cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7047275.v1
title: Additional file 7: of Whole exome sequencing in adult-onset hearing loss reveals a high load of predicted pathogenic variants in known deafness-associated genes and identifies new candidate genes

description: Table S3. listing genes reported to underlie deafness in humans and/or mice. (XLS 45 kb)
DOI: 10.6084/m9.figshare.12885536
title: R0189_20170925a_videos

description: Rat 0189, skilled reaching data collected on 9/25/2017 in Leventhal laboratory by Alexandra Bova
DOI: 10.6084/m9.figshare.7047242
title: Additional file 4: of Whole exome sequencing in adult-onset hearing loss reveals a high load of predicted pathogenic variants in known deafness-associated genes and identifies new candidate genes

description: Table S1. which lists the software prediction tools used to call and annotate variants, with relevant references. (XLS 30 kb)
DOI: 10.6084/m9.figshare.7047239
title: Additional file 9: of Draft genome sequence of wild Prunus yedoensis reveals massive inter-specific hybridization between sympatric flowering cherries

description: Table S8. Coverage of individual chromosomes of peach (Pp), sweet cherry (Pa), and Chinese plum (Pm) showing synteny with the counterpart of wild P. yedoensis (Pyn) genome. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.7047239.v1
title: Additional file 9: of Draft genome sequence of wild Prunus yedoensis reveals massive inter-specific hybridization between sympatric flowering cherries

description: Table S8. Coverage of individual chromosomes of peach (Pp), sweet cherry (Pa), and Chinese plum (Pm) showing synteny with the counterpart of wild P. yedoensis (Pyn) genome. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.7047242.v1
title: Additional file 4: of Whole exome sequencing in adult-onset hearing loss reveals a high load of predicted pathogenic variants in known deafness-associated genes and identifies new candidate genes

description: Table S1. which lists the software prediction tools used to call and annotate variants, with relevant references. (XLS 30 kb)
DOI: 10.6084/m9.figshare.7047218
title: Additional file 8: of Draft genome sequence of wild Prunus yedoensis reveals massive inter-specific hybridization between sympatric flowering cherries

description: Table S7. Summary of alternative splicing events identified in protein-coding genes. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.7047218.v1
title: Additional file 8: of Draft genome sequence of wild Prunus yedoensis reveals massive inter-specific hybridization between sympatric flowering cherries

description: Table S7. Summary of alternative splicing events identified in protein-coding genes. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.7047209
title: Additional file 2: of Early lysosomal maturation deficits in microglia triggers enhanced lysosomal activity in other brain cells of progranulin knockout mice

description: Table S1. mRNA expression of selected genes associated with the lysosome-autophagy degradation pathway in brain of Grn+/+ and Grnâ /â mice at 6 and 12 months of age. (XLSX 30 kb)
DOI: 10.6084/m9.figshare.7047206
title: Additional file 7: of Draft genome sequence of wild Prunus yedoensis reveals massive inter-specific hybridization between sympatric flowering cherries

description: Table S6. Annotation statistics of the wild P. yedoensis gene set. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.7047209.v1
title: Additional file 2: of Early lysosomal maturation deficits in microglia triggers enhanced lysosomal activity in other brain cells of progranulin knockout mice

description: Table S1. mRNA expression of selected genes associated with the lysosome-autophagy degradation pathway in brain of Grn+/+ and Grnâ /â mice at 6 and 12 months of age. (XLSX 30 kb)
DOI: 10.6084/m9.figshare.7047206.v1
title: Additional file 7: of Draft genome sequence of wild Prunus yedoensis reveals massive inter-specific hybridization between sympatric flowering cherries

description: Table S6. Annotation statistics of the wild P. yedoensis gene set. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.7047200
title: Additional file 8 of Discovering lncRNA mediated sponge interactions in breast cancer molecular subtypes

description: List of Prognostic Sponge Interactions, its corresponding pvalues and number of patients in groups are provided. (XLSX 2108 kb)
DOI: 10.6084/m9.figshare.7047200.v1
title: Additional file 8 of Discovering lncRNA mediated sponge interactions in breast cancer molecular subtypes

description: List of Prognostic Sponge Interactions, its corresponding pvalues and number of patients in groups are provided. (XLSX 2108 kb)
DOI: 10.6084/m9.figshare.7047191
title: Additional file 6: of Draft genome sequence of wild Prunus yedoensis reveals massive inter-specific hybridization between sympatric flowering cherries

description: Table S5. Statistics of gene models predicted from the draft genome of wild P. yedoensis. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.7047191.v1
title: Additional file 6: of Draft genome sequence of wild Prunus yedoensis reveals massive inter-specific hybridization between sympatric flowering cherries

description: Table S5. Statistics of gene models predicted from the draft genome of wild P. yedoensis. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.7047185
title: Additional file 7 of Discovering lncRNA mediated sponge interactions in breast cancer molecular subtypes

description: List of Spatially Proximal Sponge Interactions. Chromosome locations of the RNAs are given. Moreover, how many of the RNAs in the sponge(lncRNA, mRNA or/and miRNA) are spatially proximal are provided in this list. (XLSX 93 kb)
DOI: 10.6084/m9.figshare.7047185.v1
title: Additional file 7 of Discovering lncRNA mediated sponge interactions in breast cancer molecular subtypes

description: List of Spatially Proximal Sponge Interactions. Chromosome locations of the RNAs are given. Moreover, how many of the RNAs in the sponge(lncRNA, mRNA or/and miRNA) are spatially proximal are provided in this list. (XLSX 93 kb)
DOI: 10.6084/m9.figshare.7047173
title: Additional file 6 of Discovering lncRNA mediated sponge interactions in breast cancer molecular subtypes

description: List of mRNA clusters in sponge interactions. For the same subtype and same lncRNA:miRNA interactions mRNAs clustered. (XLSX 89 kb)
DOI: 10.6084/m9.figshare.7047176
title: Additional file 15: of Whole exome sequencing in adult-onset hearing loss reveals a high load of predicted pathogenic variants in known deafness-associated genes and identifies new candidate genes

description: Table S11. which contains further details of the validated variants listed in Table 3. (XLS 32 kb)
DOI: 10.6084/m9.figshare.7047173.v1
title: Additional file 6 of Discovering lncRNA mediated sponge interactions in breast cancer molecular subtypes

description: List of mRNA clusters in sponge interactions. For the same subtype and same lncRNA:miRNA interactions mRNAs clustered. (XLSX 89 kb)
DOI: 10.6084/m9.figshare.7047170
title: Additional file 5: of Draft genome sequence of wild Prunus yedoensis reveals massive inter-specific hybridization between sympatric flowering cherries

description: Table S4. Summary of repetitive sequences identified in the draft genome of wild P. yedoensis. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.7047176.v1
title: Additional file 15: of Whole exome sequencing in adult-onset hearing loss reveals a high load of predicted pathogenic variants in known deafness-associated genes and identifies new candidate genes

description: Table S11. which contains further details of the validated variants listed in Table 3. (XLS 32 kb)
DOI: 10.6084/m9.figshare.7047170.v1
title: Additional file 5: of Draft genome sequence of wild Prunus yedoensis reveals massive inter-specific hybridization between sympatric flowering cherries

description: Table S4. Summary of repetitive sequences identified in the draft genome of wild P. yedoensis. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.7047158
title: Additional file 5 of Discovering lncRNA mediated sponge interactions in breast cancer molecular subtypes

description: Prognostic Sponge Interactions Cytoscape Network File. (CYS 46 kb)
DOI: 10.6084/m9.figshare.7047158.v1
title: Additional file 5 of Discovering lncRNA mediated sponge interactions in breast cancer molecular subtypes

description: Prognostic Sponge Interactions Cytoscape Network File. (CYS 46 kb)
DOI: 10.6084/m9.figshare.7047149
title: Additional file 4: of Draft genome sequence of wild Prunus yedoensis reveals massive inter-specific hybridization between sympatric flowering cherries

description: Table S3. Evaluation of gene space coverage of the wild P. yedoensis genome using transcriptome unigenes. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.7047149.v1
title: Additional file 4: of Draft genome sequence of wild Prunus yedoensis reveals massive inter-specific hybridization between sympatric flowering cherries

description: Table S3. Evaluation of gene space coverage of the wild P. yedoensis genome using transcriptome unigenes. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.7047143
title: Additional file 4 of Discovering lncRNA mediated sponge interactions in breast cancer molecular subtypes

description: List of mRNAs participating in prognostic sponge interactions and their distribution over subtypes. (XLSX 18 kb)
DOI: 10.6084/m9.figshare.7047143.v1
title: Additional file 4 of Discovering lncRNA mediated sponge interactions in breast cancer molecular subtypes

description: List of mRNAs participating in prognostic sponge interactions and their distribution over subtypes. (XLSX 18 kb)
DOI: 10.6084/m9.figshare.7047131
title: Additional file 3: of Draft genome sequence of wild Prunus yedoensis reveals massive inter-specific hybridization between sympatric flowering cherries

description: Table S2. Statistics of transcriptome sequence data of wild P. yedoensis (Pyn-Jeju2) used in this study. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.7047131.v1
title: Additional file 3: of Draft genome sequence of wild Prunus yedoensis reveals massive inter-specific hybridization between sympatric flowering cherries

description: Table S2. Statistics of transcriptome sequence data of wild P. yedoensis (Pyn-Jeju2) used in this study. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.7047128
title: Additional file 13: of Sequence and structural variation in the genome of the Biomphalaria glabrata embryonic (Bge) cell line

description: Primers used for PCR and Sanger Sequencing. List of forward and reverse primers used to amplify selected fragments of Bge3 genomic DNA containing predicted high-impact mutations. Sequences were later Sanger sequenced and analyzed to confirm mutations. Amplicon sizes and annealing temperatures used for each amplification reaction are listed. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.7047128.v1
title: Additional file 13: of Sequence and structural variation in the genome of the Biomphalaria glabrata embryonic (Bge) cell line

description: Primers used for PCR and Sanger Sequencing. List of forward and reverse primers used to amplify selected fragments of Bge3 genomic DNA containing predicted high-impact mutations. Sequences were later Sanger sequenced and analyzed to confirm mutations. Amplicon sizes and annealing temperatures used for each amplification reaction are listed. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.7047119
title: Additional file 3 of Discovering lncRNA mediated sponge interactions in breast cancer molecular subtypes

description: List of mRNAs participating in sponge interactions and their distribution over subtypes. (XLSX 70 kb)
DOI: 10.6084/m9.figshare.7047119.v1
title: Additional file 3 of Discovering lncRNA mediated sponge interactions in breast cancer molecular subtypes

description: List of mRNAs participating in sponge interactions and their distribution over subtypes. (XLSX 70 kb)
DOI: 10.6084/m9.figshare.7047107
title: Additional file 2: of Draft genome sequence of wild Prunus yedoensis reveals massive inter-specific hybridization between sympatric flowering cherries

description: Table S1. Statistics of genome sequence data of wild P. yedoensis (Pyn-Jeju2) used in this study. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.7047104
title: Additional file 2 of Discovering lncRNA mediated sponge interactions in breast cancer molecular subtypes

description: List of Subtype Specific lncRNA mediated Sponge Interactions. Partial correlation and KCI values are provided in this list. Moreover, target interaction for lncRNA:miRNA and mRNA:miRNA are given with their supported databases. (XLSX 2705 kb)
DOI: 10.6084/m9.figshare.7047107.v1
title: Additional file 2: of Draft genome sequence of wild Prunus yedoensis reveals massive inter-specific hybridization between sympatric flowering cherries

description: Table S1. Statistics of genome sequence data of wild P. yedoensis (Pyn-Jeju2) used in this study. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.7047098
title: Additional file 12: of Sequence and structural variation in the genome of the Biomphalaria glabrata embryonic (Bge) cell line

description: Selected proteins of interest with high-impact mutations. Selected proteins of interest predicted to have high-impact mutations were grouped by putative functions according to current NCBI or UniProt annotations. BGLB / NCBI accession numbers and their predicted identities are provided. For each entry, the exact location of the mutation in the scaffold is indicated, followed by the nucleotide observed in the snail (reference allele) and the predicted mutated Bge nucleotide (alternative allele). DP4 scores, indicating the numbers of forward and reverse high-quality reads of the reference and the alternate, respectively, as well as the predicted high-impact effect are also presented. Eighty proteins were selected and the fragment containing the mutation submitted to PCR amplification. Each mutation was then verified by Sanger sequencing. The resulting PCR-amplification success or failure, as well as the resulting confirmation of mutation is reported. Remaining proteins are described as unchecked. (XLSX 28 kb)
DOI: 10.6084/m9.figshare.7047104.v1
title: Additional file 2 of Discovering lncRNA mediated sponge interactions in breast cancer molecular subtypes

description: List of Subtype Specific lncRNA mediated Sponge Interactions. Partial correlation and KCI values are provided in this list. Moreover, target interaction for lncRNA:miRNA and mRNA:miRNA are given with their supported databases. (XLSX 2705 kb)
DOI: 10.6084/m9.figshare.7047098.v1
title: Additional file 12: of Sequence and structural variation in the genome of the Biomphalaria glabrata embryonic (Bge) cell line

description: Selected proteins of interest with high-impact mutations. Selected proteins of interest predicted to have high-impact mutations were grouped by putative functions according to current NCBI or UniProt annotations. BGLB / NCBI accession numbers and their predicted identities are provided. For each entry, the exact location of the mutation in the scaffold is indicated, followed by the nucleotide observed in the snail (reference allele) and the predicted mutated Bge nucleotide (alternative allele). DP4 scores, indicating the numbers of forward and reverse high-quality reads of the reference and the alternate, respectively, as well as the predicted high-impact effect are also presented. Eighty proteins were selected and the fragment containing the mutation submitted to PCR amplification. Each mutation was then verified by Sanger sequencing. The resulting PCR-amplification success or failure, as well as the resulting confirmation of mutation is reported. Remaining proteins are described as unchecked. (XLSX 28 kb)
DOI: 10.6084/m9.figshare.7047062
title: Additional file 12: of Draft genome sequence of wild Prunus yedoensis reveals massive inter-specific hybridization between sympatric flowering cherries

description: Table S11. Comparison of the chloroplast genomes between Prunus accessions. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.7047059
title: Additional file 2: of “Low-” versus “high”-frequency oscillation and right ventricular function in ARDS. A randomized crossover study

description: Actual p values for results reported in Fig. 3 of the main paper. (RTF 2267 kb)
DOI: 10.6084/m9.figshare.7047062.v1
title: Additional file 12: of Draft genome sequence of wild Prunus yedoensis reveals massive inter-specific hybridization between sympatric flowering cherries

description: Table S11. Comparison of the chloroplast genomes between Prunus accessions. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.7047053
title: Additional file 11: of Draft genome sequence of wild Prunus yedoensis reveals massive inter-specific hybridization between sympatric flowering cherries

description: Table S10. Summary of accessions and Illumina short-read data used in whole-genome resequencing analysis. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.7047059.v1
title: Additional file 2: of “Low-” versus “high”-frequency oscillation and right ventricular function in ARDS. A randomized crossover study

description: Actual p values for results reported in Fig. 3 of the main paper. (RTF 2267 kb)
DOI: 10.6084/m9.figshare.7047053.v1
title: Additional file 11: of Draft genome sequence of wild Prunus yedoensis reveals massive inter-specific hybridization between sympatric flowering cherries

description: Table S10. Summary of accessions and Illumina short-read data used in whole-genome resequencing analysis. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.7047032
title: Additional file 10: of Draft genome sequence of wild Prunus yedoensis reveals massive inter-specific hybridization between sympatric flowering cherries

description: Table S9. Over- or under-represented gene families in the wild P. yedoensis genome compared to the P. avium, P. mume, and P. persica genomes. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.7047032.v1
title: Additional file 10: of Draft genome sequence of wild Prunus yedoensis reveals massive inter-specific hybridization between sympatric flowering cherries

description: Table S9. Over- or under-represented gene families in the wild P. yedoensis genome compared to the P. avium, P. mume, and P. persica genomes. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.7047023
title: Additional file 4: of Genome organization and chromatin analysis identify transcriptional downregulation of insulin-like growth factor signaling as a hallmark of aging in developing B cells

description: Chromatin segmentation output for aged pre-B cells. TXT file listing chromatin segmentation output for aged pre-B cells. (TXT 4190 kb)
DOI: 10.6084/m9.figshare.7047023.v1
title: Additional file 4: of Genome organization and chromatin analysis identify transcriptional downregulation of insulin-like growth factor signaling as a hallmark of aging in developing B cells

description: Chromatin segmentation output for aged pre-B cells. TXT file listing chromatin segmentation output for aged pre-B cells. (TXT 4190 kb)
DOI: 10.6084/m9.figshare.7046987
title: Additional file 3: of Genome organization and chromatin analysis identify transcriptional downregulation of insulin-like growth factor signaling as a hallmark of aging in developing B cells

description: Chromatin segmentation output for young pre-B cells. TXT file listing chromatin segmentation output for young pre-B cells. (TXT 4627 kb)
DOI: 10.6084/m9.figshare.7046987.v1
title: Additional file 3: of Genome organization and chromatin analysis identify transcriptional downregulation of insulin-like growth factor signaling as a hallmark of aging in developing B cells

description: Chromatin segmentation output for young pre-B cells. TXT file listing chromatin segmentation output for young pre-B cells. (TXT 4627 kb)
DOI: 10.6084/m9.figshare.7046954
title: Additional file 2: of Novel 18-gene signature for predicting relapse in ER-positive, HER2-negative breast cancer

description: Table S1. List of 585 candidate genes. Table S2. List and identifiers for the 747-patient microarray expression data cohort. Table S3. List of 454 Affymetrix probes studied. Table S4. List of 212 genes significantly prognostic (pâ
DOI: 10.6084/m9.figshare.7046954.v1
title: Additional file 2: of Novel 18-gene signature for predicting relapse in ER-positive, HER2-negative breast cancer

description: Table S1. List of 585 candidate genes. Table S2. List and identifiers for the 747-patient microarray expression data cohort. Table S3. List of 454 Affymetrix probes studied. Table S4. List of 212 genes significantly prognostic (pâ
DOI: 10.6084/m9.figshare.7046945
title: Additional file 1: of Genome organization and chromatin analysis identify transcriptional downregulation of insulin-like growth factor signaling as a hallmark of aging in developing B cells

description: Supplementary Tables S1â S16. XLSX file describing datasets generated for this study. (XLSX 369 kb)
DOI: 10.6084/m9.figshare.7046945.v1
title: Additional file 1: of Genome organization and chromatin analysis identify transcriptional downregulation of insulin-like growth factor signaling as a hallmark of aging in developing B cells

description: Supplementary Tables S1â S16. XLSX file describing datasets generated for this study. (XLSX 369 kb)
DOI: 10.6084/m9.figshare.7046831
title: Mycorrhizal status information on plant species recorded in the study

description: Table based on Gerz, M., Bueno, C. G., Zobel, M., & Moora, M. (2016). Plant community mycorrhization in temperate forests and grasslands: relations with edaphic properties and plant diversity. <i>Journal of Vegetation Science</i>, <i>27</i>(1), 89–99. https://doi.org/10.1111/jvs.12338, but has been updated significantly since original publishing.
DOI: 10.6084/m9.figshare.7046831.v1
title: Mycorrhizal status information on plant species recorded in the study

description: Table based on Gerz, M., Bueno, C. G., Zobel, M., & Moora, M. (2016). Plant community mycorrhization in temperate forests and grasslands: relations with edaphic properties and plant diversity. <i>Journal of Vegetation Science</i>, <i>27</i>(1), 89–99. https://doi.org/10.1111/jvs.12338, but has been updated significantly since original publishing.
DOI: 10.6084/m9.figshare.7046816
title: Abundances of arbuscular mycorrhizal fungal virtual taxon (VT) sequences in plant species' roots

description: Abundance data for arbuscular mycorrhizal fungal taxa sequenced from the roots of a plant species within a single semi-natural grassland community. Including the plant species mycorrhizal status and functional group.
DOI: 10.6084/m9.figshare.7046816.v1
title: Abundances of arbuscular mycorrhizal fungal virtual taxon (VT) sequences in plant species' roots

description: Abundance data for arbuscular mycorrhizal fungal taxa sequenced from the roots of a plant species within a single semi-natural grassland community. Including the plant species mycorrhizal status and functional group.
DOI: 10.6084/m9.figshare.7046804
title: ONT Minion Reads

description: ONT MinION reads after demultiplexing, basecalling (Albacore, version 1.1.0), trimming and filtering out chimeras (Porechop, version 0.2.1).These ONT MinION reads were used to perform hybrid assemblies with Illumina NextSeq/MiSeq data using Unicycler (version 0.4.1).<br>
DOI: 10.6084/m9.figshare.7046804.v1
title: ONT Minion Reads

description: ONT MinION reads after demultiplexing, basecalling (Albacore, version 1.1.0), trimming and filtering out chimeras (Porechop, version 0.2.1).These ONT MinION reads were used to perform hybrid assemblies with Illumina NextSeq/MiSeq data using Unicycler (version 0.4.1).<br>