cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.dj782
title: Data from: Constitutive turnover of histone H2A.Z at yeast promoters requires the preinitiation complex

description: The assembly of the preinitiation complex (PIC) occurs upstream of the +1
 nucleosome which, in yeast, obstructs the transcription start site and is
 frequently assembled with the histone variant H2A.Z. To understand the
 contribution of the transcription machinery in the disassembly of the +1
 H2A.Z nucleosome, conditional mutants were used to block PIC assembly. A
 quantitative ChIP-seq approach, which allows detection of global occupancy
 change, was employed to measure H2A.Z occupancy. Blocking PIC assembly
 resulted in promoter-specific H2A.Z accumulation, indicating that the PIC
 is required to evict H2A.Z. By contrast, H2A.Z eviction was unaffected
 upon depletion of INO80, a remodeler previously reported to displace
 nucleosomal H2A.Z. Robust PIC-dependent H2A.Z eviction was observed at
 active and infrequently transcribed genes, indicating that constitutive
 H2A.Z turnover is a general phenomenon. Finally, sites with strong H2A.Z
 turnover precisely mark transcript starts, providing a new metric for
 identifying cryptic and alternative sites of initiation.
description: Figure_1A--source_dataGenome-wide nucleosome tag coverage of TBP-FRB. The no RAP and +RAP datasets represent the normalized averages of 4 and 5 replicates, respectively. Data files are formatted for the Integrated Genome Browser.Figure_1B--source_dataGenome-wide nucleosome tag coverage of no FRB. The dataset represents the normalized averages of 3 replicates. Data files are formatted for the Integrated Genome Browser.Figure_1--figure_supplement_8_source_dataGenome-wide nucleosome tag coverage of RPB1-FRB. The dataset represents the normalized averages of 3 replicates. Data files are formatted for the Integrated Genome Browser.Figure_3A--source_dataGenome-wide nucleosome tag coverage of SWC5-FRB. The dataset represents the normalized averages of 2 replicates. Data files are formatted for the Integrated Genome Browser.Figure_3D--source_dataGenome-wide nucleosome tag coverage of SWC5-FRB TBP-FRB. The dataset represents the normalized averages of 2 replicates. Data files are formatted for the Integrated Genome Browser.FIgure_4A--source_dataGenome-wide nucleosome tag coverage of INO80-FRB. The dataset represents the normalized averages of 2 replicates. The data files are formatted for visualization using the Integrated Genome Browser.FIgure_6E_6F--source_dataGenome-wide nucleosome tag coverage of TBP-FRB (chromatin under-digested during the MNase treatment). The dataset represents the normalized averages of 2 replicates. Data files are formatted for visualization using the Integrated Genome Browser.
DOI: 10.5061/dryad.g9f5r
title: Data from: The population genomics of archaeological transition in west Iberia: investigation of ancient substructure using imputation and haplotype-based methods

description: We analyse new genomic data (0.05–2.95x) from 14 ancient individuals from
 Portugal distributed from the Middle Neolithic (4200–3500 BC) to the
 Middle Bronze Age (1740–1430 BC) and impute genomewide diploid genotypes
 in these together with published ancient Eurasians. While discontinuity is
 evident in the transition to agriculture across the region, sensitive
 haplotype-based analyses suggest a significant degree of local
 hunter-gatherer contribution to later Iberian Neolithic populations. A
 more subtle genetic influx is also apparent in the Bronze Age, detectable
 from analyses including haplotype sharing with both ancient and modern
 genomes, D-statistics and Y-chromosome lineages. However, the limited
 nature of this introgression contrasts with the major Steppe migration
 turnovers within third Millennium northern Europe and echoes the survival
 of non-Indo-European language in Iberia. Changes in genomic estimates of
 individual height across Europe are also associated with these major
 cultural transitions, and ancestral components continue to correlate with
 modern differences in stature.
description: Index for VCF
 fileIndex for VCF
 filepost_imputation_Martiniano_et_al_2017_public.vcf.gz.tbiVCF file containing imputed genotype data belonging to 67 newly sequenced and publicly available ancient samples.VCF file containing imputed genotype data belonging to 67 newly sequenced and publicly available ancient samples which we analysed in Martiniano et al. (2017).post_imputation_Martiniano_et_al_2017_public.vcf.gzREADME_Martiniano_et_al_2017Description of the methods used for genotype imputation.
DOI: 10.5061/dryad.n6068
title: Data from: Benefits and challenges with applying unique molecular identifiers in next generation sequencing to detect low frequency mutations

description: Indexing individual template molecules with a unique identifier (UID)
 before PCR and deep sequencing is promising for detecting low frequency
 mutations, as true mutations could be distinguished from PCR errors or
 sequencing errors based on consensus among reads sharing same index. In an
 effort to develop a robust assay to detect from urine low-abundant bladder
 cancer cells carrying well-documented mutations, we have tested the idea
 first on a set of mock templates, with wild type and known mutants mixed
 at defined ratios. We have measured the combined error rate for PCR and
 Illumina sequencing at each nucleotide position of three exons, and
 demonstrated the power of a UID in distinguishing and correcting errors.
 In addition, we have demonstrated that PCR sampling bias, rather than PCR
 errors, challenges the UID-deep sequencing method in faithfully detecting
 low frequency mutation.
description: 7Mix_E7
 (3)3rd part of the 7Mix_E7
 fastq data7mixac7Mix_E7 (1)1st part of 7Mix_E7 fastq data7mixaa7Mix E7 (2)2nd part of 7Mix_E7 fastq data7mixab7Mix_E7 (4)4th part of 7Mix_E7 fastq data7mixadREADME_plosone
DOI: 10.5061/dryad.p1r02
title: Data from: Host genotype is an important determinant of the cereal phyllosphere mycobiome

description: The phyllosphere mycobiome in cereals is an important determinant of crop
 health. However, an understanding of the factors shaping this community is
 lacking. Fungal diversity in leaves from a range of cultivars of winter
 wheat (Triticum aestivum), winter and spring barley (Hordeum vulgare) and
 a smaller number of samples from oat (Avena sativa), rye (Secale cereale)
 and triticale (Triticum × Secale) was studied using next-generation
 sequencing. The effects of host genotype, fungicide treatment and location
 on fungal communities were explored. In total, 635 251 fungal internal
 transcribed spacer (ITS) reads were obtained from 210 leaf samples. Visual
 disease assessments and relative read abundance of Zymoseptoria tritici
 and Ramularia collo-cygni were strongly positively related. Crop genotype
 at the species level explained 43% of the variance in the total dataset,
 followed by fungicide treatment (13%) and location (4%). Indicator
 species, including plant pathogens, responding to factors such as crop
 species, location and treatment were identified. Host genotype at both the
 species and cultivar level is important in shaping phyllosphere fungal
 communities, whereas fungicide treatment and location have minor effects.
 We found many host-specific fungal pathogens, but also a large diversity
 of fungi that were relatively insensitive to host genetic background,
 indicating that host-specific pathogens live in a ‘sea’ of nonspecific
 fungi.
description: Winter barley
 01.sff file containing raw
 data from a 454 sequencing run. Fungal ITS reads from winter
 barleyW_barley_01.sffWheat 02sff file containing raw data from a 454 sequencing run. Fungal ITS reads from wheatWheat_02.sffSpring barley 03.sff file containing raw data from a 454 sequencing run. Fungal ITS reads from spring barleyS_barley_03.sffWinter barley 04.sff file containing raw data from a 454 sequencing run. Fungal ITS reads from winter barleyW_barley_04.sffWheat 05.sff file containing raw data from a 454 sequencing run. Fungal ITS reads from wheatWheat_05.sffSpring barley 06.sff file containing raw data from a 454 sequencing run. Fungal ITS reads from spring barleyS_barley_06.sffOat, wheat and triticale 07.sff file containing raw data from a 454 sequencing run. Fungal ITS reads from oat, rye and triticaleOBS_07.sffMapping fileMapping file including metadataTable S2.txt
DOI: 10.5061/dryad.kk40s
title: Data from: Breakdown of local information processing may underlie isoflurane anesthesia effects

description: The disruption of coupling between brain areas has been suggested as the
 mechanism underlying loss of consciousness in anesthesia. This hypothesis
 has been tested previously by measuring the information transfer between
 brain areas, and by taking reduced information transfer as a proxy for
 decoupling. Yet, information transfer is a function of the amount of
 information available in the information source—such that transfer
 decreases even for unchanged coupling when less source information is
 available. Therefore, we reconsidered past interpretations of reduced
 information transfer as a sign of decoupling, and asked whether impaired
 local information processing leads to a loss of information transfer. An
 important prediction of this alternative hypothesis is that changes in
 locally available information (signal entropy) should be at least as
 pronounced as changes in information transfer. We tested this prediction
 by recording local field potentials in two ferrets after administration of
 isoflurane in concentrations of 0.0%, 0.5%, and 1.0%. We found strong
 decreases in the source entropy under isoflurane in area V1 and the
 prefrontal cortex (PFC)—as predicted by our alternative hypothesis. The
 decrease in source entropy was stronger in PFC compared to V1. Information
 transfer between V1 and PFC was reduced bidirectionally, but with a
 stronger decrease from PFC to V1. This links the stronger decrease in
 information transfer to the stronger decrease in source entropy—suggesting
 reduced source entropy reduces information transfer. This conclusion fits
 the observation that the synaptic targets of isoflurane are located in
 local cortical circuits rather than on the synapses formed by interareal
 axonal projections. Thus, changes in information transfer under isoflurane
 seem to be a consequence of changes in local processing more than of
 decoupling between brain areas. We suggest that source entropy changes
 must be considered whenever interpreting changes in information transfer
 as decoupling.
description: Simultaneous local field
 potential recordings in prefrontal and primary visual area of the ferret
 cortex (animal 1)Simultaneous local field
 potential recordings in prefrontal and primary visual areas of the ferret
 cortex (animal 1) in the awake state and after administration of
 isoflurane in concentrations of 0.5 % and 1.0 %.lfp_raw_data_animal_1.zipSimultaneous local field potential recordings in prefrontal and primary visual area of the ferret cortex (animal 2)Simultaneous local field potential recordings in prefrontal and primary visual areas of the ferret cortex (animal 2) in the awake state and after administration of isoflurane in concentrations of 0.5 % and 1.0 %.lfp_raw_data_animal_2.zip
DOI: 10.5061/dryad.jv42j
title: Data from: A quantitative theory of gamma synchronization in macaque V1

description: Gamma-band synchronization coordinates brief periods of excitability in
 oscillating neuronal populations to optimize information transmission
 during sensation and cognition. Commonly, a stable, shared frequency over
 time is considered a condition for functional neural synchronization.
 Here, we demonstrate the opposite: instantaneous frequency modulations are
 critical to regulate phase relations and synchronization. In monkey visual
 area V1, nearby local populations driven by different visual stimulation
 showed different gamma frequencies. When similar enough, these frequencies
 continually attracted and repulsed each other, which enabled preferred
 phase relations to be maintained in periods of minimized frequency
 difference. Crucially, the precise dynamics of frequencies and phases
 across a wide range of stimulus conditions was predicted from a physics
 theory that describes how weakly coupled oscillators influence each
 other’s phase relations. Hence, the fundamental mathematical principle of
 synchronization through instantaneous frequency modulations applies to
 gamma in V1, and is likely generalizable to other brain regions and
 rhythms.
description: M1_session_1Contains current-source density (CSD) signals from 3X 16-contact laminar probes inserted in macaque cortical area V1. Horizontal and vertical eye positions are added. Each trial consists of 1 sec baseline (gray screen while monkey is looking on fixation point) and 2sec stimulation period (square-wave grating with spatially varying contrast; monkey remains fixating). Information about the receptive field positions as well as seen local stimulus contrast for each probe is added to the data structure.M1_session_2M1_session_3M1_session_4M1_session_5M1_session_6M2_session_1M1_session_7M2_session_2M2_session_3M2_session_4M2_session_5M2_session_6coupled_oscillators_elifeMatlab code to simulate coupled phase oscillators. With this code the effects of detuning and coupling are illustrated.coupled_PING_elifeMatlab simulation code of two coupled pyramidal-interneuron gamma networks (PING). It is based on the izhikevich-type neuronal model. With this code the effect of detuning (shifting preferred frequency by increasing input current) and coupling on their phase dynamics are illustrated.Please_read_this
DOI: 10.5061/dryad.48t6710
title: Data from: Limited dietary overlap amongst resident Arctic herbivores in winter - complementary insights from complementary methods

description: Snow may prevent Arctic herbivores from accessing their forage in winter,
 forcing them to aggregate in the few patches with limited snow. In High
 Arctic Greenland, Arctic hare and rock ptarmigan often forage in muskox
 feeding craters. We therefore hypothesized that due to limited
 availability of forage, the dietary niches of these resident herbivores
 overlap considerably, and that the overlap increases as winter progresses.
 To test this, we analyzed fecal samples collected in early and late
 winter. We used molecular analysis to identify the plant taxa consumed,
 and stable isotope ratios of carbon and nitrogen to quantify the dietary
 niche breadth and dietary overlap. The plant taxa found indicated only
 limited dietary differentiation between the herbivores. As expected,
 dietary niches exhibited a strong contraction from early to late winter,
 especially for rock ptarmigan. This may indicate increasing reliance on
 particular plant resources as winter progresses. In early winter, the diet
 of rock ptarmigan overlapped slightly with that of muskox and Arctic hare.
 Contrary to our expectations, no inter-specific dietary niche overlap was
 observed in late winter. This overall pattern was specifically revealed by
 combined analysis of molecular data and stable isotope contents. Hence,
 despite foraging in the same areas and generally feeding on the same plant
 taxa, the quantitative dietary overlap between the three herbivores was
 limited. This may be attributable to species-specific consumption rates of
 plant taxa. Yet, Arctic hare and rock ptarmigan may benefit from muskox
 opening up the snow pack, thereby allowing them to access the plants.
description: ZOTUsDenoised,
 chimera-filtered, and clustered ZOTUs from the sequence
 data.ZOTUtabsZOTUtab linking ZOTUs to samples (and replicates).Raw Fastq filesRaw fastq files from the first (primers pairs ch, gh, and ITS; all samples pooled and then index-tagged) and second run (primer pairs ch and gh, all reactions and replicates tagged individually) for the study. The file names refer to the sample and replicate as follows: HA=Arctic hare, PT=ptarmigan, MX=muskox; A=replicate 1; B=replicate 2; E=efterår (late winter); and F=förår (early winter)Raw_Fastq_files.tar.gz
DOI: 10.5061/dryad.qd300cb
title: Data from: Differential effect of selection against LINE retrotransposons among vertebrates inferred from whole-genome data and demographic modeling

description: Variation in LINE composition is one of the major determinants for the
 substantial size and structural differences among vertebrate genomes. In
 particular, the larger genomes of mammals are characterized by hundreds of
 thousands of copies from a single LINE clade, L1, whereas nonmammalian
 vertebrates possess a much greater diversity of LINEs, yet with orders of
 magnitude less in copy number. It has been proposed that such variation in
 copy number among vertebrates is due to differential effect of LINE
 insertions on host fitness. To investigate LINE selection, we deployed a
 framework of demographic modeling, coalescent simulations, and
 probabilistic inference against population-level whole-genome data sets
 for four model species: one population each of threespine stickleback,
 green anole, and house mouse, as well as three human populations.
 Specifically, we inferred a null demographic background utilizing SNP
 data, which was then exploited to simulate a putative null distribution of
 summary statistics that was compared with LINE data. Subsequently,we
 applied the inferred null demographic model with an additional exponential
 size change parameter, coupled with model selection, to test for
 neutrality as well as estimate the strength of either negative or positive
 selection. We found a robust signal for purifying selection in anole and
 mouse, but a lack of clear evidence for selection in stickleback and
 human. Overall, we demonstrated LINE insertion dynamics that are not in
 accordance to a mammalian versus nonmammalian dichotomy, and instead the
 degree of existing LINE activity together with host-specific demographic
 history may be the main determinants of LINE abundance.
description: Scripts, results, and
 LINE VCFsNote: Filenames
 containing "PositiveSelection" actually refer to negative
 selection experiments, and likewise, filenames containing only
 "Selection" actually refer to positive selection experiments,
 due to an initial naming confusion earlier in the
 project.Anatomically_Modern_Human.tarCarolina_Anole_House_Mouse_Threespine_SticklebackNote: Filenames containing "PositiveSelection" actually refer to negative selection experiments, and likewise, filenames containing only "Selection" actually refer to positive selection experiments, due to an initial naming confusion earlier in the project.
DOI: 10.5061/dryad.7b8vb
title: Data from: Sequence entropy of folding and the absolute rate of amino acid substitutions

description: Adequate representations of protein evolution should consider how the
 acceptance of mutations depends on the sequence context in which they
 arise. However, epistatic interactions among sites in a protein result in
 hererogeneities in the substitution rate, both temporal and spatial, that
 are beyond the capabilities of current models. Here we use parallels
 between amino acid substitutions and chemical reaction kinetics to develop
 an improved theory of protein evolution. We constructed a mechanistic
 framework for modelling amino acid substitution rates that uses the
 formalisms of statistical mechanics, with principles of population
 genetics underlying the analysis. Theoretical analyses and computer
 simulations of proteins under purifying selection for thermodynamic
 stability show that substitution rates and the stabilization of resident
 amino acids (the ‘evolutionary Stokes shift’) can be predicted from
 biophysics and the effect of sequence entropy alone. Furthermore, we
 demonstrate that substitutions predominantly occur when epistatic
 interactions result in near neutrality; substitution rates are determined
 by how often epistasis results in such nearly neutral conditions. This
 theory provides a general framework for modelling protein sequence change
 under purifying selection, potentially explains patterns of convergence
 and mutation rates in real proteins that are incompatible with previous
 models, and provides a better null model for the detection of adaptive
 changes.
description: Simulation results: Ne =
 1.0E6Results of evolutionary
 simulations for Ne = 1.0E6NE1E6.tarSimulation results: Ne = 1.0E4Results of evolutionary simulations for Ne = 1.0E4NE1E4.tarSimulation results: Ne = 1.0E8Results of evolutionary simulations for Ne = 1.0E8NE1E8.tarSimulation results (null amino acid): Ne = 1.0E4Results of evolutionary simulations for Ne = 1.0E4: One residue is fixed to be a non-interacting 'null' residue 'X'. Identity of fixed residue indicated by number at end of file name. (zero based numbering)NE1E4_null.tarReadMe fileDescription of data filesSimulation results (null amino acid): Ne = 1.0E6Results of evolutionary simulations for Ne = 1.0E6: One residue is fixed to be a non-interacting 'null' residue 'X'. Identity of fixed residue indicated by number at end of file name. (zero based numbering)NE1E6_null.tarSimulation results (null amino acid): Ne = 1.0E8Results of evolutionary simulations for Ne = 1.0E8: One residue is fixed to be a non-interacting 'null' residue 'X'. Identity of fixed residue indicated by number at end of file name. (zero based numbering)NE1E8_null.tar
DOI: 10.5061/dryad.c0g0p
title: Data from: Output variability across animals and levels in a motor system

description: Rhythmic behaviors vary across individuals. We investigated the sources of
 this output variability across a motor system, from the central pattern
 generator (CPG) to the motor plant. In the bilaterally symmetric leech
 heartbeat system, the CPG orchestrates two coordinations in the bilateral
 hearts with different intersegmental phase relations (Δφ) and periodic
 side-to-side switches. Population variability is large. We show that the
 system is precise within a coordination, that differences in repetitions
 of a coordination contribute little to population output variability, but
 that differences between bilaterally homologous cells may contribute to
 some of this variability. Nevertheless, much output variability is likely
 associated with genetic and life history differences among individuals.
 Variability of Δφ were coordination-specific: similar at all levels in
 one, but significantly lower for the motor pattern than the CPG pattern in
 the other. Mechanisms that transform CPG output to motor neurons may limit
 output variability in the motor pattern.
description: Heart_OpticalSignalProcessingFolder contains for each movie its digitized optical signals and the code to analyze them, each in a separate folder.HeartAnalysis_VideoProcessingDummyData file contains 13 movies and the code to analyze them.HeartAnalysis_VideoProcessing.zipCPGtoMotorPattern_synapticsElectrophysiologcal recordings to determine the synaptic strength between interneurons and motor neuronsCPG&MotorPattern_data&codetxtExtracellular recordings from interneurons and motor neurons to determine burst and phase characteristics.CPG&MotorPattern_data&code.7zVariances; data sourceMatlab code and *txt files to calculate the cycle-to-cycle variances, the population variances, the repetition variances, and the bilateral variances as well as the code for bootstrapping and scramblingVariances.zip