cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.13467581.v1
title: Additional file 2 of Quality assessment of a clinical next-generation sequencing melanoma panel within the Italian Melanoma Intergroup (IMI)

description: Additional file 2. List of exonic genetic variants called by PGM™ VC for the eleven tumor samples. All variants are annotated with the gene ID and locus RefSeq, and the mutation nomenclature is based on the convention recommended by the Human Genome Variation Society ( http://www.hgvs.org/mutnomen/ ) other than the variant allele and the nature of the allele call (heterozygous or homozygous). Frequency data indicate the percentage of the variant allele detected by PGM VC. Moreover, they are annotated for dbSNP (rs number) or COSMIC v86 database, together with FATHMM score. The FATHMM is a functional score for individual mutations from FATHMM-MKL are in the form of a single p-value, ranging from 0 to 1. Scores above 0.5 are deleterious, but in order to highlight the most significant data in COSMIC, only scores ≥0.7 are classified as ‘Pathogenic’ whereas mutations are classed as ‘Neutral’ if the score is ≤0.5 [47]. The “Effect” column reports the effect of nucleotide change on the protein. The last three columns of the table report the GnomAD Frequency, the predictive effect on the protein based on SIFT, and the conservation score, namely GERP. Converted rankscore is reported for SIFT. To obtain the rankscore, Sorting Intolerant from Tolerant (SIFT) scores were first converted to SIFTnew = (1-SIFTori), then ranked among all SIFTnew scores in dbNSFP. The rankscore is the ratio of the rank the SIFTnew score over the total number of SIFTnew scores in dbNSFP. If there are multiple scores, only the largest (most damaging) rankscore is presented. Rankscores range from 0.02654 to 0.87932. Genomic Evolutionary Rate Profiling (GERP) is a conservation score calculated by quantifying substitution deficits across multiple alignments of orthologues using the genomes of 35 mammals. It ranges from − 12.3 to 6.17, with 6.17 being the most conserved [48]. Abbreviations: VC: Variant Caller; −: no available data; GERP: genomic evolutionary rate profiling. SIFT: Sorts Intolerant From Tolerant. GnomAD: Genome Aggregation Database
DOI: 10.6084/m9.figshare.13467581
title: Additional file 2 of Quality assessment of a clinical next-generation sequencing melanoma panel within the Italian Melanoma Intergroup (IMI)

description: Additional file 2. List of exonic genetic variants called by PGM™ VC for the eleven tumor samples. All variants are annotated with the gene ID and locus RefSeq, and the mutation nomenclature is based on the convention recommended by the Human Genome Variation Society ( http://www.hgvs.org/mutnomen/ ) other than the variant allele and the nature of the allele call (heterozygous or homozygous). Frequency data indicate the percentage of the variant allele detected by PGM VC. Moreover, they are annotated for dbSNP (rs number) or COSMIC v86 database, together with FATHMM score. The FATHMM is a functional score for individual mutations from FATHMM-MKL are in the form of a single p-value, ranging from 0 to 1. Scores above 0.5 are deleterious, but in order to highlight the most significant data in COSMIC, only scores ≥0.7 are classified as ‘Pathogenic’ whereas mutations are classed as ‘Neutral’ if the score is ≤0.5 [47]. The “Effect” column reports the effect of nucleotide change on the protein. The last three columns of the table report the GnomAD Frequency, the predictive effect on the protein based on SIFT, and the conservation score, namely GERP. Converted rankscore is reported for SIFT. To obtain the rankscore, Sorting Intolerant from Tolerant (SIFT) scores were first converted to SIFTnew = (1-SIFTori), then ranked among all SIFTnew scores in dbNSFP. The rankscore is the ratio of the rank the SIFTnew score over the total number of SIFTnew scores in dbNSFP. If there are multiple scores, only the largest (most damaging) rankscore is presented. Rankscores range from 0.02654 to 0.87932. Genomic Evolutionary Rate Profiling (GERP) is a conservation score calculated by quantifying substitution deficits across multiple alignments of orthologues using the genomes of 35 mammals. It ranges from − 12.3 to 6.17, with 6.17 being the most conserved [48]. Abbreviations: VC: Variant Caller; −: no available data; GERP: genomic evolutionary rate profiling. SIFT: Sorts Intolerant From Tolerant. GnomAD: Genome Aggregation Database
DOI: 10.6084/m9.figshare.13467585
title: Additional file 4 of Quality assessment of a clinical next-generation sequencing melanoma panel within the Italian Melanoma Intergroup (IMI)

description: Additional file 4. List of exonic genetic variants called by MiSeq™ Illumina Variant interpreter for the eleven tumor samples. All variants are annotated with the gene ID and locus RefSeq, and the mutation nomenclature is based on the convention recommended by the Human Genome Variation Society ( http://www.hgvs.org/mutnomen/ ) other than the variant allele and the nature of the allele call (heterozygous or homozygous). Frequency data indicate the percentage of the variant allele detected by Illumina. Moreover, they are annotated for dbSNP (rs number) or COSMIC v86 database, together with FATHMM score. The FATHMM is a functional score for individual mutations from FATHMM-MKL are in the form of a single p-value, ranging from 0 to 1. Scores above 0.5 are deleterious, but in order to highlight the most significant data in COSMIC, only scores ≥0.7 are classified as ‘Pathogenic’ whereas mutations are classed as ‘Neutral’ if the score is ≤0.5 [47]. The “Effect” column reports the effect of nucleotide change on the protein. The last three columns of the table report the GnomAD Frequency, the predictive effect on the protein based on SIFT, and the conservation score, namely GERP. Converted rankscore is reported for SIFT. To obtain the rankscore, Sorting Intolerant from Tolerant (SIFT) scores were first converted to SIFTnew = (1-SIFTori), then ranked among all SIFTnew scores in dbNSFP. The rankscore is the ratio of the rank the SIFTnew score over the total number of SIFTnew scores in dbNSFP. If there are multiple scores, only the largest (most damaging) rankscore is presented. Rankscores range from 0.02654 to 0.87932. Genomic Evolutionary Rate Profiling (GERP) is a conservation score calculated by quantifying substitution deficits across multiple alignments of orthologues using the genomes of 35 mammals. It ranges from − 12.3 to 6.17, with 6.17 being the most conserved [48]. Abbreviations: VC: Variant Caller; −: no available data; GERP: Genomic Evolutionary Rate Profiling. SIFT: Sorts Intolerant From Tolerant. GnomAD: Genome Aggregation Database.
DOI: 10.6084/m9.figshare.13467587
title: Additional file 5 of Quality assessment of a clinical next-generation sequencing melanoma panel within the Italian Melanoma Intergroup (IMI)

description: Additional file 5. Coding genetic variants called by all platforms for the eleven tumor samples. Abbreviations: VC: Variant Caller; −: no available data; GERP: Genomic Evolutionary Rate Profiling. SIFT: Sorts Intolerant From Tolerant. GnomAD: Genome Aggregation Database.
DOI: 10.6084/m9.figshare.13467585.v1
title: Additional file 4 of Quality assessment of a clinical next-generation sequencing melanoma panel within the Italian Melanoma Intergroup (IMI)

description: Additional file 4. List of exonic genetic variants called by MiSeq™ Illumina Variant interpreter for the eleven tumor samples. All variants are annotated with the gene ID and locus RefSeq, and the mutation nomenclature is based on the convention recommended by the Human Genome Variation Society ( http://www.hgvs.org/mutnomen/ ) other than the variant allele and the nature of the allele call (heterozygous or homozygous). Frequency data indicate the percentage of the variant allele detected by Illumina. Moreover, they are annotated for dbSNP (rs number) or COSMIC v86 database, together with FATHMM score. The FATHMM is a functional score for individual mutations from FATHMM-MKL are in the form of a single p-value, ranging from 0 to 1. Scores above 0.5 are deleterious, but in order to highlight the most significant data in COSMIC, only scores ≥0.7 are classified as ‘Pathogenic’ whereas mutations are classed as ‘Neutral’ if the score is ≤0.5 [47]. The “Effect” column reports the effect of nucleotide change on the protein. The last three columns of the table report the GnomAD Frequency, the predictive effect on the protein based on SIFT, and the conservation score, namely GERP. Converted rankscore is reported for SIFT. To obtain the rankscore, Sorting Intolerant from Tolerant (SIFT) scores were first converted to SIFTnew = (1-SIFTori), then ranked among all SIFTnew scores in dbNSFP. The rankscore is the ratio of the rank the SIFTnew score over the total number of SIFTnew scores in dbNSFP. If there are multiple scores, only the largest (most damaging) rankscore is presented. Rankscores range from 0.02654 to 0.87932. Genomic Evolutionary Rate Profiling (GERP) is a conservation score calculated by quantifying substitution deficits across multiple alignments of orthologues using the genomes of 35 mammals. It ranges from − 12.3 to 6.17, with 6.17 being the most conserved [48]. Abbreviations: VC: Variant Caller; −: no available data; GERP: Genomic Evolutionary Rate Profiling. SIFT: Sorts Intolerant From Tolerant. GnomAD: Genome Aggregation Database.
DOI: 10.6084/m9.figshare.13467587.v1
title: Additional file 5 of Quality assessment of a clinical next-generation sequencing melanoma panel within the Italian Melanoma Intergroup (IMI)

description: Additional file 5. Coding genetic variants called by all platforms for the eleven tumor samples. Abbreviations: VC: Variant Caller; −: no available data; GERP: Genomic Evolutionary Rate Profiling. SIFT: Sorts Intolerant From Tolerant. GnomAD: Genome Aggregation Database.
DOI: 10.6084/m9.figshare.13467583
title: Additional file 3 of Quality assessment of a clinical next-generation sequencing melanoma panel within the Italian Melanoma Intergroup (IMI)

description: Additional file 3. List of exonic genetic variants called by Proton™ VC for the eleven tumor samples. All variants are annotated with the gene ID and locus RefSeq, and the mutation nomenclature is based on the convention recommended by the Human Genome Variation Society ( http://www.hgvs.org/mutnomen/ ) other than the variant allele and the nature of the allele call (heterozygous or homozygous). Frequency data indicate the percentage of the variant allele detected by Proton VC. Moreover, they are annotated for dbSNP (rs number) or COSMIC v86 database, together with FATHMM score. The FATHMM is a functional score for individual mutations from FATHMM-MKL are in the form of a single p-value, ranging from 0 to 1. Scores above 0.5 are deleterious, but in order to highlight the most significant data in COSMIC, only scores ≥0.7 are classified as ‘Pathogenic’ whereas mutations are classed as ‘Neutral’ if the score is ≤0.5 [47]. The “Effect” column reports the effect of nucleotide change on the protein. The last three columns of the table report the GnomAD Frequency, the predictive effect on the protein based on SIFT, and the conservation score, namely GERP. Converted rankscore is reported for SIFT. To obtain the rankscore, Sorting Intolerant from Tolerant (SIFT) scores were first converted to SIFTnew = (1-SIFTori), then ranked among all SIFTnew scores in dbNSFP. The rankscore is the ratio of the rank the SIFT new score over the total number of SIFTnew scores in dbNSFP. If there are multiple scores, only the largest (most damaging) rankscore is presented. Rank scores range from 0.02654 to 0.87932. Genomic Evolutionary Rate Profiling (GERP) is a conservation score calculated by quantifying substitution deficits across multiple alignments of orthologues using the genomes of 35 mammals. It ranges from − 12.3 to 6.17, with 6.17 being the most conserved [48]. Abbreviations: VC: Variant Caller; −: no available data; GERP: Genomic Evolutionary Rate Profiling. SIFT: Sorts Intolerant From Tolerant. GnomAD: Genome Aggregation Database.
DOI: 10.6084/m9.figshare.13467583.v1
title: Additional file 3 of Quality assessment of a clinical next-generation sequencing melanoma panel within the Italian Melanoma Intergroup (IMI)

description: Additional file 3. List of exonic genetic variants called by Proton™ VC for the eleven tumor samples. All variants are annotated with the gene ID and locus RefSeq, and the mutation nomenclature is based on the convention recommended by the Human Genome Variation Society ( http://www.hgvs.org/mutnomen/ ) other than the variant allele and the nature of the allele call (heterozygous or homozygous). Frequency data indicate the percentage of the variant allele detected by Proton VC. Moreover, they are annotated for dbSNP (rs number) or COSMIC v86 database, together with FATHMM score. The FATHMM is a functional score for individual mutations from FATHMM-MKL are in the form of a single p-value, ranging from 0 to 1. Scores above 0.5 are deleterious, but in order to highlight the most significant data in COSMIC, only scores ≥0.7 are classified as ‘Pathogenic’ whereas mutations are classed as ‘Neutral’ if the score is ≤0.5 [47]. The “Effect” column reports the effect of nucleotide change on the protein. The last three columns of the table report the GnomAD Frequency, the predictive effect on the protein based on SIFT, and the conservation score, namely GERP. Converted rankscore is reported for SIFT. To obtain the rankscore, Sorting Intolerant from Tolerant (SIFT) scores were first converted to SIFTnew = (1-SIFTori), then ranked among all SIFTnew scores in dbNSFP. The rankscore is the ratio of the rank the SIFT new score over the total number of SIFTnew scores in dbNSFP. If there are multiple scores, only the largest (most damaging) rankscore is presented. Rank scores range from 0.02654 to 0.87932. Genomic Evolutionary Rate Profiling (GERP) is a conservation score calculated by quantifying substitution deficits across multiple alignments of orthologues using the genomes of 35 mammals. It ranges from − 12.3 to 6.17, with 6.17 being the most conserved [48]. Abbreviations: VC: Variant Caller; −: no available data; GERP: Genomic Evolutionary Rate Profiling. SIFT: Sorts Intolerant From Tolerant. GnomAD: Genome Aggregation Database.
DOI: 10.15468/jg7ajf
title: Description of two new Proceroecia species (Ostracoda: Halocyprididae) from neritic waters off South Korea with an insight into the morphological and molecular diversity of the genus

description: This dataset contains the digitized treatments in Plazi based on the original journal article Choi, Eunha, Karanovic, Ivana, Lee, Wonchoel, Angel, Martin V. (2020): Description of two new Proceroecia species (Ostracoda: Halocyprididae) from neritic waters off South Korea with an insight into the morphological and molecular diversity of the genus. Zootaxa 4896 (2): 180-200, DOI: https://doi.org/10.11646/zootaxa.4896.2.2
DOI: 10.6084/m9.figshare.13467631
title: Additional file 7 of Altered metabolism of mothers of young children with Autism Spectrum Disorder: a case control study

description: Additional File 7: Raw Data File. The excel file contains the raw data of the metabolite measurements analyzed in this paper. The metabolite measurements are separated by tabs by what lab measured them. The three labs included the Metabolic and Oxidative Stress Laboratory (MOSL), the Mayo Clinic, and Metabolon.
DOI: 10.6084/m9.figshare.13467631.v1
title: Additional file 7 of Altered metabolism of mothers of young children with Autism Spectrum Disorder: a case control study

description: Additional File 7: Raw Data File. The excel file contains the raw data of the metabolite measurements analyzed in this paper. The metabolite measurements are separated by tabs by what lab measured them. The three labs included the Metabolic and Oxidative Stress Laboratory (MOSL), the Mayo Clinic, and Metabolon.
DOI: 10.6084/m9.figshare.13467645.v1
title: Additional file 1 of Minocycline reduces inflammatory response and cell death in a S100B retina degeneration model

description: Additional file 1: Supplementary table 1. Experimental design of proteomics analysis.
DOI: 10.6084/m9.figshare.13467647
title: Additional file 2 of Minocycline reduces inflammatory response and cell death in a S100B retina degeneration model

description: Additional file 2: Supplementary table 2a. MaxQuant parameters. Supplementary table 2b. List of proteins identified employing MaxQuant (Rattus and Homo sapiens).
DOI: 10.6084/m9.figshare.13467653.v1
title: Additional file 4 of Minocycline reduces inflammatory response and cell death in a S100B retina degeneration model

description: Additional file 4: Supplementary table 4A. Protein-protein relations types of the differentially expressed proteins in S100B vs. PBS. Supplementary table 4B. Protein-protein relations types of the differentially expressed proteins in 13.5 mg/kg mino vs. PBS. Supplementary table 4C. Protein-protein relations types of the differentially expressed proteins in 25 mg/kg mino vs. PBS. Supplementary table 4D. Protein-protein relations types of the differentially expressed proteins in 13.5 mg/kg mino vs. S100B. Supplementary table 4E. Protein-protein relations types of the differentially expressed proteins in 25 mg/kg mino vs. S100B. Supplementary table 4F. Protein-protein relations types of the differentially expressed proteins in 25 mg/kg mino vs. 13.5 mg/kg mino.
DOI: 10.6084/m9.figshare.13467655
title: Additional file 5 of Minocycline reduces inflammatory response and cell death in a S100B retina degeneration model

description: Additional file 5: Supplementary table 5. Functional annotation analysis of the differentially abundant proteins.
DOI: 10.6084/m9.figshare.13467655.v1
title: Additional file 5 of Minocycline reduces inflammatory response and cell death in a S100B retina degeneration model

description: Additional file 5: Supplementary table 5. Functional annotation analysis of the differentially abundant proteins.
DOI: 10.6084/m9.figshare.13467647.v1
title: Additional file 2 of Minocycline reduces inflammatory response and cell death in a S100B retina degeneration model

description: Additional file 2: Supplementary table 2a. MaxQuant parameters. Supplementary table 2b. List of proteins identified employing MaxQuant (Rattus and Homo sapiens).
DOI: 10.6084/m9.figshare.13467645
title: Additional file 1 of Minocycline reduces inflammatory response and cell death in a S100B retina degeneration model

description: Additional file 1: Supplementary table 1. Experimental design of proteomics analysis.
DOI: 10.6084/m9.figshare.13467651.v1
title: Additional file 3 of Minocycline reduces inflammatory response and cell death in a S100B retina degeneration model

description: Additional file 3: Supplementary table 3. Differentially expressed proteins in the designated groups.
DOI: 10.6084/m9.figshare.13467653
title: Additional file 4 of Minocycline reduces inflammatory response and cell death in a S100B retina degeneration model

description: Additional file 4: Supplementary table 4A. Protein-protein relations types of the differentially expressed proteins in S100B vs. PBS. Supplementary table 4B. Protein-protein relations types of the differentially expressed proteins in 13.5 mg/kg mino vs. PBS. Supplementary table 4C. Protein-protein relations types of the differentially expressed proteins in 25 mg/kg mino vs. PBS. Supplementary table 4D. Protein-protein relations types of the differentially expressed proteins in 13.5 mg/kg mino vs. S100B. Supplementary table 4E. Protein-protein relations types of the differentially expressed proteins in 25 mg/kg mino vs. S100B. Supplementary table 4F. Protein-protein relations types of the differentially expressed proteins in 25 mg/kg mino vs. 13.5 mg/kg mino.
DOI: 10.6084/m9.figshare.13467651
title: Additional file 3 of Minocycline reduces inflammatory response and cell death in a S100B retina degeneration model

description: Additional file 3: Supplementary table 3. Differentially expressed proteins in the designated groups.
DOI: 10.6084/m9.figshare.13467713.v1
title: Additional file 1 of Stability of canine and feline cerebrospinal fluid samples regarding total cell count and cell populations stored in “TransFix®/EDTA CSF sample storage tubes”

description: Additional file 1.
DOI: 10.6084/m9.figshare.13467713
title: Additional file 1 of Stability of canine and feline cerebrospinal fluid samples regarding total cell count and cell populations stored in “TransFix®/EDTA CSF sample storage tubes”

description: Additional file 1.
DOI: 10.6084/m9.figshare.13467735
title: Additional file 3 of Identification of biological correlates associated with respiratory failure in COVID-19

description: Additional file 3. For 708 candidate SNPs, eQTL information obtained from GTEx V8 for 6 tissues, including the aorta, coronary artery, skeletal muscle, lung, and atrial appendage and left ventricle in the heart.
DOI: 10.6084/m9.figshare.13467731
title: Additional file 1 of Identification of biological correlates associated with respiratory failure in COVID-19

description: Additional file 1. 144 genes identified based on the proximity of 708 candidate SNPs.
DOI: 10.6084/m9.figshare.13467735.v1
title: Additional file 3 of Identification of biological correlates associated with respiratory failure in COVID-19

description: Additional file 3. For 708 candidate SNPs, eQTL information obtained from GTEx V8 for 6 tissues, including the aorta, coronary artery, skeletal muscle, lung, and atrial appendage and left ventricle in the heart.
DOI: 10.6084/m9.figshare.13467731.v1
title: Additional file 1 of Identification of biological correlates associated with respiratory failure in COVID-19

description: Additional file 1. 144 genes identified based on the proximity of 708 candidate SNPs.
DOI: 10.6084/m9.figshare.13467737
title: Additional file 4 of Identification of biological correlates associated with respiratory failure in COVID-19

description: Additional file 4. SNPs with eQTL associations in multiple tissues.
DOI: 10.6084/m9.figshare.13467737.v1
title: Additional file 4 of Identification of biological correlates associated with respiratory failure in COVID-19

description: Additional file 4. SNPs with eQTL associations in multiple tissues.
DOI: 10.6084/m9.figshare.13467745
title: Additional file 2 of RNA sequencing identifies transcriptional changes in the rabbit larynx in response to low humidity challenge

description: Additional file 2: Table S2. Functional enrichment analyses of differentially expressed genes identified in the larynges of low humidity exposure group. Excel table containing the functional annotation enrichments divided into GO categories and KEGG obtained with DAVID (first tab), the functional annotation enrichments obtained by STRING (second tab), and the enrichement data for moderate and low humidity groups by GSEA.
DOI: 10.6084/m9.figshare.13467743.v1
title: Additional file 1 of RNA sequencing identifies transcriptional changes in the rabbit larynx in response to low humidity challenge

description: Additional file 1: Table S1. Complete list of genes identified by RNA-Seq analysis and differentially expressed genes (DEG) identified in the larynges of low humidity exposure group by Cufflinks. Excel table of all DEGs obtained by Cufflinks analysis, including Ensembl gene IDs, statistics, and Biomart annotations. Color code Ensembl_ID: green (FDR
DOI: 10.6084/m9.figshare.13467745.v1
title: Additional file 2 of RNA sequencing identifies transcriptional changes in the rabbit larynx in response to low humidity challenge

description: Additional file 2: Table S2. Functional enrichment analyses of differentially expressed genes identified in the larynges of low humidity exposure group. Excel table containing the functional annotation enrichments divided into GO categories and KEGG obtained with DAVID (first tab), the functional annotation enrichments obtained by STRING (second tab), and the enrichement data for moderate and low humidity groups by GSEA.