cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12629885.v3
title: The assembled transcriptome of the tidal reeds and freshwater reeds in Yellow River Delta responding to salt stress

description: Transcriptome assemblyWe used Trinity software for transcriptome assembly. The basic process of assembly is shown in the following link: http://trinityrnaseq.github.io .The results of transcriptional assembly were as follows:1.Trinity.fasta: FASTA sequences of Trinity assembly2.cluster_ all.fasta: The sequence obtained by removing redundancy in the TRINITY.fasta by corset clustering.3.unigene.fasta: Select the longest transcript of each gene from the cluster_ all.fasta to store in FASTA format as a unigene of the gene.4.Sampled_ trinity.fasta: Some examples of Trinity.fasta sequence, and the format of the sequence is the same as the Trinity.fasta.5.Sampled_ cluster_ all.fasta: Some examples of Clusters_ all.fasta sequence, and the format of the sequence is the same as the cluster_ all.fasta.6.Sampled_ unigene.fasta: Some examples of the unigene.fasta sequence, and the format of the sequence is the same as the unigene.fasta.
DOI: 10.6084/m9.figshare.12629754
title: Additional file 8 of SLFinder, a pipeline for the novel identification of splice-leader sequences: a good enough solution for a complex problem

description: Additional file 8: Supplementary Table 6. Putative SL loci identified by SLFinder in the H. vulgaris dataset. Annotated protein-coding genes closer than 100 pb are also indicated.
DOI: 10.6084/m9.figshare.12629751
title: Additional file 7 of SLFinder, a pipeline for the novel identification of splice-leader sequences: a good enough solution for a complex problem

description: Additional file 7: Supplementary Table 5. Putative SL loci identified by SLFinder in the C. intestinalis dataset. Annotated lncRNA and protein-coding genes closer than 100 pb are also indicated.
DOI: 10.6084/m9.figshare.12629754.v1
title: Additional file 8 of SLFinder, a pipeline for the novel identification of splice-leader sequences: a good enough solution for a complex problem

description: Additional file 8: Supplementary Table 6. Putative SL loci identified by SLFinder in the H. vulgaris dataset. Annotated protein-coding genes closer than 100 pb are also indicated.
DOI: 10.6084/m9.figshare.12629751.v1
title: Additional file 7 of SLFinder, a pipeline for the novel identification of splice-leader sequences: a good enough solution for a complex problem

description: Additional file 7: Supplementary Table 5. Putative SL loci identified by SLFinder in the C. intestinalis dataset. Annotated lncRNA and protein-coding genes closer than 100 pb are also indicated.
DOI: 10.6084/m9.figshare.12629730
title: Additional file 11 of SLFinder, a pipeline for the novel identification of splice-leader sequences: a good enough solution for a complex problem

description: Additional file 11: Supplementary Table 8. Putative SL loci identified by SLFinder in the S. mansoni dataset using GeneDB’s genome assembly as reference. Annotated protein-coding genes closer than 100 bp are indicated.
DOI: 10.6084/m9.figshare.12629733
title: Additional file 1 of SLFinder, a pipeline for the novel identification of splice-leader sequences: a good enough solution for a complex problem

description: Additional file 1: Supplementary Table 1. Reported SL sequences for the species C. elegans, C. intestinalis, H. vulgaris and S. mansoni.
DOI: 10.6084/m9.figshare.12629736
title: Additional file 2 of SLFinder, a pipeline for the novel identification of splice-leader sequences: a good enough solution for a complex problem

description: Additional file 2: Supplementary Table 2. Basic descriptors of the analyzed datasets. Data Set, GenBank SRA ID, N° Reads, N° Trimmed Reads, Assembled Bases, Total Transcripts, N50, Median Contig Length, Average Contig Length, Genes predicted by Trinity (Trinity Genes) and GC content.
DOI: 10.6084/m9.figshare.12629739
title: Additional file 3 of SLFinder, a pipeline for the novel identification of splice-leader sequences: a good enough solution for a complex problem

description: Additional file 3: Supplementary Table 3. Hook hits obtained for each dataset (Step 1 - F in Fig. 1). Hit counts according to position and orientation in the contig, coi score and observation count cutoff (occ) are indicated. Selected Best Hooks are highlighted in bold. Results for C. intestinalis include those obtained with default and custom values (see main text).
DOI: 10.6084/m9.figshare.12629742
title: Additional file 4 of SLFinder, a pipeline for the novel identification of splice-leader sequences: a good enough solution for a complex problem

description: Additional file 4: Supplementary Table 4. Putative SLs loci identified by SLFinder in the C. elegans dataset. Previously reported SL-RNAs are also indicated.
DOI: 10.6084/m9.figshare.12629730.v1
title: Additional file 11 of SLFinder, a pipeline for the novel identification of splice-leader sequences: a good enough solution for a complex problem

description: Additional file 11: Supplementary Table 8. Putative SL loci identified by SLFinder in the S. mansoni dataset using GeneDB’s genome assembly as reference. Annotated protein-coding genes closer than 100 bp are indicated.
DOI: 10.6084/m9.figshare.12629736.v1
title: Additional file 2 of SLFinder, a pipeline for the novel identification of splice-leader sequences: a good enough solution for a complex problem

description: Additional file 2: Supplementary Table 2. Basic descriptors of the analyzed datasets. Data Set, GenBank SRA ID, N° Reads, N° Trimmed Reads, Assembled Bases, Total Transcripts, N50, Median Contig Length, Average Contig Length, Genes predicted by Trinity (Trinity Genes) and GC content.
DOI: 10.6084/m9.figshare.12629727
title: Additional file 10 of SLFinder, a pipeline for the novel identification of splice-leader sequences: a good enough solution for a complex problem

description: Additional file 10: Supplementary Table 7. Putative SL loci identified by SLFinder in the S. mansoni dataset using Wormbase’s genome assembly as reference (WBPS). Annotated protein-coding genes closer than 100 bp are indicated.
DOI: 10.6084/m9.figshare.12629733.v1
title: Additional file 1 of SLFinder, a pipeline for the novel identification of splice-leader sequences: a good enough solution for a complex problem

description: Additional file 1: Supplementary Table 1. Reported SL sequences for the species C. elegans, C. intestinalis, H. vulgaris and S. mansoni.
DOI: 10.6084/m9.figshare.12629739.v1
title: Additional file 3 of SLFinder, a pipeline for the novel identification of splice-leader sequences: a good enough solution for a complex problem

description: Additional file 3: Supplementary Table 3. Hook hits obtained for each dataset (Step 1 - F in Fig. 1). Hit counts according to position and orientation in the contig, coi score and observation count cutoff (occ) are indicated. Selected Best Hooks are highlighted in bold. Results for C. intestinalis include those obtained with default and custom values (see main text).
DOI: 10.6084/m9.figshare.12629725
title: Additional file 2 of A quasi-experimental approach using telemetry to assess migration-strategy-specific differences in the decision-making processes at stopover

description: Additional file 2: Table S1. Raw data of the study. Time: local time; Species: CR = common redstart, ER = European robin; Muscle: muscle score; Wing: wing length in mm; Bodymass: body mass in g; take.off: local time of take off; dep.dir: direction at departure; days.on.island: days spent on the island; dep.min.sunset: departure in min after sunset; dep.realtive.night: departure relative to night length; wind.speed: wind speed in m/s at departure; wind.dir: wind direction at departure.
DOI: 10.6084/m9.figshare.12629742.v1
title: Additional file 4 of SLFinder, a pipeline for the novel identification of splice-leader sequences: a good enough solution for a complex problem

description: Additional file 4: Supplementary Table 4. Putative SLs loci identified by SLFinder in the C. elegans dataset. Previously reported SL-RNAs are also indicated.
DOI: 10.6084/m9.figshare.12629725.v1
title: Additional file 2 of A quasi-experimental approach using telemetry to assess migration-strategy-specific differences in the decision-making processes at stopover

description: Additional file 2: Table S1. Raw data of the study. Time: local time; Species: CR = common redstart, ER = European robin; Muscle: muscle score; Wing: wing length in mm; Bodymass: body mass in g; take.off: local time of take off; dep.dir: direction at departure; days.on.island: days spent on the island; dep.min.sunset: departure in min after sunset; dep.realtive.night: departure relative to night length; wind.speed: wind speed in m/s at departure; wind.dir: wind direction at departure.
DOI: 10.6084/m9.figshare.12629727.v1
title: Additional file 10 of SLFinder, a pipeline for the novel identification of splice-leader sequences: a good enough solution for a complex problem

description: Additional file 10: Supplementary Table 7. Putative SL loci identified by SLFinder in the S. mansoni dataset using Wormbase’s genome assembly as reference (WBPS). Annotated protein-coding genes closer than 100 bp are indicated.
DOI: 10.6084/m9.figshare.12629683
title: Additional file 2 of Production and verification of the first Atlantic salmon (Salmo salar L.) clonal lines

description: Additional file 2 Table S2. Microsatellite analysis of 2 parents and 362 offspring from Exp2011 (row 1–366). The first 45 individuals (controls) were fertilized with diluted, but unirradiated milt. The others were fertilized with UV-irradiated milt and pressure shocked. Alleles that are exclusive for the Sire (sperm donor) are in green and blue and for the female in red and yellow. Only two individuals from the putative mitotic gynogenetic groups showed any paternal contribution (rows 55 and 216). The females that matured in 2014 and were used to produce the isogenic lines are shown in col. A with the number indicating which line they originated from. Rows 369 to 424 compares the microsatellites of the clonal founders with their progeny. Microsatellite data from Exp2012 is shown in lines 430 to 702 with the parents in lines 430 and 431, the doubled haploid progeny in lines 433 to 672 and the controls in lines 673 to 702.
DOI: 10.6084/m9.figshare.12629683.v1
title: Additional file 2 of Production and verification of the first Atlantic salmon (Salmo salar L.) clonal lines

description: Additional file 2 Table S2. Microsatellite analysis of 2 parents and 362 offspring from Exp2011 (row 1–366). The first 45 individuals (controls) were fertilized with diluted, but unirradiated milt. The others were fertilized with UV-irradiated milt and pressure shocked. Alleles that are exclusive for the Sire (sperm donor) are in green and blue and for the female in red and yellow. Only two individuals from the putative mitotic gynogenetic groups showed any paternal contribution (rows 55 and 216). The females that matured in 2014 and were used to produce the isogenic lines are shown in col. A with the number indicating which line they originated from. Rows 369 to 424 compares the microsatellites of the clonal founders with their progeny. Microsatellite data from Exp2012 is shown in lines 430 to 702 with the parents in lines 430 and 431, the doubled haploid progeny in lines 433 to 672 and the controls in lines 673 to 702.
DOI: 10.6084/m9.figshare.12629668
title: Additional file 5 of Tongue microbiome of smokeless tobacco users

description: Additional file 5.
DOI: 10.6084/m9.figshare.12629662
title: Additional file 3 of Tongue microbiome of smokeless tobacco users

description: Additional file 3.
DOI: 10.6084/m9.figshare.12629665
title: Additional file 4 of Tongue microbiome of smokeless tobacco users

description: Additional file 4.
DOI: 10.6084/m9.figshare.12629665.v1
title: Additional file 4 of Tongue microbiome of smokeless tobacco users

description: Additional file 4.
DOI: 10.6084/m9.figshare.12629659
title: Additional file 2 of Tongue microbiome of smokeless tobacco users

description: Additional file 2.
DOI: 10.6084/m9.figshare.12629662.v1
title: Additional file 3 of Tongue microbiome of smokeless tobacco users

description: Additional file 3.
DOI: 10.6084/m9.figshare.12629668.v1
title: Additional file 5 of Tongue microbiome of smokeless tobacco users

description: Additional file 5.
DOI: 10.6084/m9.figshare.12629659.v1
title: Additional file 2 of Tongue microbiome of smokeless tobacco users

description: Additional file 2.
DOI: 10.15161/oar.it/30643
title: CovidStat project data

description: This record contains the daily updated data of the CovidStat project. CovidStat is a project carried out by the CovidStat Working Group at INFN, whose creation was promoted within the Italian National Institute of Nuclear Physics with the aim of making a statistical analysis of the data provided daily by the Civil Protection on the spread of the pandemic in Italy. CovidStat data can interactively be browsed at https://covid19.infn.it.
description: The software to process this Root TTree is in the related identifier. Be sure to use the right corresponding version, based on the data in which Root TTree was generated.
DOI: 10.6084/m9.figshare.12629626
title: Additional file 3 of Molecular docking and machine learning analysis of Abemaciclib in colon cancer

description: Additional file 3 Additional file S3. Clinical data of patients involved in classification between tumour and health tissue. In this excel file it can be found several clinical variables that correspond to patients involved in tumour and health tissue classification.
DOI: 10.6084/m9.figshare.12629620
title: Additional file 1 of Molecular docking and machine learning analysis of Abemaciclib in colon cancer

description: Additional file 1 Additional file S1. List of ligands with their corresponding annotation in ChEMBL. It showed a list of ligand used in the docking experiment. A total of 159 ChEMBL coumpounds are listed from 81 anti-cancer drugs downloaded.
DOI: 10.6084/m9.figshare.12629623
title: Additional file 2 of Molecular docking and machine learning analysis of Abemaciclib in colon cancer

description: Additional file 2 Additional file S2. Top 50 interactions from docking experiment. In this excel file it can be found the interaction force between ligand (drug) and target (protein). The interaction force is measured by kcal/mol.
DOI: 10.6084/m9.figshare.12629626.v1
title: Additional file 3 of Molecular docking and machine learning analysis of Abemaciclib in colon cancer

description: Additional file 3 Additional file S3. Clinical data of patients involved in classification between tumour and health tissue. In this excel file it can be found several clinical variables that correspond to patients involved in tumour and health tissue classification.
DOI: 10.6084/m9.figshare.12629623.v1
title: Additional file 2 of Molecular docking and machine learning analysis of Abemaciclib in colon cancer

description: Additional file 2 Additional file S2. Top 50 interactions from docking experiment. In this excel file it can be found the interaction force between ligand (drug) and target (protein). The interaction force is measured by kcal/mol.
DOI: 10.6084/m9.figshare.12629613
title: Additional file 6 of Sierra: discovery of differential transcript usage from polyA-captured single-cell RNA-seq data

description: Additional file 6 List of the primers used in qRT-PCR. Format: XLSX file.
DOI: 10.6084/m9.figshare.12629616
title: Additional file 7 of Sierra: discovery of differential transcript usage from polyA-captured single-cell RNA-seq data

description: Additional file 7 Review history. Format: DOCX file.
DOI: 10.6084/m9.figshare.12629620.v1
title: Additional file 1 of Molecular docking and machine learning analysis of Abemaciclib in colon cancer

description: Additional file 1 Additional file S1. List of ligands with their corresponding annotation in ChEMBL. It showed a list of ligand used in the docking experiment. A total of 159 ChEMBL coumpounds are listed from 81 anti-cancer drugs downloaded.
DOI: 10.6084/m9.figshare.12629610
title: Additional file 5 of Sierra: discovery of differential transcript usage from polyA-captured single-cell RNA-seq data

description: Additional file 5 Output for DTU testing between activated/proliferating fibroblast populations and the resting populations. DTU testing based on 3’UTR peaks, after filtering out peaks tagged as proximal to an A-rich region. Format: XLSX file.
DOI: 10.6084/m9.figshare.12629616.v1
title: Additional file 7 of Sierra: discovery of differential transcript usage from polyA-captured single-cell RNA-seq data

description: Additional file 7 Review history. Format: DOCX file.
DOI: 10.6084/m9.figshare.12629604
title: Additional file 3 of Sierra: discovery of differential transcript usage from polyA-captured single-cell RNA-seq data

description: Additional file 3 Comparison of overlapping detected differential transcript usage genes and differentially expressed genes for different cell-type comparisons between the PBMC 7k and PBMC 4k datasets. Format: XLSX file.
DOI: 10.6084/m9.figshare.12629607
title: Additional file 4 of Sierra: discovery of differential transcript usage from polyA-captured single-cell RNA-seq data

description: Additional file 4 Output for DTU testing between cell-types from the TIP dataset. Format: XLSX file.
DOI: 10.6084/m9.figshare.12629610.v1
title: Additional file 5 of Sierra: discovery of differential transcript usage from polyA-captured single-cell RNA-seq data

description: Additional file 5 Output for DTU testing between activated/proliferating fibroblast populations and the resting populations. DTU testing based on 3’UTR peaks, after filtering out peaks tagged as proximal to an A-rich region. Format: XLSX file.
DOI: 10.6084/m9.figshare.12629613.v1
title: Additional file 6 of Sierra: discovery of differential transcript usage from polyA-captured single-cell RNA-seq data

description: Additional file 6 List of the primers used in qRT-PCR. Format: XLSX file.
DOI: 10.6084/m9.figshare.12629604.v1
title: Additional file 3 of Sierra: discovery of differential transcript usage from polyA-captured single-cell RNA-seq data

description: Additional file 3 Comparison of overlapping detected differential transcript usage genes and differentially expressed genes for different cell-type comparisons between the PBMC 7k and PBMC 4k datasets. Format: XLSX file.
DOI: 10.6084/m9.figshare.12629607.v1
title: Additional file 4 of Sierra: discovery of differential transcript usage from polyA-captured single-cell RNA-seq data

description: Additional file 4 Output for DTU testing between cell-types from the TIP dataset. Format: XLSX file.
DOI: 10.6084/m9.figshare.12629598
title: Additional file 1 of Sierra: discovery of differential transcript usage from polyA-captured single-cell RNA-seq data

description: Additional file 1 Metrics from peak calling, counting and annotation for the 19 individual datasets analysed is this study. Shown are 1) the number of peaks, 2) number of genes, 3) median peaks per-gene, 4-7) % of peaks falling on 3’UTRs, exons, introns or 5’UTRs, 8-11) % of peaks with a polyA motif according to 3’UTRs, exons, introns or 5’UTRs and 12-5) % of peaks down-stream from an A-rich stretch according to 3’UTRs, exons, introns or 5’UTRs. Format: XLSX file.
DOI: 10.6084/m9.figshare.12629598.v1
title: Additional file 1 of Sierra: discovery of differential transcript usage from polyA-captured single-cell RNA-seq data

description: Additional file 1 Metrics from peak calling, counting and annotation for the 19 individual datasets analysed is this study. Shown are 1) the number of peaks, 2) number of genes, 3) median peaks per-gene, 4-7) % of peaks falling on 3’UTRs, exons, introns or 5’UTRs, 8-11) % of peaks with a polyA motif according to 3’UTRs, exons, introns or 5’UTRs and 12-5) % of peaks down-stream from an A-rich stretch according to 3’UTRs, exons, introns or 5’UTRs. Format: XLSX file.
DOI: 10.6084/m9.figshare.12629583
title: Additional file 1 of Harnessing repeated measurements of predictor variables for clinical risk prediction: a review of existing methods

description: Additional file 1: Table 1 Reference List. Title of data: Journal articles included in the review, ordered alphabetically by first author surname. Description of data: A list of all articles included in the review, including author names, title of publication, journal of publication, volume, pages and DOI number.
DOI: 10.6084/m9.figshare.12629578
title: Additional file 1 of DNA methylation biomarkers of future health outcomes in children

description: Additional file 1: Table 1. Included articles.
DOI: 10.6084/m9.figshare.12629583.v1
title: Additional file 1 of Harnessing repeated measurements of predictor variables for clinical risk prediction: a review of existing methods

description: Additional file 1: Table 1 Reference List. Title of data: Journal articles included in the review, ordered alphabetically by first author surname. Description of data: A list of all articles included in the review, including author names, title of publication, journal of publication, volume, pages and DOI number.
DOI: 10.6084/m9.figshare.12629578.v1
title: Additional file 1 of DNA methylation biomarkers of future health outcomes in children

description: Additional file 1: Table 1. Included articles.
DOI: 10.6084/m9.figshare.12629560
title: Additional file 2 of Clinical efficacy and safety in patients treated with teicoplanin with a target trough concentration of 20 μg/mL using a regimen of 12 mg/kg for five doses within the initial 3 days

description: Additional file 2.
DOI: 10.6084/m9.figshare.12629560.v1
title: Additional file 2 of Clinical efficacy and safety in patients treated with teicoplanin with a target trough concentration of 20 μg/mL using a regimen of 12 mg/kg for five doses within the initial 3 days

description: Additional file 2.
DOI: 10.6084/m9.figshare.12629431
title: Additional file 2 of The MLH1 polymorphism rs1800734 and risk of endometrial cancer with microsatellite instability

description: Additional file 2: Supplementary figure 2. Results of meta-analysis of all MSI cases versus controls (from ANECS – Illumina genotyped, ANECS – iCOGS genotyped, RENDOCAS, MCCS; MSI n = 225, controls n = 13,582) showing association statistics for all SNPs in the MLH1 promoter region (chr3:36,000,000-38,000,000 hg38; chr3:36024996-38024996 hg19) and in silico predicted transcription factor binding sites (SNP2TFBS).
DOI: 10.6084/m9.figshare.12629434
title: Additional file 3 of The MLH1 polymorphism rs1800734 and risk of endometrial cancer with microsatellite instability

description: Additional file 3: Supplementary figure 3. Results of meta-analysis of cases with loss of MLH1/PMS2 protein expression only versus controls (from ANECS – Illumina genotyped, ANECS – iCOGS genotyped, RENDOCAS, MCCS; MLH1 loss cases n = 157, controls n = 13,582) showing association statistics for all SNPs in the MLH1 promoter region (chr3:36,000,000-38,000,000 hg38; chr3:36024996-38024996 hg19).
DOI: 10.6084/m9.figshare.12629431.v1
title: Additional file 2 of The MLH1 polymorphism rs1800734 and risk of endometrial cancer with microsatellite instability

description: Additional file 2: Supplementary figure 2. Results of meta-analysis of all MSI cases versus controls (from ANECS – Illumina genotyped, ANECS – iCOGS genotyped, RENDOCAS, MCCS; MSI n = 225, controls n = 13,582) showing association statistics for all SNPs in the MLH1 promoter region (chr3:36,000,000-38,000,000 hg38; chr3:36024996-38024996 hg19) and in silico predicted transcription factor binding sites (SNP2TFBS).
DOI: 10.6084/m9.figshare.12629434.v1
title: Additional file 3 of The MLH1 polymorphism rs1800734 and risk of endometrial cancer with microsatellite instability

description: Additional file 3: Supplementary figure 3. Results of meta-analysis of cases with loss of MLH1/PMS2 protein expression only versus controls (from ANECS – Illumina genotyped, ANECS – iCOGS genotyped, RENDOCAS, MCCS; MLH1 loss cases n = 157, controls n = 13,582) showing association statistics for all SNPs in the MLH1 promoter region (chr3:36,000,000-38,000,000 hg38; chr3:36024996-38024996 hg19).