cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.13467743
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.13467753
title: Additional file 4 of RNA sequencing identifies transcriptional changes in the rabbit larynx in response to low humidity challenge

description: Additional file 4 Cuffdiff Cmd. Syntax used for Cufflinks analysis.
DOI: 10.6084/m9.figshare.13467753.v1
title: Additional file 4 of RNA sequencing identifies transcriptional changes in the rabbit larynx in response to low humidity challenge

description: Additional file 4 Cuffdiff Cmd. Syntax used for Cufflinks analysis.
DOI: 10.6084/m9.figshare.13467789
title: Additional file 2 of In vivo assessment of glutamine anaplerosis into the TCA cycle in human pre-malignant and malignant clonal plasma cells

description: Additional file 2: Supplementary Table 1. Comparisons of the levels of mRNA of select genes associated with glutamine metabolism via RNA sequencing between MM and MGUS groups and CD138 +/- cells.
DOI: 10.6084/m9.figshare.13467789.v1
title: Additional file 2 of In vivo assessment of glutamine anaplerosis into the TCA cycle in human pre-malignant and malignant clonal plasma cells

description: Additional file 2: Supplementary Table 1. Comparisons of the levels of mRNA of select genes associated with glutamine metabolism via RNA sequencing between MM and MGUS groups and CD138 +/- cells.
DOI: 10.6084/m9.figshare.13467801
title: Additional file 1 of Repeatability and reproducibility of the wzi high resolution melting-based clustering analysis for Klebsiella pneumoniae typing

description: Additional file 1: Table S1. Strains genomic information and Results of clustering analysis. For each strain included in the study the cluster assigned by MeltingPlot tool on the basis of wzi-3 and wzi-4 melting temperatures obtained by each instrument and operator (“CFX96” for Biorad CFX96; “Eco_RT” for Illumina Eco Real-Time; “QS_6Flex“for Applied Biosystem QuantStudio 6 Flex) are reported. The relative hospital of isolation (Hospital), Multi Locus Sequence Typing (MLST) profiles, the wzi alleles (wzi) and the clusters described in Perini et al. 2020b (Perini et al. 2020b) (Perini et al. 2020b Clusters)are also reported.
DOI: 10.6084/m9.figshare.13467801.v1
title: Additional file 1 of Repeatability and reproducibility of the wzi high resolution melting-based clustering analysis for Klebsiella pneumoniae typing

description: Additional file 1: Table S1. Strains genomic information and Results of clustering analysis. For each strain included in the study the cluster assigned by MeltingPlot tool on the basis of wzi-3 and wzi-4 melting temperatures obtained by each instrument and operator (“CFX96” for Biorad CFX96; “Eco_RT” for Illumina Eco Real-Time; “QS_6Flex“for Applied Biosystem QuantStudio 6 Flex) are reported. The relative hospital of isolation (Hospital), Multi Locus Sequence Typing (MLST) profiles, the wzi alleles (wzi) and the clusters described in Perini et al. 2020b (Perini et al. 2020b) (Perini et al. 2020b Clusters)are also reported.
DOI: 10.6084/m9.figshare.13467803
title: Additional file 2 of Repeatability and reproducibility of the wzi high resolution melting-based clustering analysis for Klebsiella pneumoniae typing

description: Additional file 2: Table S2. Instruments information. For each instrument used in this work, the model, the short name (used in manuscript, tables and figure), the sensitivity and the location are reported.
DOI: 10.6084/m9.figshare.13467807
title: Additional file 4 of Repeatability and reproducibility of the wzi high resolution melting-based clustering analysis for Klebsiella pneumoniae typing

description: Additional file 4: Table S4. Melting temperature differences among instruments and operators. The median of the average melting temperatures differences for each strain among instruments and operators are reported. In brackets, minimum and maximum difference values are reported. The comparisons between the two operators on the same instrument are reported in bold.
DOI: 10.6084/m9.figshare.13467811
title: Additional file 6 of Repeatability and reproducibility of the wzi high resolution melting-based clustering analysis for Klebsiella pneumoniae typing

description: Additional file 6: Table S6. Cross table of the clusters found in Perini et al. 2020b and the clusters of each instrument used in this work is reported. The discrepancies from the clusters found in Perini et al. 2020b are reported in bold.
DOI: 10.6084/m9.figshare.13467815.v1
title: Additional file 1 of Genome-wide identification and expression analysis of the CLC gene family in pomegranate (Punica granatum) reveals its roles in salt resistance

description: Additional file 1: Table S1. A summary of 15 species for phylogenetic analysis and their genomic sources. Table S2. List of CLC proteins used for constructing the phylogenetic tree. Table S3. Primers used in qRT-PCR analysis for PgCLCs. Table S4. Dry weights of pomegranate cuttings under NaCl stress. (XLS 67 kb)
DOI: 10.6084/m9.figshare.13467809
title: Additional file 5 of Repeatability and reproducibility of the wzi high resolution melting-based clustering analysis for Klebsiella pneumoniae typing

description: Additional file 5: Table S5. Results of statistical analyses. The results of statistical analyses are reported.
DOI: 10.6084/m9.figshare.13467811.v1
title: Additional file 6 of Repeatability and reproducibility of the wzi high resolution melting-based clustering analysis for Klebsiella pneumoniae typing

description: Additional file 6: Table S6. Cross table of the clusters found in Perini et al. 2020b and the clusters of each instrument used in this work is reported. The discrepancies from the clusters found in Perini et al. 2020b are reported in bold.
DOI: 10.6084/m9.figshare.13467815
title: Additional file 1 of Genome-wide identification and expression analysis of the CLC gene family in pomegranate (Punica granatum) reveals its roles in salt resistance

description: Additional file 1: Table S1. A summary of 15 species for phylogenetic analysis and their genomic sources. Table S2. List of CLC proteins used for constructing the phylogenetic tree. Table S3. Primers used in qRT-PCR analysis for PgCLCs. Table S4. Dry weights of pomegranate cuttings under NaCl stress. (XLS 67 kb)
DOI: 10.6084/m9.figshare.13467817
title: Additional file 2 of Detecting missing IS-A relations in the NCI Thesaurus using an enhanced hybrid approach

description: Additional file 2.. Causes for false positives.
DOI: 10.6084/m9.figshare.13467813
title: Additional file 1 of Detecting missing IS-A relations in the NCI Thesaurus using an enhanced hybrid approach

description: Additional file 1. Evaluation results for 55 potentially missing IS-A relations identified by our method.
DOI: 10.6084/m9.figshare.13467813.v1
title: Additional file 1 of Detecting missing IS-A relations in the NCI Thesaurus using an enhanced hybrid approach

description: Additional file 1. Evaluation results for 55 potentially missing IS-A relations identified by our method.
DOI: 10.6084/m9.figshare.13467817.v1
title: Additional file 2 of Detecting missing IS-A relations in the NCI Thesaurus using an enhanced hybrid approach

description: Additional file 2.. Causes for false positives.
DOI: 10.6084/m9.figshare.13467805
title: Additional file 3 of Repeatability and reproducibility of the wzi high resolution melting-based clustering analysis for Klebsiella pneumoniae typing

description: Additional file 3: Table S3. Strains melting temperatures. The instrument used for the HRM analysis, the operator who performed the HRM analysis, the primer set used, the melting temperature replicates (T1, T2 and T3) and their average melting temperature (aTm) are reported for each strain.
DOI: 10.6084/m9.figshare.13467859.v1
title: Additional file 3 of Effects of habitat edges on vegetation structure and the vulnerable golden-brown mouse lemur (Microcebus ravelobensis) in northwestern Madagascar

description: Additional file 3. Dataset that was used for the regression analyses between all vegetation parameters and the two animal parameters abundance and body mass (one value per 100 m per transect).
DOI: 10.6084/m9.figshare.13467857
title: Additional file 2 of Effects of habitat edges on vegetation structure and the vulnerable golden-brown mouse lemur (Microcebus ravelobensis) in northwestern Madagascar

description: Additional file 2. Dataset that was used for the statistical comparison of all vegetation and animal parameters (one value per double plot per transect if applicable) between the “edge habitats” and the “interior habitats”.
DOI: 10.6084/m9.figshare.13467859
title: Additional file 3 of Effects of habitat edges on vegetation structure and the vulnerable golden-brown mouse lemur (Microcebus ravelobensis) in northwestern Madagascar

description: Additional file 3. Dataset that was used for the regression analyses between all vegetation parameters and the two animal parameters abundance and body mass (one value per 100 m per transect).
DOI: 10.6084/m9.figshare.13467857.v1
title: Additional file 2 of Effects of habitat edges on vegetation structure and the vulnerable golden-brown mouse lemur (Microcebus ravelobensis) in northwestern Madagascar

description: Additional file 2. Dataset that was used for the statistical comparison of all vegetation and animal parameters (one value per double plot per transect if applicable) between the “edge habitats” and the “interior habitats”.
DOI: 10.6084/m9.figshare.13467875.v1
title: Additional file 5 of A highly contiguous genome assembly of Brassica nigra (BB) and revised nomenclature for the pseudochromosomes

description: Additional file 5: Supplementary Table 4. Genes predicted on different pseudochromosomes of Brassica nigra Sangam and their orthologs in Arabidopsis thaliana (along with their respective gene blocks) and B. juncea Varuna B genome (BjuB) and B. rapa Chiifu V3.0 (BraA) genome. Column A – gene blocks as identified in A. thaliana; Column B – A. thaliana orthologs with gene id; Column C – paleogenome of B. nigra to which the gene belongs; Column D – predicted B. nigra gene id; Column E – physical position of the genes on the pseudochromosomes; Column F – expression status of the predicted B. nigra genes (“Expressed” means that the gene was found in the transcriptome analysis in this study or other studies described in Supplementary File 2, “Not expressed” represents – expression not found); Column G – B. juncea B genome (BjuB) orthologs with the gene id; Column H –B. rapa V3.0 (BraA) orthologs with the gene id.
DOI: 10.6084/m9.figshare.13467875
title: Additional file 5 of A highly contiguous genome assembly of Brassica nigra (BB) and revised nomenclature for the pseudochromosomes

description: Additional file 5: Supplementary Table 4. Genes predicted on different pseudochromosomes of Brassica nigra Sangam and their orthologs in Arabidopsis thaliana (along with their respective gene blocks) and B. juncea Varuna B genome (BjuB) and B. rapa Chiifu V3.0 (BraA) genome. Column A – gene blocks as identified in A. thaliana; Column B – A. thaliana orthologs with gene id; Column C – paleogenome of B. nigra to which the gene belongs; Column D – predicted B. nigra gene id; Column E – physical position of the genes on the pseudochromosomes; Column F – expression status of the predicted B. nigra genes (“Expressed” means that the gene was found in the transcriptome analysis in this study or other studies described in Supplementary File 2, “Not expressed” represents – expression not found); Column G – B. juncea B genome (BjuB) orthologs with the gene id; Column H –B. rapa V3.0 (BraA) orthologs with the gene id.
DOI: 10.6084/m9.figshare.13467939.v1
title: Additional file 1 of SeqURE – a new copy-capture based method for sequencing of unknown Retroposition events

description: Additional file 1: Supplementary Table 1. A detailed description of individual-specific Alu insertions.
DOI: 10.6084/m9.figshare.13467939
title: Additional file 1 of SeqURE – a new copy-capture based method for sequencing of unknown Retroposition events

description: Additional file 1: Supplementary Table 1. A detailed description of individual-specific Alu insertions.
DOI: 10.6084/m9.figshare.13467941.v1
title: Additional file 2 of SeqURE – a new copy-capture based method for sequencing of unknown Retroposition events

description: Additional file 2: Supplementary Table 2. TSD identification.
DOI: 10.6084/m9.figshare.13467941
title: Additional file 2 of SeqURE – a new copy-capture based method for sequencing of unknown Retroposition events

description: Additional file 2: Supplementary Table 2. TSD identification.
DOI: 10.6084/m9.figshare.13467945
title: Additional file 3 of SeqURE – a new copy-capture based method for sequencing of unknown Retroposition events

description: Additional file 3: Supplementary Table 3. Oligonucleotide sequences used for library preparation and locus-specific PCR.
DOI: 10.6084/m9.figshare.13467945.v1
title: Additional file 3 of SeqURE – a new copy-capture based method for sequencing of unknown Retroposition events

description: Additional file 3: Supplementary Table 3. Oligonucleotide sequences used for library preparation and locus-specific PCR.
DOI: 10.6084/m9.figshare.13467975
title: Additional file 2 of Feedback inhibition of AMT1 NH4+-transporters mediated by CIPK15 kinase

description: Additional file 2. Individual values for figures where the number of independent replicates is less than 6 (n
DOI: 10.6084/m9.figshare.13467975.v1
title: Additional file 2 of Feedback inhibition of AMT1 NH4+-transporters mediated by CIPK15 kinase

description: Additional file 2. Individual values for figures where the number of independent replicates is less than 6 (n
DOI: 10.6084/m9.figshare.13468005
title: Additional file 2 of Improving maternal health services through social accountability interventions in Nepal: an analytical review of existing literature

description: Additional file 2: Appendix 2. References details
DOI: 10.6084/m9.figshare.13468003
title: Additional file 1 of Improving maternal health services through social accountability interventions in Nepal: an analytical review of existing literature

description: Additional file 1: Appendix 1. Search strategy
DOI: 10.6084/m9.figshare.13468003.v1
title: Additional file 1 of Improving maternal health services through social accountability interventions in Nepal: an analytical review of existing literature

description: Additional file 1: Appendix 1. Search strategy
DOI: 10.6084/m9.figshare.13468005.v1
title: Additional file 2 of Improving maternal health services through social accountability interventions in Nepal: an analytical review of existing literature

description: Additional file 2: Appendix 2. References details
DOI: 10.6084/m9.figshare.13468021.v1
title: Additional file 5 of Corticosteroid use in COVID-19 patients: a systematic review and meta-analysis on clinical outcomes

description: Additional file 5. NOS score.
DOI: 10.6084/m9.figshare.13468021
title: Additional file 5 of Corticosteroid use in COVID-19 patients: a systematic review and meta-analysis on clinical outcomes

description: Additional file 5. NOS score.
DOI: 10.6084/m9.figshare.13468077.v1
title: Additional file 3 of Identification of FMRP target mRNAs in the developmental brain: FMRP might coordinate Ras/MAPK, Wnt/β-catenin, and mTOR signaling during corticogenesis

description: Additional file 3: Table S3. Hypergeometric distribution analyses between FMRP target genes.
DOI: 10.6084/m9.figshare.13468077
title: Additional file 3 of Identification of FMRP target mRNAs in the developmental brain: FMRP might coordinate Ras/MAPK, Wnt/β-catenin, and mTOR signaling during corticogenesis

description: Additional file 3: Table S3. Hypergeometric distribution analyses between FMRP target genes.
DOI: 10.6084/m9.figshare.13468075
title: Additional file 2 of Identification of FMRP target mRNAs in the developmental brain: FMRP might coordinate Ras/MAPK, Wnt/β-catenin, and mTOR signaling during corticogenesis

description: Additional file 2: Table S2. Gene ontology (biological process) analysis of the 118 shared genes.
DOI: 10.6084/m9.figshare.13468073.v1
title: Additional file 1 of Identification of FMRP target mRNAs in the developmental brain: FMRP might coordinate Ras/MAPK, Wnt/β-catenin, and mTOR signaling during corticogenesis

description: Additional file 1: Table S1. 865 FMRP target genes identified using RIP-seq.
DOI: 10.6084/m9.figshare.13468073
title: Additional file 1 of Identification of FMRP target mRNAs in the developmental brain: FMRP might coordinate Ras/MAPK, Wnt/β-catenin, and mTOR signaling during corticogenesis

description: Additional file 1: Table S1. 865 FMRP target genes identified using RIP-seq.
DOI: 10.6084/m9.figshare.13468079.v1
title: Additional file 4 of Identification of FMRP target mRNAs in the developmental brain: FMRP might coordinate Ras/MAPK, Wnt/β-catenin, and mTOR signaling during corticogenesis

description: Additional file 4: Table S4. Primer sequences used for RIP-qPCR and RT-qPCR.
DOI: 10.6084/m9.figshare.13468079
title: Additional file 4 of Identification of FMRP target mRNAs in the developmental brain: FMRP might coordinate Ras/MAPK, Wnt/β-catenin, and mTOR signaling during corticogenesis

description: Additional file 4: Table S4. Primer sequences used for RIP-qPCR and RT-qPCR.
DOI: 10.6084/m9.figshare.13468109.v1
title: Additional file 2 of Male recombination map of the autosomal genome in German Holstein

description: Additional file 2: Table S1. Genetic-map coordinates. The table contains the genetic-map coordinates that were estimated from deterministic (cM_deterministic) and likelihood-based (cM_likelihood) approaches in Holstein cattle. Marker physical coordinates (Mbp_position) are based on the ARS-UCD1.2 genome assembly. Furthermore, recrate_adjacent_deterministic denotes the recombination rate between adjacent markers based on the deterministic approach.
DOI: 10.6084/m9.figshare.13468109
title: Additional file 2 of Male recombination map of the autosomal genome in German Holstein

description: Additional file 2: Table S1. Genetic-map coordinates. The table contains the genetic-map coordinates that were estimated from deterministic (cM_deterministic) and likelihood-based (cM_likelihood) approaches in Holstein cattle. Marker physical coordinates (Mbp_position) are based on the ARS-UCD1.2 genome assembly. Furthermore, recrate_adjacent_deterministic denotes the recombination rate between adjacent markers based on the deterministic approach.
DOI: 10.6084/m9.figshare.13468115.v1
title: Additional file 5 of Male recombination map of the autosomal genome in German Holstein

description: Additional file 5: Table S2. Panel of misplaced candidates in the ARS-UCD1.2 genome assembly. The table lists all the markers that are putatively misplaced in the underlying genome assembly, as revealed by the likelihood-based approach. Physical position (bp) corresponds to ARS-UCD1.2 genome assembly; the index refers to consecutive numbering of SNPs to facilitate the identification of clusters.
DOI: 10.6084/m9.figshare.13468115
title: Additional file 5 of Male recombination map of the autosomal genome in German Holstein

description: Additional file 5: Table S2. Panel of misplaced candidates in the ARS-UCD1.2 genome assembly. The table lists all the markers that are putatively misplaced in the underlying genome assembly, as revealed by the likelihood-based approach. Physical position (bp) corresponds to ARS-UCD1.2 genome assembly; the index refers to consecutive numbering of SNPs to facilitate the identification of clusters.
DOI: 10.6084/m9.figshare.13468143
title: Additional file 1 of Identification of candidate genes controlling fiber quality traits in upland cotton through integration of meta-QTL, significant SNP and transcriptomic data

description: Additional file 1: Table S1 Initial QTL location on upland cotton TM-1 reference genome. Table S2. The information of the meta-QTL. Table S3. SNPs associated with fiber quality traits from 15 papers. Table S4. Significant SNPs location on upland cotton TM-1 reference genome. Table S5. Significant SNPs in the mQTL. Table S6. Candidate genes closely linked SNPs in the meta-QTL. Table S7. GO enrichment of candidate genes. Table S8. The expression of candidate genes in ten tissues.
DOI: 10.6084/m9.figshare.13468143.v1
title: Additional file 1 of Identification of candidate genes controlling fiber quality traits in upland cotton through integration of meta-QTL, significant SNP and transcriptomic data

description: Additional file 1: Table S1 Initial QTL location on upland cotton TM-1 reference genome. Table S2. The information of the meta-QTL. Table S3. SNPs associated with fiber quality traits from 15 papers. Table S4. Significant SNPs location on upland cotton TM-1 reference genome. Table S5. Significant SNPs in the mQTL. Table S6. Candidate genes closely linked SNPs in the meta-QTL. Table S7. GO enrichment of candidate genes. Table S8. The expression of candidate genes in ten tissues.
DOI: 10.6084/m9.figshare.13468193
title: Additional file 2 of High-resolution analyses of human sperm dynamic methylome reveal thousands of novel age-related epigenetic alterations

description: Additional file 2: Table S4. Age related hypermethylated DMRs and closest genes with OMIM genes annotated.
DOI: 10.6084/m9.figshare.13468193.v1
title: Additional file 2 of High-resolution analyses of human sperm dynamic methylome reveal thousands of novel age-related epigenetic alterations

description: Additional file 2: Table S4. Age related hypermethylated DMRs and closest genes with OMIM genes annotated.
DOI: 10.6084/m9.figshare.13468197.v1
title: Additional file 3 of High-resolution analyses of human sperm dynamic methylome reveal thousands of novel age-related epigenetic alterations

description: Additional file 3: Table S5. Enriched gene lists by GREAT in hyper- or Hypomethylated regions.
DOI: 10.6084/m9.figshare.13468201.v1
title: Additional file 4 of High-resolution analyses of human sperm dynamic methylome reveal thousands of novel age-related epigenetic alterations

description: Additional file 4: Table S6. WGCNA module enriched genes and CpGs.
DOI: 10.6084/m9.figshare.13468197
title: Additional file 3 of High-resolution analyses of human sperm dynamic methylome reveal thousands of novel age-related epigenetic alterations

description: Additional file 3: Table S5. Enriched gene lists by GREAT in hyper- or Hypomethylated regions.
DOI: 10.6084/m9.figshare.13468201
title: Additional file 4 of High-resolution analyses of human sperm dynamic methylome reveal thousands of novel age-related epigenetic alterations

description: Additional file 4: Table S6. WGCNA module enriched genes and CpGs.
DOI: 10.6084/m9.figshare.13468213
title: Additional file 2 of The identification of co-expressed gene modules in Streptococcus pneumonia from colonization to infection to predict novel potential virulence genes

description: Additional file 2:. DEGs. Differentially expressed genes.
DOI: 10.6084/m9.figshare.13468209
title: Additional file 1 of The identification of co-expressed gene modules in Streptococcus pneumonia from colonization to infection to predict novel potential virulence genes

description: Additional file 1:. SPD genes. All genes were detected by the SPD algorithm.
DOI: 10.6084/m9.figshare.13468209.v1
title: Additional file 1 of The identification of co-expressed gene modules in Streptococcus pneumonia from colonization to infection to predict novel potential virulence genes

description: Additional file 1:. SPD genes. All genes were detected by the SPD algorithm.