cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.c.3643076_d1
title: Additional file 3: of Genome-wide analysis of the transcriptional response to porcine reproductive and respiratory syndrome virus infection at the maternal/fetal interface and in the fetus

description: Gene function enrichment analysis results on DEG lists. Excel (.xlsx) file of three function enrichment analyses from the IPA software: biological function (BF), canonical Pathway (CP), and upstream regulator (UR), for each of the six DEG lists (18 tabs in total). (XLSX 801 kb)
DOI: 10.6084/m9.figshare.c.3643076_d2
title: Additional file 2: of Genome-wide analysis of the transcriptional response to porcine reproductive and respiratory syndrome virus infection at the maternal/fetal interface and in the fetus

description: Lists of differentially expressed genes. Excel (.xlsx) file of the differentially expressed genes (DEGs) identified by the edgeR software from the six contrasts of the transcriptomic analysis. Results for each contrast are on a separate tab (6 tabs in total). (XLSX 656 kb)
DOI: 10.6084/m9.figshare.c.3643076_d3
title: Additional file 6: of Genome-wide analysis of the transcriptional response to porcine reproductive and respiratory syndrome virus infection at the maternal/fetal interface and in the fetus

description: Gene function enrichment analysis results on WGCNA data. Excel (.xlsx) file of three function enrichment analyses from the IPA software: biological function (BF), canonical Pathway (CP), and upstream regulator (UR), for each of the modules from the six contrasts mentioned in the Results section (36 tabs in total). (XLSX 7834 kb)
DOI: 10.6084/m9.figshare.c.3643076_d4
title: Additional file 7: of Genome-wide analysis of the transcriptional response to porcine reproductive and respiratory syndrome virus infection at the maternal/fetal interface and in the fetus

description: Comparison of RNA-seq and RT-qPCR expression data for individual genes. Excel (.xlsx) file of log2 transformed fold differences, for both RNA-seq and RT-qPCR, for genes used for RT-qPCR validation of RNA-seq data from endometrium and thymus (2 tabs in total). (XLSX 37 kb)
DOI: 10.6084/m9.figshare.c.3643076_d5
title: Additional file 4: of Genome-wide analysis of the transcriptional response to porcine reproductive and respiratory syndrome virus infection at the maternal/fetal interface and in the fetus

description: WGCNA module trait correlations. Excel file (.xlsx) of the modules identified for each of the six contrasts by the WGCNA software, their correlation with the traits of interest, and the statistical significance of that correlation (6 tabs in total). (XLSX 70 kb)
DOI: 10.6084/m9.figshare.c.3643076_d7
title: Additional file 5: of Genome-wide analysis of the transcriptional response to porcine reproductive and respiratory syndrome virus infection at the maternal/fetal interface and in the fetus

description: Gene significance and module membership results. Excel file (.xlsx) of the gene significance and module membership results from the WGCNA analysis for each of the six contrasts (6 tabs in total). (XLSX 1631 kb)
DOI: 10.6084/m9.figshare.c.3643319_d6
title: MOESM2 of Evaluation of breeding strategies for polledness in dairy cattle using a newly developed simulation framework for quantitative and Mendelian traits

description: Additional file 2. AF2_QUALsim.
DOI: 10.6084/m9.figshare.c.3643322_d2
title: Additional file 2 of Design and engineering of a transmissible antiviral defense

description: Mathematica file used to generate Fig. 4d. Changes in parameters and initial densities are needed to generate the other panels.
DOI: 10.6084/m9.figshare.c.3643322_d1
title: Additional file 1 of Design and engineering of a transmissible antiviral defense

description: Original data file used to generate estimates in Table 2.
DOI: 10.6084/m9.figshare.c.3643331_d1
title: Additional file 4: of Cell wall proteome of sugarcane stems: comparison of a destructive and a non-destructive extraction method showed differences in glycoside hydrolases and peroxidases

description: Raw MS data from sugarcane culms using Method 2, biological replicate2. (XLS 1.39 MB)
DOI: 10.6084/m9.figshare.c.3643328_d1
title: Additional file 1: of Training tomorrowâ  s leaders in global health: impact of the Afya Bora Consortium Fellowship on the careers of its alumni

description: Afya Bora Alumni Impact Survey: Survey used in this assessment. (CSV 1 kb)
DOI: 10.5281/zenodo.10991872
title: Pore-Scale Investigation of MICP in Simplified Pores through Microfluidic Tests

description: This file contains all raw and binarized images used to analyze the pore filling ratios, count of crystals and size of crystals. The processed data used for producing figures also included in the Data Excel. The MATLAB script used for subimage segmentation was also included.
DOI: 10.5281/zenodo.10992955
title: Pore-Scale Investigation of MICP in Simplified Pores through Microfluidic Tests

description: This file contains all raw and binarized images and movies used to analyze the pore filling ratios, count of crystals, size of crystals, and flow fields in pore networks. The processed data used for producing figures also included in the Data Excel. The MATLAB script used for subimage segmentation was also included.
DOI: 10.5281/zenodo.14466805
title: Pore-Scale Investigation of MICP in Simplified Pores through Microfluidic Tests

description: This file contains all raw and binarized images and movies used to analyze the pore filling ratios, count of crystals, size of crystals, and flow fields in pore networks. The processed data used for producing figures also included in the Data Excel. The MATLAB script used for subimage segmentation was also included. The COMSOL models used for calculating flow field.
DOI: 10.6084/m9.figshare.c.3643331_d2
title: Additional file 6: of Cell wall proteome of sugarcane stems: comparison of a destructive and a non-destructive extraction method showed differences in glycoside hydrolases and peroxidases

description: Proteins of sugarcane young culms identified using Method 1 or 2 and predicted to be intracellular. (XLSX 21.2 kb)
DOI: 10.5281/zenodo.14213299
title: Pore-Scale Investigation of MICP in Simplified Pores through Microfluidic Tests

description: This file contains all raw and binarized images and movies used to analyze the pore filling ratios, count of crystals, size of crystals, and flow fields in pore networks. The processed data used for producing figures also included in the Data Excel. The MATLAB script used for subimage segmentation was also included.
DOI: 10.6084/m9.figshare.c.3643331_d3
title: Additional file 3: of Cell wall proteome of sugarcane stems: comparison of a destructive and a non-destructive extraction method showed differences in glycoside hydrolases and peroxidases

description: Raw MS data from sugarcane culms using Method 2, biological replicate1. (XLS 2.33 MB)
DOI: 10.6084/m9.figshare.c.3643331_d4
title: Additional file 5: of Cell wall proteome of sugarcane stems: comparison of a destructive and a non-destructive extraction method showed differences in glycoside hydrolases and peroxidases

description: CWPs identified in 2 month-old sugarcane culms. (XLSX 30.3 kb)
DOI: 10.6084/m9.figshare.c.3643331_d5
title: Additional file 7: of Cell wall proteome of sugarcane stems: comparison of a destructive and a non-destructive extraction method showed differences in glycoside hydrolases and peroxidases

description: Important features identified by Volcano plot. (XLSX 10.0 kb)
DOI: 10.6084/m9.figshare.c.3643331_d6
title: Additional file 2: of Cell wall proteome of sugarcane stems: comparison of a destructive and a non-destructive extraction method showed differences in glycoside hydrolases and peroxidases

description: Raw MS data from sugarcane culms using Method 1, biological replicate 2. (XLS 3.02 MB)
DOI: 10.6084/m9.figshare.c.3643331_d7
title: Additional file 1: of Cell wall proteome of sugarcane stems: comparison of a destructive and a non-destructive extraction method showed differences in glycoside hydrolases and peroxidases

description: Raw MS data from sugarcane culms using Method 1, biological replicate1. (XLS 2.26 MB)
DOI: 10.6084/m9.figshare.c.3643493_d17
title: Additional file 4: Table S2. of Distinct gene expression program dynamics during erythropoiesis from human induced pluripotent stem cells compared with adult and cord blood progenitors

description: Linear expression values of all genes from all HSC sources studied that exceed a threshold linear expression level of 100 in all replicates of at least one population. (CSV 17480 kb)
DOI: 10.6084/m9.figshare.c.3643502_d1
title: Additional file 3: of dupRadar: a Bioconductor package for the assessment of PCR artifacts in RNA-Seq data

description: Methods 2. Instructions to reproduce main images. (MD 4 kb)
DOI: 10.6084/m9.figshare.c.3643502_d2
title: Additional file 6: of dupRadar: a Bioconductor package for the assessment of PCR artifacts in RNA-Seq data

description: Methods 3. Simulation of datasets and differential expression. (RMD 7 kb)
DOI: 10.6084/m9.figshare.c.3643502_d3
title: Additional file 4: Table S1. of dupRadar: a Bioconductor package for the assessment of PCR artifacts in RNA-Seq data

description: Mapping statistics of the data set used to generate Fig.Â 1. (CSV 520 bytes)
DOI: 10.6084/m9.figshare.c.3643502_d6
title: Additional file 7: Table S2. of dupRadar: a Bioconductor package for the assessment of PCR artifacts in RNA-Seq data

description: Full version of TableÂ 1 from manuscript. (CSV 2183 kb)
DOI: 10.6084/m9.figshare.c.3643514_d2
title: Additional file 3: of Development of a community health inclusion index: an evaluation tool for improving inclusion of people with disabilities in community health initiatives

description: Expert Panel Results.xlsx: A database of the items kept and removed by the Expert Panel as part of the development of the CHII. (XLSX 25 kb)
DOI: 10.6084/m9.figshare.c.3643769_d1
title: Additional file 2: Figure S1. of Exploring how individuals complete the choice tasks in a discrete choice experiment: an interview study

description: Example of choice task rotavirus DCE, word document. Figure S2. Example of choice task prostate cancer-screening DCE, word document (ZIP 172 kb)
DOI: 10.6084/m9.figshare.c.3643949_d16
title: Additional file 1: of Relationships between putative G-quadruplex-forming sequences, RecQ helicases, and transcription

description: Genomic coordinates and motif features for all PQS. Reference coordinates from GRCh37 calculated using the Quadparser algorithm, and analysis of individual PQS sequence features including total length, loop lengths, number of G stacks, and base fractions of adenine, thymine, and cytosine. (ZIP 13239 kb)
DOI: 10.6084/m9.figshare.c.3643949_d17
title: Additional file 20: of Relationships between putative G-quadruplex-forming sequences, RecQ helicases, and transcription

description: R code for PQS feature analysis in BS and WS via ANOVA. Program written in R that analyses promoter-proximal PQS motif length, loop lengths, and base fraction in differentially expressed genes in BS and WS and compares the result to the genomic distribution. Takes Additional file 1 an Additional file 4 as input. (R 78 kb)
DOI: 10.6084/m9.figshare.c.3643949_d18
title: Additional file 15: of Relationships between putative G-quadruplex-forming sequences, RecQ helicases, and transcription

description: HepG2 epigenetic modeling of gene expression dataset. Expression modeling dataset used for epigenetic modeling of gene expression analysis. Each row corresponds to a TSS and contains information on positions of PQS within 2 kbp of the TSS as well as â  bestbinâ   epigenomic track signals for DNase hypersensitivity and histone modifications. This file is an output of Additional file 11 and is taken as input by Additional file 19. (CSV 4911 kb)
DOI: 10.6084/m9.figshare.c.3643949_d19
title: Additional file 6: of Relationships between putative G-quadruplex-forming sequences, RecQ helicases, and transcription

description: R code for GENCODE annotation processing protocol for epigenetic modeling of gene expression method. Program written in R for filtering low quality transcript annotations, assigning unique TSS numberings, and unique gene numberings. Takes GENCODE annotations in .gtf format as input. (R 3 kb)
DOI: 10.6084/m9.figshare.c.3643949_d21
title: Additional file 11: of Relationships between putative G-quadruplex-forming sequences, RecQ helicases, and transcription

description: R code for determining optimal pseudocount and bin for epigenetic modeling of gene expression method. Program written in R that identifies optimal pseudocount and bin for calculating correlations of epigenomic track signals with gene expression. Takes output of Additional file 10 as input. (R 5 kb)
DOI: 10.6084/m9.figshare.c.3643949_d20
title: Additional file 12: of Relationships between putative G-quadruplex-forming sequences, RecQ helicases, and transcription

description: GM12878 epigenetic modeling of gene expression dataset. Expression modeling dataset used for epigenetic modeling of gene expression analysis. Each row corresponds to a TSS and contains information on positions of PQS within 2 kbp of the TSS as well as â  bestbinâ   epigenomic track signals for DNase hypersensitivity and histone modifications. This file is an output of Additional file 11 and is taken as input by Additional file 19. (CSV 2493 kb)
DOI: 10.6084/m9.figshare.c.3643949_d23
title: Additional file 5: of Relationships between putative G-quadruplex-forming sequences, RecQ helicases, and transcription

description: R code for PQS abundance analysis in BS and WS differentially-expressed genes. Program written in R for analyzing differences in PQS abundance between BS/WS differentially-expressed genes and the rest of the genes in the genome. Takes Additional files 3 and 5 as input. (R 50 kb)
DOI: 10.6084/m9.figshare.c.3643949_d22
title: Additional file 9: of Relationships between putative G-quadruplex-forming sequences, RecQ helicases, and transcription

description: R code for extracting DNAse 1 genomic track signal near TSS for epigenetic modeling of gene expression method. Program written in R that calculates DNAse track signal in 100 bp bins spanning 1 kbp upstream and downstream of the TSS. Takes .bigwig file of DNAse 1 hypersesitivity epigenomic track and output of Additional file 8 as input. (R 4 kb)
DOI: 10.15156/bio/sh1126432.10fu
title: SH1126432.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1126437.10fu
title: SH1126437.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1126438.10fu
title: SH1126438.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1126439.10fu
title: SH1126439.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1126440.10fu
title: SH1126440.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1126441.10fu
title: SH1126441.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1126442.10fu
title: SH1126442.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1126443.10fu
title: SH1126443.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.