI: 10.5061/dryad.7625d/2
title: Chloroplast alignment Figure 4.

description: Chloroplast alignment used for constructing MrBayes phylogeny in Figure 4.
DOI: 10.5061/dryad.7625d/3
title: Nuclear alignment for Figures 5, 6 and Supplementary Figure 10

description: Nuclear alignment used for Figures 5, 6 (STEM analyses )and Supplementary Figure 10 (BEAST analysis)
DOI: 10.5061/dryad.7625d/4
title: Chloroplast alignment Figure 5.

description: Chloroplast alignment used for constructing STEM species tree in Figure 5.
DOI: 10.5061/dryad.7625d/5
title: Chloroplast alignment Figure 6.

description: Chloroplast alignment used for constructing STEM species tree in Figure 6.
DOI: 10.5061/dryad.7kp78/2
title: Bythotrephes Remnant Spines Lake Michigan

description: See ReadMe file.
DOI: 10.5061/dryad.8q02m/1
title: DRYAD_Leinaas_et_al_2015

description: Number of Collembola in litter traps (h=4 cm, Ø = 7.5 cm) at three sampling dates after the traps were placed out in a renosterveld vegetation in Western Cape, South Africa
DOI: 10.5061/dryad.9p31r/1
title: Inhibition growth

description: Inhibition zones (mm) exhibited by each of the treatment.
DOI: 10.5061/dryad.b8465/5
title: Mitochondrial maximum-likelihood phylogeny

description: Maximum-likelihood tree constructed from concatenated maxicircle sequences for 78 sylvatic Bolivian TcI clones and 24 additional TcI isolates from across the Americas.
DOI: 10.5061/dryad.d3k37/3
title: Y-tube bioassay
DOI: 10.5061/dryad.d3k37/4
title: Field data
DOI: 10.5061/dryad.d3k37/5
title: qPCR raw data
DOI: 10.5061/dryad.ns7bv/1
title: SmithandReynolds_Ecology_2015_dataset

description: File includes biomass data from a two-phase greenhouse experiment designed to measure net pairwise plant-soil feedback in understory species from Eastern deciduous forests of the United States. In Phase I each species was grown under each light treatment.  In Phase II, soil from each Phase I pot was divided and used to inoculate a new set of plants so that each species was grown in soil conditioned by a conspecific and all possible heterospecifics.
DOI: 10.5061/dryad.s38n5/1
title: data_and_plotting_scripts

description: The data were generated by experiments in the Sferes evolutionary algorithm framework. Source code for our experiments are available at: http://evolvingai.org/code/modularity_forgetting.tar.gz
DOI: 10.5061/dryad.1pj04/10
title: CEL file for isolate IC1410

description: aCGH raw data submitted to Gene Expression Omnibus
DOI: 10.5061/dryad.1pj04/11
title: CEL file for isolate IC313

description: aCGH raw data submitted to Gene Expression Omnibus
DOI: 10.5061/dryad.1pj04/3
title: CEL file for isolate IC158

description: aCGH raw data submitted to Gene Expression Omnibus
DOI: 10.5061/dryad.1pj04/4
title: CEL file for isolate IC277

description: aCGH raw data submitted to Gene Expression Omnibus
DOI: 10.5061/dryad.1pj04/5
title: CEL file for isolate IC903

description: aCGH raw data submitted to Gene Expression Omnibus
DOI: 10.5061/dryad.1pj04/6
title: CEL file for isolate IC902

description: aCGH raw data submitted to Gene Expression Omnibus
DOI: 10.5061/dryad.1pj04/7
title: CEL file for isolate IC1

description: aCGH raw data submitted to Gene Expression Omnibus
DOI: 10.5061/dryad.1pj04/8
title: CEL file for isolate IC33

description: aCGH raw data submitted to Gene Expression Omnibus
DOI: 10.5061/dryad.1pj04/9
title: CEL file for isolate IC75

description: aCGH raw data submitted to Gene Expression Omnibus
DOI: 10.5061/dryad.21s3t/1
title: mtDNA haplotypes of Iberian Honey bee

description: Alignment of mtDNA haplotypes
DOI: 10.5061/dryad.3vc83/16
title: Fig8B

description: The initial MEF cells seeding number was 105. The doubling generation curve was generated by dividing the cell number with 104 and then transferring the quotient to the logarithm to the base2.
DOI: 10.5061/dryad.5g1k6/10
title: script_construction_deoxy
DOI: 10.5061/dryad.5g1k6/11
title: script_construction_oxy
DOI: 10.5061/dryad.5g1k6/12
title: script_construction_oxy-FA-complex
DOI: 10.5061/dryad.5g1k6/13
title: horse_oxy_only_wbi_10ns_compressed
DOI: 10.5061/dryad.5g1k6/14
title: horse_oxy-OLE_wbi_100ns_compressed
DOI: 10.5061/dryad.5g1k6/15
title: mutant_complex_wbi_compressed
DOI: 10.5061/dryad.5g1k6/16
title: horse_oxy-PLM_wbi_100ns_compressed
DOI: 10.5061/dryad.5g1k6/17
title: Read_Me
DOI: 10.5061/dryad.5g1k6/9
title: top_heme
DOI: 10.5061/dryad.7625d/6
title: Chloroplast alignment Supplementary Figure 10.

description: Chloroplast alignment used for constructing BEAST phylogeny in Supplementary Figure 10.