cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8857436.v1
title: Additional file 6: of Paired-end mappability of transposable elements in the human genome

description: Table S2. Ancient TE families with unusually low mappability and accompanying segmental duplications. This table enumerates a number of ancient TE families which have unusually low mappability scores. Though some of these scores can be accounted for by recent segmental duplications, there still remains a substantial portion of older elements with low mappability scores that could be furthered explored. (XLSX 5 kb)
DOI: 10.6084/m9.figshare.8857430.v1
title: Additional file 5: of Paired-end mappability of transposable elements in the human genome

description: Table S1. TE class and family mappability scores. Percent of elements in each TE class and family with completely unique mappability scores based on Bowtie alignment of 76â bp simulated reads allowing for 3 mismatches. (XLSX 8 kb)
DOI: 10.6084/m9.figshare.8857193
title: MOESM7 of Studies of a rice sterile mutant sstl from the TRIM collection

description: Additional file 7: Table S4. Prediction of gene function in RNA-seq heat-map analysis result.
DOI: 10.6084/m9.figshare.8857193.v1
title: MOESM7 of Studies of a rice sterile mutant sstl from the TRIM collection

description: Additional file 7: Table S4. Prediction of gene function in RNA-seq heat-map analysis result.
DOI: 10.6084/m9.figshare.8857157
title: MOESM1 of Studies of a rice sterile mutant sstl from the TRIM collection

description: Additional file 1: Table S1. Primers list.
DOI: 10.6084/m9.figshare.8857157.v1
title: MOESM1 of Studies of a rice sterile mutant sstl from the TRIM collection

description: Additional file 1: Table S1. Primers list.
DOI: 10.6084/m9.figshare.12869894
title: WB and Pulse Chase Quantification for PNAS Manuscript.xlsx

description: Raw data including all western blots and radioactive pulse chase experiments for our PNAS manuscript are presented in this Excel document.
DOI: 10.6084/m9.figshare.12869894.v1
title: WB and Pulse Chase Quantification for PNAS Manuscript.xlsx

description: Raw data including all western blots and radioactive pulse chase experiments for our PNAS manuscript are presented in this Excel document.
DOI: 10.6084/m9.figshare.8856974
title: Dataset

description: The materials provide the raw data generate for publication '<b>"novel analytical platform for </b><b>robust identification of cell migration inhibitors"</b><b></b><b></b>
DOI: 10.6084/m9.figshare.8856974.v1
title: Dataset for Figure 1B-E

description: The materials provide the raw data generate for publication '<b>"novel analytical platform for </b><b>robust identification of cell migration inhibitors"</b><b></b><b></b>
DOI: 10.6084/m9.figshare.8856974.v2
title: Dataset for Fig. 1

description: The materials provide the raw data generate for publication '<b>"novel analytical platform for </b><b>robust identification of cell migration inhibitors"</b><b></b><b></b>
DOI: 10.6084/m9.figshare.8856890
title: Influence of groundwater table fluctuation on the transport of volatile organic contaminants in the vadose zone

description: The data included all the information about the unpublished paper about the influence of groundwater table fluctuation on the transport of VOCs in the underground environment.
DOI: 10.6084/m9.figshare.8856974.v3
title: Dataset

description: The materials provide the raw data generate for publication '<b>"novel analytical platform for </b><b>robust identification of cell migration inhibitors"</b><b></b><b></b>
DOI: 10.6084/m9.figshare.8856890.v1
title: Influence of groundwater table fluctuation on the transport of volatile organic contaminants in the vadose zone

description: The data included all the information about the unpublished paper about the influence of groundwater table fluctuation on the transport of VOCs in the underground environment.
DOI: 10.6084/m9.figshare.8856974.v4
title: Dataset

description: The materials provide the raw data generate for publication '<b>"novel analytical platform for </b><b>robust identification of cell migration inhibitors"</b><b></b><b></b>
DOI: 10.6084/m9.figshare.8856974.v5
title: Dataset

description: The materials provide the raw data generate for publication '<b>"novel analytical platform for </b><b>robust identification of cell migration inhibitors"</b><b></b><b></b>
DOI: 10.6084/m9.figshare.8856698
title: different coat color sheep skin

description: Transcriptome results of different coat of sheep skin
DOI: 10.6084/m9.figshare.8856698.v1
title: different coat color sheep skin

description: Transcriptome results of different coat of sheep skin
DOI: 10.6084/m9.figshare.8856641
title: dN/dS analysis on substitution in CenAsiaIII Shigella sonnei

description: For the 395 CenAsiaIII sequences, substitutions across the reference Ss046 were summarized and annotated using SnpEff v4.1b. Point mutations present within mobile, repetitive, or recombination elements were excluded, resulting in a set of 4,230 mutations available for examination. Due to the limited temporal sampling period, we assessed the dN/dS ratio (non-synonymous to synonymous substitution rate) to detect potential signals of selection, adopted from a previously recommended approach. In brief, a phylogenetic tree was constructed using these 4,230 SNPs in RAxML v8.1.3, and PAML was used for ancestral state reconstruction of all SNPs. Mutations were classified as intergenic, synonymous, or non-synonymous based on comparison of each SNP to its annotation and the reconstructed ancestral state. The dN/dS rate was adjusted for transition/transversion rate and codon frequencies under the NY98 model. Genes were determined to be under positive selection if their adjusted dN/dS ratio were &gt;1.5 or if they possessed no synonymous and at least five non-synonymous mutations.
DOI: 10.6084/m9.figshare.8856638
title: Stochastic mapping of geographical trait for phylogeography inference

description: The reference-based maximum likelihood phylogeny of 395 CenAsiaIII S. sonnei served as an input for reconstructing the ancestral geographical states of each isolate, as adopted from a recently described approach. We treated geographical source (sub-continental level) of the organisms as discrete characters. Due to biased sampling toward South Asia, we sub-sampled the phylogeny to include equal numbers of isolates from each character state (i.e. geographical region; n=13 from South Asia, Africa, Europe, and combined Southeast Asia/East Asia), generating 1,000 subsampled trees. Regions with fewer than 13 isolates (i.e. Middle East and America) were excluded. We utilized stochastic mapping to quantify transition events between geographical characters as well as the total time spent within each character state, separately for each subsampled tree. Stochastic mapping, implemented as the function make.simmap in the R package phytools v0.6.0, was performed under an asymmetric model of character change (ARD) with the rate matrix sampled from the posterior probability distribution using MCMC (Q=mcmc) for 100 simulations. To ensure that resultant phylogeographical signal was not an artefact due to over-sampling in South Asia, we permuted (without replacement) the tip-location of the original maximum likelihood phylogeny, generating ten independent randomization sets. We repeated stochastic mapping analysis for each randomization as detailed above, using only 500 subsampled trees from each randomization to reduce computational expense. Results from the ‘true’ and ‘randomization’ runs were compared by analysis of variance (ANOVA) with post-hoc Tukey test.
DOI: 10.6084/m9.figshare.8856641.v1
title: dN/dS analysis on substitution in CenAsiaIII Shigella sonnei

description: For the 395 CenAsiaIII sequences, substitutions across the reference Ss046 were summarized and annotated using SnpEff v4.1b. Point mutations present within mobile, repetitive, or recombination elements were excluded, resulting in a set of 4,230 mutations available for examination. Due to the limited temporal sampling period, we assessed the dN/dS ratio (non-synonymous to synonymous substitution rate) to detect potential signals of selection, adopted from a previously recommended approach. In brief, a phylogenetic tree was constructed using these 4,230 SNPs in RAxML v8.1.3, and PAML was used for ancestral state reconstruction of all SNPs. Mutations were classified as intergenic, synonymous, or non-synonymous based on comparison of each SNP to its annotation and the reconstructed ancestral state. The dN/dS rate was adjusted for transition/transversion rate and codon frequencies under the NY98 model. Genes were determined to be under positive selection if their adjusted dN/dS ratio were &gt;1.5 or if they possessed no synonymous and at least five non-synonymous mutations.
DOI: 10.6084/m9.figshare.8856638.v1
title: Stochastic mapping of geographical trait for phylogeography inference

description: The reference-based maximum likelihood phylogeny of 395 CenAsiaIII S. sonnei served as an input for reconstructing the ancestral geographical states of each isolate, as adopted from a recently described approach. We treated geographical source (sub-continental level) of the organisms as discrete characters. Due to biased sampling toward South Asia, we sub-sampled the phylogeny to include equal numbers of isolates from each character state (i.e. geographical region; n=13 from South Asia, Africa, Europe, and combined Southeast Asia/East Asia), generating 1,000 subsampled trees. Regions with fewer than 13 isolates (i.e. Middle East and America) were excluded. We utilized stochastic mapping to quantify transition events between geographical characters as well as the total time spent within each character state, separately for each subsampled tree. Stochastic mapping, implemented as the function make.simmap in the R package phytools v0.6.0, was performed under an asymmetric model of character change (ARD) with the rate matrix sampled from the posterior probability distribution using MCMC (Q=mcmc) for 100 simulations. To ensure that resultant phylogeographical signal was not an artefact due to over-sampling in South Asia, we permuted (without replacement) the tip-location of the original maximum likelihood phylogeny, generating ten independent randomization sets. We repeated stochastic mapping analysis for each randomization as detailed above, using only 500 subsampled trees from each randomization to reduce computational expense. Results from the ‘true’ and ‘randomization’ runs were compared by analysis of variance (ANOVA) with post-hoc Tukey test.
DOI: 10.6084/m9.figshare.8856539
title: Bayesian phylogenetic inference of CenAsiaIII Shigella sonnei

description: Bayesian phylogenetic inference of 144 CenAsiaIII S. sonnei. The samples include 72 from each hierBAPS determined population (Pop1 and Pop2). The best model used in this BEAST analysis is a combination of a strict molecular clock with a piecewise Bayesian skyline demographic model.
DOI: 10.6084/m9.figshare.8856539.v1
title: Bayesian phylogenetic inference of CenAsiaIII Shigella sonnei

description: Bayesian phylogenetic inference of 144 CenAsiaIII S. sonnei. The samples include 72 from each hierBAPS determined population (Pop1 and Pop2). The best model used in this BEAST analysis is a combination of a strict molecular clock with a piecewise Bayesian skyline demographic model.
DOI: 10.6084/m9.figshare.8856512
title: Maximum likelihood phylogeny of 395 CenAsiaIII Shigella sonnei

description: A newick format of the maximum likelihood phylogeny of CenAsiaIII S. sonnei, generated by RAxML. Details are described in the paper.
DOI: 10.6084/m9.figshare.8856371
title: CCDB_8063.jpg

description: Processed mosaic of a sagittal section through the brain of mouse model of glioma. To produce transformed cells, creGFAP mice were injected in the cortex with Ras/s.i.p53 virus and perfused after 5 weeks. In this system, GFP is introduced by the virus and expression is induced by an IRES site in the mRNA. Thus, the GFP gene is expressed whenever the virus infects a cell expressing GFAP (green). The section was immunolabeled for nestin (red) and counterstained with DAPI (blue). See MP:7857 for a section from the same brain labeled with GFAP.
DOI: 10.6084/m9.figshare.8856371.v1
title: CCDB_8063.jpg

description: Processed mosaic of a sagittal section through the brain of mouse model of glioma. To produce transformed cells, creGFAP mice were injected in the cortex with Ras/s.i.p53 virus and perfused after 5 weeks. In this system, GFP is introduced by the virus and expression is induced by an IRES site in the mRNA. Thus, the GFP gene is expressed whenever the virus infects a cell expressing GFAP (green). The section was immunolabeled for nestin (red) and counterstained with DAPI (blue). See MP:7857 for a section from the same brain labeled with GFAP.
DOI: 10.6084/m9.figshare.8856368
title: microDamID raw read data

description: Illumina MiniSeq sequencing data from DNA amplified by DamID on a microfluidic device by Altemose et al. 2019 (microDamID). Data are from 18 individual HEK293T cells transiently transfected with m6A-Tracer and Dam or Dam-LMNB1. NA001-015 are Dam-LMNB1 expressing cells. NA016-018 are Dam-only expressing cells. Imaging data for each cell are available in a separate folder.
DOI: 10.6084/m9.figshare.8856368.v1
title: microDamID raw read data

description: Illumina MiniSeq sequencing data from DNA amplified by DamID on a microfluidic device by Altemose et al. 2019 (microDamID). Data are from 18 individual HEK293T cells transiently transfected with m6A-Tracer and Dam or Dam-LMNB1. NA001-015 are Dam-LMNB1 expressing cells. NA016-018 are Dam-only expressing cells. Imaging data for each cell are available in a separate folder.
DOI: 10.6084/m9.figshare.8856161
title: Data and code for: Range of motion in the avian wing is strongly associated with flight behavior and body mass

description: Data and code for:<br>Baliga VB, Szabo I, and Altshuler DL. 2019. Range of motion in the avian wing is strongly associated with flight behavior and body mass. <em>Science Advances. </em>5, eaaw6670. doi:10.1126/sciadv.aaw6670
DOI: 10.6084/m9.figshare.8856092
title: Bphy SNPs 2011_05_26.csv

description: Spreadsheet of 23 SNPs from 159 fin whale (Balaenoptera physalus) samples. Data used in<br>Archer et al. 2019. Revision of fin whale Balaenoptera physalus (Linnaeus, 1758) subspecies using genetics. Journal of Mammalogy
DOI: 10.6084/m9.figshare.8856161.v1
title: Data and code for: Range of motion in the avian wing is strongly associated with flight behavior and body mass

description: Data and code for manuscript entitled "Range of motion in the avian wing is strongly associated with flight behavior and body mass"
DOI: 10.6084/m9.figshare.8856161.v2
title: Data and code for: Range of motion in the avian wing is strongly associated with flight behavior and body mass

description: Data and code for manuscript entitled "Range of motion in the avian wing is strongly associated with flight behavior and body mass"
DOI: 10.6084/m9.figshare.8855795
title: Reproducible results for: Releasing a preprint is associated with more attention and citations for the peer-reviewed article

description: Zip file contains scripts, parameters, data, and results. API keys for Entrez, Altmetric, and CrossRef are not included.<br>In accordance with Altmetric's data use agreement, the raw data from Altmetric and the Attention Score for each article are not included. These data can be obtained by running the code after acquiring an API key from Altmetric. Files from which the Attention Score have been removed have a suffix of "_edit".<br>Citation counts come from CrossRef, all other article metadata come from PubMed.
DOI: 10.6084/m9.figshare.8855750
title: Fast and selective organocatalytic ring-opening polymerization by fluorinated alcohol without a cocatalystm

description: source data for -"Fast and selective organocatalytic ring-opening polymerization by fluorinated alcohol without a cocatalyst"The source data for Figures 3-6 and Supplementary Figures 2-10, 12-22 and 24-26<br>
DOI: 10.6084/m9.figshare.8855681
title: Taxonomy of New Zealand plant species within 100 km of soil sampling sites

description: All records were derived from the New Zealand National Vegetation Survey databank (https://landcareresearch.co.nz/) and were accessed from the Global Biodiversity Information Facility (https://www.bgif.org/) in December 2018. Only plant species from vegetation plots surveyed after 1960 and within 100 km of the soil sampling sites are provided in this tab-delimited taxonomy file.<br>
DOI: 10.6084/m9.figshare.8855795.v1
title: Reproducible results for: Releasing a preprint is associated with more attention and citations

description: Zip file contains scripts, parameters, data, and results. API keys for Entrez, Altmetric, and CrossRef are not included.<br>In accordance with Altmetric's data use agreement, the raw data from Altmetric and the Attention Score for each article are not included. These data can be obtained by running the code after acquiring an API key from Altmetric.<br>Citation counts come from CrossRef, all other article metadata come from PubMed.
DOI: 10.6084/m9.figshare.8855681.v1
title: Taxonomy of New Zealand plant species within 100 km of soil sampling sites

description: All records were derived from the New Zealand National Vegetation Survey databank (https://landcareresearch.co.nz/) and were accessed from the Global Biodiversity Information Facility (https://www.bgif.org/) in December 2018. Only plant species from vegetation plots surveyed after 1960 and within 100 km of the soil sampling sites are provided in this tab-delimited taxonomy file.<br>
DOI: 10.6084/m9.figshare.8855657
title: New Zealand plant species data within 100 km of sites

description: All records were derived from the New Zealand National Vegetation Survey databank (https://landcareresearch.co.nz/) and were accessed from the Global Biodiversity Information Facility (https://www.bgif.org/) in December 2018. Only species presence/absence data from vegetation plots surveyed after 1960 and within 100 km of the soil sampling sites are present in this csv file.<br>
DOI: 10.6084/m9.figshare.8855795.v2
title: Reproducible results for: Releasing a preprint is associated with more attention and citations for the peer-reviewed article

description: Zip file contains scripts, parameters, data, and results. API keys for Entrez, Altmetric, and CrossRef are not included.<br>In accordance with Altmetric's data use agreement, the raw data from Altmetric and the Attention Score for each article are not included. These data can be obtained by running the code after acquiring an API key from Altmetric. Files from which the Attention Score have been removed have a suffix of "_edit".<br>Citation counts come from CrossRef, all other article metadata come from PubMed.
DOI: 10.6084/m9.figshare.8855657.v1
title: New Zealand plant species data within 100 km of sites

description: All records were derived from the New Zealand National Vegetation Survey databank (https://landcareresearch.co.nz/) and were accessed from the Global Biodiversity Information Facility (https://www.bgif.org/) in December 2018. Only species presence/absence data from vegetation plots surveyed after 1960 and within 100 km of the soil sampling sites are present in this csv file.<br>
DOI: 10.6084/m9.figshare.8855585
title: New Zealand plant species presence/absence OTU table

description: A presence/absence OTU table of plant species recorded within 100 km of 15 sites located in New Zealand. All records were derived from the New Zealand National Vegetation Survey databank (https://landcareresearch.co.nz/) and were accessed from the Global Biodiversity Information Facility (https://www.bgif.org/) in December 2018. Only species presence/absence data from vegetation plots surveyed after 1960 and within 100 km of the soil sampling sites were included to generate the OTU table. To control for sampling effort among sites, data were rarefied to the minimum number of observations (9,790) per site and resampling with replacement 999 times.<br>
DOI: 10.6084/m9.figshare.8854352
title: Raw voltage and current traces for current-voltage (IV) relationships for cochlear nucleus neurons.

description: Whole-cell tight seal current-clamp recordings from neurons in brain slices of mouse cochlear nucleus. These data are the responses to series of current steps (100 and 500 ms in duration), used to derive measures of intrinsic excitability, including input resistance, resting membrane potential, time constants, spike shape parameters, coefficient of variation of spike rate, and adaptation. The data were analyzed using the package ephysanalysis (https://github.com/pbmanis/ephysanalysis). The raw data here are in NWB format(https://neurodatawithoutborders.github.io/pynwb), and have been extracted from the main dataset.<br>Additional files include the extracted parameters (pickled Pandas database), and Python source files used for the analysis. <br>See README.md for more details.<br>Source file CN_LDA.py updated, 9/4/2019. Minor edits to remove unused statements and update docstrings; no change in results.<br>Preprint: bioRxiv 594713; doi: https://doi.org/10.1101/594713<br><br>
DOI: 10.6084/m9.figshare.8855585.v1
title: New Zealand plant species presence/absence OTU table

description: A presence/absence OTU table of plant species recorded within 100 km of 15 sites located in New Zealand. All records were derived from the New Zealand National Vegetation Survey databank (https://landcareresearch.co.nz/) and were accessed from the Global Biodiversity Information Facility (https://www.bgif.org/) in December 2018. Only species presence/absence data from vegetation plots surveyed after 1960 and within 100 km of the soil sampling sites were included to generate the OTU table. To control for sampling effort among sites, data were rarefied to the minimum number of observations (9,790) per site and resampling with replacement 999 times.<br>
DOI: 10.6084/m9.figshare.8853764
title: JulieKim06 Differential Expression.xlsx

description: RNA-seq data comparing treatment of normal follicular phase estradiol and testosterone to PCOS levels of estradiol and testosterone for 14 days on endometrial organoids in vitro.
DOI: 10.6084/m9.figshare.8854352.v1
title: Raw voltage and current traces for current-voltage (IV) relationships for cochlear nucleus neurons.

description: Whole-cell tight seal current-clamp recordings from neurons in brain slices of mouse cochlear nucleus. These data are the responses to series of current steps (100 and 500 ms in duration), used to derive measures of intrinsic excitability, including input resistance, resting membrane potential, time constants, spike shape parameters, coefficient of variation of spike rate, and adaptation. The data were analyzed using the package ephysanalysis (https://github.com/pbmanis/ephysanalysis). The raw data here are in NWB format(https://neurodatawithoutborders.github.io/pynwb), and have been extracted from the main dataset.<br>Additional files include the extracted parameters (pickled Pandas database), and Python source files used for the analysis. <br>See README.md for more details.<br>Source file CN_LDA.py updated, 9/4/2019. Minor edits to remove unused statements and update docstrings; no change in results.<br>Preprint: bioRxiv 594713; doi: https://doi.org/10.1101/594713<br><br>
DOI: 10.6084/m9.figshare.8852351
title: Cadmium-induced hypertension is associated with renal myosin light chain phosphatase inhibition at Thr697 and p44 mitogen-activated protein kinase elevation

description: The data provide blood pressures of Sprague-Dawley rats, taken from the tail vein using a non-invasive CODA machine. Rats received cadmium and/or potassium and were compared to a control group.
DOI: 10.6084/m9.figshare.8852354
title: Supp materials final.docx

description: Supplemental information for Sorrentino et al final version<br>