cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.4288j/10
title: Supplemental File 1

description: CU full network session
DOI: 10.5061/dryad.4288j/2
title: Supplemental Dataset 1

description: Supplemental Data. Walker et al. (2017). Plant Cell 10.1105/tpc.16.00961.Supplemental Dataset 1. RMA-normalised Nimblegen microarray data for all transcripts measured. The table lists the TAIR10 Arabidopsis Genome Initiative (AGI) gene IDs represented on the array (for design see GEO record GPL18735 for Nimblegen probe design) and their expression values in all 6 time series, averaged (“Mean”) for each replicate set; see GEO GSE91379 for complete raw and normalised individual replicate values. Gene symbols and gene descriptions are listed according to the TAIR10 annotation. If significantly differentially expressed within a time series (BATS), the cluster number is listed. If significantly differentially expressed between treated and untreated time series (CN GP2S etc), the cluster number is listed. Cluster numbers described in the manuscript text always refer to the within-CU/PU or N/Rhizobia vs. U clusters (orange columns). Empty cells indicate no evidence of DE within/between time series. Transcripts associated with genes that have previously been found to be affected by the protoplast generation treatment or FACS (as [18]) are marked (Proto-flagged) but not removed from the analysis.
DOI: 10.5061/dryad.4288j/3
title: Supplemental Dataset 2

description: Supplemental Data. Walker et al. (2017). Plant Cell 10.1105/tpc.16.00961.Supplemental Dataset 2. Cluster designations for differentially expressed transcripts. The table lists the TAIR10 AGI IDs and descriptions (as Supplemental Dataset 1), whether these are classed as transcriptional regulators for network analysis (‘TF category’) and the cluster numbers for DE transcripts. In addition, transcripts that are differentially expressed in both CU and PU (‘Core CU/PU’), are ‘N-response’ marker genes, clock genes or are CTSEs in cortex or pericycle are indicated (as referred to in the text).
DOI: 10.5061/dryad.4288j/4
title: Supplemental Dataset 3

description: Supplemental Data. Walker et al. (2017). Plant Cell 10.1105/tpc.16.00961.																								
Supplemental Dataset 3. Phenotypic analysis. (A) Average (ave) and standard error (SE) root trait values measured from 9 day old Col0 seedlings and for the same seedlings after 4 days of N, rhizobial or control/mock treatment with T-test values comparing phenotype values (bold=P&lt;0.01). (B-C) Average (ave) and standard error (SE) root trait values measured from 12 day old wrky15 (B) and nlp8 (C) mutant plants on replete and deplete N with T-test values comparing phenotype values in mutant and silbling WT (bold=P&lt;0.01); LR = lateral root, PR = primary root. (D) Average and SE (n=3 biological replicates) of qPCR measurement, qPCR primer sequences and qPCR product lengths.
DOI: 10.5061/dryad.4288j/5
title: Supplemental Dataset 4

description: Supplemental Data. Walker et al. (2017). Plant Cell 10.1105/tpc.16.00961. Supplemental Dataset 4. GO term overrepresentation analysis. GO terms (biological process/molecular function/cellular component) found to be overrepresented within CN/PN/CR/PR clusters (according to GOrilla [79] with hypergeometric test correction) or within core N-response groups (Figure 6C) (according to BioMaps implemented in VirtualPlant [80] using a Fisher exact test with FDR correction) are listed, together with the corrected P value																								
and gene membership; x=number of genes with GO term in test cluster/group; X=total number of genes in test cluster/group; n=number of genes with GO term in background; N=total number of genes in background.
DOI: 10.5061/dryad.4288j/6
title: Supplemental Dataset 5

description: Supplemental Data. Walker et al. (2017). Plant Cell 10.1105/tpc.16.00961. Supplemental Dataset 5. Network edge designations with validation information. For each causal regulatory network (A) CU, (B) CN, (C) CR, (D) PU, (E) PN, (F) PR, edges between regulator and target are listed with their posterior probability (pp), regulation type (induce or repress), and whether they are validated according to the O'Malley et al 2016 ampDAP-Seq data or DAP-seq data [42] (1=validated, 0=not validated, NT=not tested).
DOI: 10.5061/dryad.4288j/7
title: Supplemental Dataset 6

description: Supplemental Data. Walker et al. (2017). Plant Cell 10.1105/tpc.16.00961. Supplemental Dataset 6. Network statistics and module annotation and characteristics .(A) For each causal regulatory network 8 statistics are shown: number of edges, number of nodes, the node/edge ratio, number of connected TFs, number of targets of those TFs (including TFs that are targets), average targets per TF, the network clustering coefficient and the characteristic path length as given in Cytoscape. (B) Comparison of TF module size and timing response category for CN and PN networks.  (C) Network statistics for major modules in each experiment are shown with a cut off of &gt;=10 targets in at least one experiment. The status of each TF in the network in each experiment is shown (DE (0 not DE, 1 DE), indegree, outdegree). The combined outdegree is the sum of the shown out degrees across the six experiments, the number of experiments where outdegree is &gt;7 is also shown. Maximum module size was in part dictated by the number of genes in the network, while the mean number of targets per TF was larger in CU and CN. This indicates that the pericycle and cortex networks have statistically different structures and this was confirmed  by analysis of the network connectivity using size independent statistics; specifically there were differing levels of clustering, CN was the least clustered whereas PN had the longest path length while still being highly clustered. This indicates that the cortex is dominated by a few large  modules, while the pericycle is more distributed amongst a larger number of modules, in fact extending to very large sizes. (D) Corroborated interactions based on the presence of cis-acting TF family binding sites for networks. Data derived from Franco-Zorrilla et al 2014 [83]. Source contains TFs that interact with a putative regulated gene (Target) and the type of interaction (activation/inhibition) is shown.
DOI: 10.5061/dryad.4288j/8
title: Supplemental Dataset 7

description: Supplemental Data. Walker et al. (2017). Plant Cell 10.1105/tpc.16.00961. Supplemental Dataset 7. Glutathione S-transferase gene family expression is highly variable. All members of the GST family the time series within which differential expression was found are indicated (or not DE), together with the cluster number for that time series. Genes shown on Figure 6 are highlighted in yellow and the time series that has been shown is indicated.
DOI: 10.5061/dryad.4288j/9
title: Supplemental Dataset 8

description: Supplemental Data. Walker et al. (2017). Plant Cell 10.1105/tpc.16.00961. Supplemental Dataset 8. Gene family regulation across cell types and treatments. (A) Summary of gene family regulation: number DE/non-DE, in which timeseries they are regulated and if transcripts are DE in one or both cell types. (B) Lists of the genes in each family together with cluster numbers if differentially expressed in a timeseries.
DOI: 10.5061/dryad.6cs14/1
title: Soil food webs chronosequences Western Australia

description: Biotic and abiotic soil properties measured along four long-term  chronosequences in Western Australia.
DOI: 10.5061/dryad.6j205/1
title: Input file for entropy analysis

description: Genotype likelihoods (simplified from VCF) at 11,221 SNPs for 2785 individual Catostomus fish. This file was used for analyses of hybridization.
DOI: 10.5061/dryad.6j205/2
title: artificial reference genome

description: This reference was made by completing a denovo assembly of a subset of the data using smng (see manuscript text) and all reads were assembled to this reference for variant calling.
DOI: 10.5061/dryad.6j205/3
title: Full VCF file

description: All variant sites initially identified for analysis of hybridization. This VCF was produced using samtools and bcftools, and contains information for 2785 Catostomus individuals.
DOI: 10.5061/dryad.7p05v/1
title: Landscape genetics of Alaska salmon

description: The nine files contain genotypic and environmental data for Chinook, Coho, and Chum Salmon (three files per species).  For more detail see the README.pdf file.
DOI: 10.5061/dryad.80dk1/1
title: Osur CHCs

description: cuticular hydrocarbons measured by GC/MS of O.surinamensis adults with and without symbionts, reared at 30 or 60% relative humidity before and after acute desiccation stress (Fig. 4)
DOI: 10.5061/dryad.80dk1/2
title: Osur cuticle melanization

description: Melanization of O.surinamensis cuticle with and without symbionts, reared at 30 and 60% relative humidity, measured as redness of thorax and cuticle (Fig. 3a and S3)
DOI: 10.5061/dryad.80dk1/3
title: Osur cuticle thickness

description: Cuticle thicknes of O.surinamensis with and without symbionts, reared at 30 and 60% relative humidity, larvae and adults.(Fig. 3b and S4)
DOI: 10.5061/dryad.80dk1/4
title: Osur water loss

description: weight (water) loss of O.surinamensis under acute desiccation stress (&lt;5%relative humidity). Beetles were beforehand reared with and without symbionts, at 30 or 60% relative humidity (Fig. 5a and S5)
DOI: 10.5061/dryad.97cj5/1
title: Maseyk et al_BiodivConserv_Data&RScripts

description: 1. R code DataPrep (R script for data compilation and file preparation); 2. R code LMM and graphs (R script for Linear Mixed Models and plotting); 3. Masterfile.csv (raw data file); 4. Abandoned.csv, Mowed.csv and Grazed.csv (input data by management type); 5. Count.csv, Cover.csv, Evar.csv, InvSimpson.csv (input data by metric).
DOI: 10.5061/dryad.b0ck8/1
title: Relatedness_Odisjunctus

description: This spreadsheet contains a summary sheet of all relatedness values between all individuals sequenced (first sheet). All other sheets contain the data that was used in the R-script “LogRelatedness_wilcoxon_sim.R” to compare relatedness between individuals residing in the same log vs those residing in different logs across different categories of individuals. Simply copy and paste each sheet in a separate .csv document and rename the file appropriately to analyze data and replicate the results of the paper.
DOI: 10.5061/dryad.b0ck8/2
title: LogRelatedness_wilcoxon_sim

description: This file contains the R script used to analyze relatedness between different categories of individuals within and between logs using permuted Wilcoxon Rank Sum test following the methods of Wolf & Trillmich (2008). Use data from “Relatedness_Odisjunctus.xls” to create .csv files to run with this code to replicate results.
DOI: 10.5061/dryad.bh78m/1
title: Matala et al_7-20-17
DOI: 10.5061/dryad.c1j01/2
title: 6hmms_makerStandard_noTEs.gff3

description: Genome annotation for Six HMMs gene predictions in rice.
DOI: 10.5061/dryad.c1j01/3
title: 6hmms_makerStandard_noTEs_proteins.fasta

description: Predicted proteins from the Six HMMs gene predictions in rice.
DOI: 10.5061/dryad.c1j01/4
title: 6hmms_makerStandard_noTEs_transcripts.fasta

description: Predicted transcripts from Six HMMs gene predictions in rice.
DOI: 10.5061/dryad.cb448/2
title: Buschcricket_file_and_entropy_data_Chiversetal_after_revision

description: Data file of species, acoustic, and morphological information for 40 species of bush-cricket.
DOI: 10.5061/dryad.cb448/3
title: Data_file_images_Chiversetal

description: Folder contains SEM images of the stridulatory file of 40 species of bush-cricket.
DOI: 10.5061/dryad.cb448/4
title: Data_sound_text_files_Chiversetal

description: Folder contains acoustic recordings of 40 species of bush-cricket presented ascii files. Each file contains time and signal data.
DOI: 10.5061/dryad.dg072/1
title: Variables in model examining effect of road crossing on bear max. heart rate

description: This csv file contains all of the processed values of variables included in the first model (generalized additive model)  examining the influence of road crossings on bears' maximum heart rate (MAXHRstep), including other considered covariates.
DOI: 10.5061/dryad.dg072/2
title: Variables in model examining effect of distance to roadway on bear max. heart rate

description: This csv file contains all of the processed values of variables included in the second model (generalized additive model)  examining the influence distance to roadways on bears' maximum heart rate (MAXHRstep), including other considered covariates.
DOI: 10.5061/dryad.f357r/15
title: Processed behavioral and neurophysiological data 15
DOI: 10.5061/dryad.f357r/16
title: Processed behavioral and neurophysiological data 16
DOI: 10.5061/dryad.f357r/17
title: Processed behavioral and neurophysiological data 17
DOI: 10.5061/dryad.f357r/18
title: Processed behavioral and neurophysiological data 18
DOI: 10.5061/dryad.f357r/19
title: Processed behavioral and neurophysiological data 19
DOI: 10.5061/dryad.f357r/20
title: Supplementary Materials: Subject 1-4
DOI: 10.5061/dryad.f357r/21
title: Subject 5-8
DOI: 10.5061/dryad.g3qh8/1
title: Benthic infauna from grab samples - Irish Sea

description: Abundance and biomass of benthic invertebrates from the Day  grab samples per species and per station. Benthic invertebrates were sampled by taking six 0.1 m2 grabs at haphazard locations within the station box.  All samples were sieved and preserved in 4% formalin for identification. All invertebrates were identified to the highest practicable taxonomic resolution (mostly genus or family) and the wet weight of species was estimated after blotting.
DOI: 10.5061/dryad.gm073.2/10.2
title: div_imputed.hmp.txt
DOI: 10.5061/dryad.gm073.2/11.2
title: div_raw.hmp.txt
DOI: 10.5061/dryad.gm073.2/12.2
title: map.composite
DOI: 10.5061/dryad.gm073.2/13.2
title: div_rec_dist.chr_def
DOI: 10.5061/dryad.gm073.2/4.2
title: genotypes_weslaco
DOI: 10.5061/dryad.gm073.2/5.2
title: genotypes_grin
DOI: 10.5061/dryad.gm073.2/6.2
title: geno_sap60K
DOI: 10.5061/dryad.gm073.2/7.2
title: geno_nam60K
DOI: 10.5061/dryad.gm073.2/8.2
title: geno_grin60K
DOI: 10.5061/dryad.gm073.2/9.2
title: script_simulation
DOI: 10.5061/dryad.gq93s/1
title: concatenated DNA matrix

description: DNA matrix used for BEAST analysis
DOI: 10.5061/dryad.gq93s/2
title: MCC_17.7.2

description: Maximum Clade Credibility obtained in BEAST
DOI: 10.5061/dryad.m1v40/1
title: STAPLER_pipeline

description: A zip  archive containing input file for STAPLER pipeline tool
DOI: 10.5061/dryad.m1v40/2
title: Data processing pipeline

description: A zip  archive containing pipeline scripts for mapping data processing
DOI: 10.5061/dryad.m1v40/3
title: Stairwayplot_pipelines

description: A zip  archive containing files for Stairwayplot analysis
DOI: 10.5061/dryad.m1v40/4
title: ANGSD_pipelines

description: A zip  archive containing pipelines for population genetics analyses with ANGSD
DOI: 10.5061/dryad.m1v40/5
title: fastsimcoal2_models

description: A zip  archive containing fastsimcoal2 model and prior specification files
DOI: 10.5061/dryad.m1v40/6
title: admixture_pipeline_REVISION

description: A file containing commands to run ADMIXTURE analysis
DOI: 10.5061/dryad.m1v40/7
title: NGSadmix pipeline

description: A file containing commands for NGSadmix  analysis
DOI: 10.5061/dryad.mk4r5/5
title: Figure 5
DOI: 10.5061/dryad.rp011/1
title: zipped folder containing files related to analyses

description: All other scripts, final datasets, the probe set, and the U. beldingi transcritpome
DOI: 10.5061/dryad.th160/1
title: spectral_meassurements

description: Measurements of the dorsal and ventral spectral reflectance variables (ΔL, ΔS, L, S, ΣR(λ))
DOI: 10.5061/dryad.th160/2
title: PC_scores.DORSAL

description: Individual scores on the principal components derived from the dorsal spectral measurements
DOI: 10.5061/dryad.th160/3
title: PC_scores.VENTRAL

description: Individual scores on the principal components derived from the ventral spectral measurements
DOI: 10.17632/hpjkdz8b6f.1
title: Data for: Circulating microRNAs and depression: Many candidates, few finalists

description: Research data accompanying revised paper on circulating microRNAs and depression.
DOI: 10.5061/dryad.2p6b5/1
title: Raw sequences

description: All the markers which were newly sequenced for this study.
DOI: 10.5061/dryad.3dt70/1
title: Gibb et al Ecography - Data

description: Data from 371 locations showing whole assemblage ant body size, including min, max, mean, variance and percentiles from 10th to 90th.
DOI: 10.5061/dryad.4288j/11
title: Supplemental File 2

description: CN full network session
DOI: 10.5061/dryad.4288j/12
title: Supplemental File 3

description: CR full network session
DOI: 10.5061/dryad.4288j/13
title: Supplemental File 4

description: PU full network session
DOI: 10.5061/dryad.4288j/14
title: Supplemental File 5

description: PN full network session
DOI: 10.5061/dryad.4288j/15
title: Supplemental File 6

description: PR full network session
DOI: 10.5061/dryad.4288j/16
title: Supplemental File 7

description: CU backbone network session
DOI: 10.5061/dryad.4288j/17
title: Supplemental File 8

description: CN backbone network session
DOI: 10.5061/dryad.4288j/18
title: Supplemental File 9

description: CR backbone network session
DOI: 10.5061/dryad.4288j/19
title: Supplemental File 10

description: PU backbone network session
DOI: 10.5061/dryad.42d2r/1
title: Tamburini et al. DATA

description: Sunflower yield, yield parameters and visitation rate
DOI: 10.5061/dryad.6200g/1
title: Figure 3 R script

description: R script to recreate Figure 3 summarising simulated fire patterns
DOI: 10.5061/dryad.6200g/2
title: Summary data on simulated fires

description: Two files that provide information on the timing and location of simulated fires, and on the landscape patterns of fire history resulting from the fire simulations.
DOI: 10.5061/dryad.6200g/3
title: Simulation outputs for T1W1 scenarios

description: Individual genotypes, locations and environmental info for T1W1 scenarios
DOI: 10.5061/dryad.6200g/4
title: Simulation outputs for T1W2 scenario

description: Individual genotype, location and environment outputs fro T1W2 simulation scenarios
DOI: 10.5061/dryad.6200g/5
title: Sulation outputs for T2W1 scenarios

description: Individual genotype, location and environment outputs fro T1W2 simulation scenarios
DOI: 10.5061/dryad.66s9h/1
title: Hist_1000_Chars

description: The number of incorrect nodes found within each consensus subtracted from the number of correct nodes found tree within the same consensus trees constructed from 100 replicate matrices of 1000 morphological characters.
DOI: 10.5061/dryad.758g8/1
title: Microbiome JEXBIO/2017/169227 data file
DOI: 10.5061/dryad.80dk1/5
title: Osur mortality

description: Mortality of O.surinamensis under acute desiccation stress (&lt;5%relative humidity). Beetles were beforehand reared with and without symbionts, at 30 or 60% relative humidity. (Fig. 5b)
DOI: 10.5061/dryad.80dk1/6
title: Osur population growth

description: Population growth of O.surinamensis, with and without symbionts, reared at 30 and 60% relative humidity. (Fig. 6 and S3b)
DOI: 10.5061/dryad.80dk1/7
title: Osur symbiont elimination qPCR

description: Quantification of symbiont titer after heat and tetracyclin treatments in offspring eggs. Abundance measured as DNA amount of 16S / 28S rDNA.
DOI: 10.5061/dryad.84397/1
title: Seedling winter survival in 4 bryophyte treatment under different snow treatments and elevations

description: Field experimental data of winter survival of transplanted seedlings. Experiment had two elevational sites to which bryophytes cores were transplanted. These were subjected to snow treatments(addition, control, reduction). Seedling were transplanted into bryophyte cores in at the end of 2013 growing season and survival was assessed in june and august 2014. See published article for full description of the experimental details
DOI: 10.5061/dryad.8gr16/1
title: Species presence in plotgroups

description: The file “Nabe-Nielsen etal 2017 Young Sund spp pres in plotgrps” contains data on the number of plots where each vascular plant species was present within each of the 48 plot groups. Species names are based on nomenclature in Supplementary Information in the published paper.
DOI: 10.5061/dryad.8gr16/2
title: Vegetation cover and environmental data per plot group

description: The file “Nabe-Nielsen etal 2017 Young Sund plotgroup data.csv” contains data on average vegetation cover, average number of plant species per plot and average environmental variables in each of 48 plot groups distributed along Young Sund, a High Arctic fjord in Northeast Greenland. The plots are located in three sites: “Zackenberg”, “Blæsedalen” and “Tyrolerfjord”. Each plot group consists of six plots. See the published paper for further details. Environemental variables include: altitude [m], continentality index [*], slope [degrees], solar radiation index [*], soil water [percent], and temperature [degrees celsius]. *See the paper for definitions of the indices.
DOI: 10.5061/dryad.9fp38/1
title: AllData_PLoSONE_SI_2017_v1
DOI: 10.5061/dryad.b0ck8/3
title: figure4data

description: Data used to create figure 4 (within and between log relatedness)
DOI: 10.5061/dryad.b0ck8/4
title: figure4_RCODE

description: R-code used to create figure 4 – use with “figure4data.csv”
DOI: 10.5061/dryad.b0ck8/5
title: beetleweight

description: Longitudinal data of beetle weight through time. Individuals identified by solitary treatment or by group and leg modification (e.g., G1LMT would indicate a beetle from group 1 that has had its left mesal tarsus clipped).
DOI: 10.5061/dryad.b0ck8/6
title: beetlespec

description: Longitudinal data of beetle reflectance (spec) through time. Like “beetleweight.xls”, individuals identified by solitary treatment or by group and leg modification (e.g., G1LMT would indicate a beetle from group 1 that has had its left mesal tarsus clipped).
DOI: 10.5061/dryad.b0ck8/7
title: fungal growth summary

description: Summary of fungal growth in petri dish experiment containing a frass and a deceased beetle either alone or with a living beetle.
DOI: 10.5061/dryad.b0ck8/8
title: Odontotaenius_SNPdata

description: All SNPs which passed our filtering processes are contained in this file, which is in SPAGeDi format and includes a distance matrix in meters at the end of the file.
DOI: 10.5061/dryad.b0ck8/9
title: Odontotaenius_GPScoords

description: This file contains GPS coordinates for each of the six logs we sampled in the field.
DOI: 10.5061/dryad.b1t42/1
title: return rates

description: table showing return rates of geolocator and control birds in form of aggregated data (one record per year, study site and species of birds) for Italian and Swiss study sites.This data were used for the analysis shown in Table 4 of main text.
DOI: 10.5061/dryad.b1t42/2
title: swift biometries

description: file containing measures of wing and weight of Apus apus and Apus pallidus from the study sites for which these were available.
DOI: 10.5061/dryad.b1t42/3
title: geolocator birds

description: Table having 372 records exclusively belonging to geolocators birds from all the 14 study sites.  Geolocator type, weight and appearence (flat vs with light stalk) are indicated. Dataset used to run the model shown in Table 5 of the main text.
DOI: 10.5061/dryad.b1t42/4
title: capture recapture histories for MARK

description: Capture-recapture histories in format 01 used to run the MARK analysis described in the paper. Look at the legend for details.
DOI: 10.5061/dryad.c1j01/1
title: md5_values

description: The md5 values for the files in this data submission.
DOI: 10.5061/dryad.c1j01/10
title: novel_low_maker_standard_proteins.fasta

description: Predicted proteins of novel genes predicted by the low GC HMM in rice.
DOI: 10.5061/dryad.c1j01/11
title: novel_low_maker_standard_transcripts.fasta

description: Predicted transcripts of novel genes predicted by the low GC HMM in rice.
DOI: 10.5061/dryad.c1j01/6
title: novel_high_maker_standard_genes.gff3

description: Gene annotations of novel genes predicted by the high GC HMM in rice.