cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.11769600.v1
title: Additional file 1 of New insights on intercontinental origins of paternal lineages in Northeast Brazil

description: Additional file 1. Genotypic and SNP data. All genotypes found for the samples analysed in this study as well as chosen SNP information can be found in Additional file 1.
DOI: 10.6084/m9.figshare.11769549
title: Additional file 9 of Genome-wide analyses of cassava Pathogenesis-related (PR) gene families reveal core transcriptome responses to whitefly infestation, salicylic acid and jasmonic acid

description: Additional file 9 PR gene expression values (log2FC) during biotic stress. This table compiles DEGs identified in response to: SA, JA and whitefly (this study); Xanthomonas (bacteria) [27, 28]; C. gloeosporioides (fungi) [29]; and the viruses South African CMV [30] and CBSV [31â€“33].
DOI: 10.6084/m9.figshare.11769549.v1
title: Additional file 9 of Genome-wide analyses of cassava Pathogenesis-related (PR) gene families reveal core transcriptome responses to whitefly infestation, salicylic acid and jasmonic acid

description: Additional file 9 PR gene expression values (log2FC) during biotic stress. This table compiles DEGs identified in response to: SA, JA and whitefly (this study); Xanthomonas (bacteria) [27, 28]; C. gloeosporioides (fungi) [29]; and the viruses South African CMV [30] and CBSV [31â€“33].
DOI: 10.6084/m9.figshare.11769546
title: Additional file 1 of Quality of whole genome sequencing from blood versus saliva derived DNA in cardiac patients

description: Additional file 1: Table S1. Coordinates of all Consensus Coding Sequence (CCDS) transcripts in the hg19 genome build. Table S2. Coordinates of all cardiovascular disease (CVD) gene transcripts in the hg19 genome build. Table S3. Concordance of SNVs and CNVs between saliva and blood whole genomes. Table S4. Comparison of SNVs genome-wide in each paired blood and saliva genome. Table S5. Comparison of SNVs within CCDS transcripts in each paired blood and saliva genome. Table S6. Comparison of SNVs within CVD gene transcripts in each paired blood and saliva genome. Table S7. Comparison of rare SNVs genome-wide in each paired blood and saliva genome. Table S8. Comparison of rare SNVs within CCDS transcripts in each paired blood and saliva genome. Table S9. Comparison of rare SNVs within CVD gene transcripts in each paired blood and saliva genome. Table S10. Comparison of all CNVs genome-wide, within CCDS transcripts, and within CVD gene transcripts.
DOI: 10.6084/m9.figshare.11769546.v1
title: Additional file 1 of Quality of whole genome sequencing from blood versus saliva derived DNA in cardiac patients

description: Additional file 1: Table S1. Coordinates of all Consensus Coding Sequence (CCDS) transcripts in the hg19 genome build. Table S2. Coordinates of all cardiovascular disease (CVD) gene transcripts in the hg19 genome build. Table S3. Concordance of SNVs and CNVs between saliva and blood whole genomes. Table S4. Comparison of SNVs genome-wide in each paired blood and saliva genome. Table S5. Comparison of SNVs within CCDS transcripts in each paired blood and saliva genome. Table S6. Comparison of SNVs within CVD gene transcripts in each paired blood and saliva genome. Table S7. Comparison of rare SNVs genome-wide in each paired blood and saliva genome. Table S8. Comparison of rare SNVs within CCDS transcripts in each paired blood and saliva genome. Table S9. Comparison of rare SNVs within CVD gene transcripts in each paired blood and saliva genome. Table S10. Comparison of all CNVs genome-wide, within CCDS transcripts, and within CVD gene transcripts.
DOI: 10.6084/m9.figshare.11769540
title: Additional file 8 of Genome-wide analyses of cassava Pathogenesis-related (PR) gene families reveal core transcriptome responses to whitefly infestation, salicylic acid and jasmonic acid

description: Additional file 8. Whitefly-responsive DEGs: Temporal expression programs and hormone-response clusters.
DOI: 10.6084/m9.figshare.11769537
title: Additional file 7 of Genome-wide analyses of cassava Pathogenesis-related (PR) gene families reveal core transcriptome responses to whitefly infestation, salicylic acid and jasmonic acid

description: Additional file 7. Mean log2FC of SA and/or JA DEGs.
DOI: 10.6084/m9.figshare.11769540.v1
title: Additional file 8 of Genome-wide analyses of cassava Pathogenesis-related (PR) gene families reveal core transcriptome responses to whitefly infestation, salicylic acid and jasmonic acid

description: Additional file 8. Whitefly-responsive DEGs: Temporal expression programs and hormone-response clusters.
DOI: 10.6084/m9.figshare.11769537.v1
title: Additional file 7 of Genome-wide analyses of cassava Pathogenesis-related (PR) gene families reveal core transcriptome responses to whitefly infestation, salicylic acid and jasmonic acid

description: Additional file 7. Mean log2FC of SA and/or JA DEGs.
DOI: 10.6084/m9.figshare.11769516
title: Additional file 4 of Genome-wide analyses of cassava Pathogenesis-related (PR) gene families reveal core transcriptome responses to whitefly infestation, salicylic acid and jasmonic acid

description: Additional file 4 Table S15. Expression profile clusters for PR responses to whitefly feeding. Table S16. Expression profile clusters for PR responses to whitefly, SA and JA.
DOI: 10.6084/m9.figshare.11769513
title: Additional file 3 of Genome-wide analyses of cassava Pathogenesis-related (PR) gene families reveal core transcriptome responses to whitefly infestation, salicylic acid and jasmonic acid

description: Additional file 3 PR gene expression after whitefly, SA and JA treatments of cassava. Table S3. log2FC and FDR values of DEGs identified in whitefly-susceptible genotypes (COL2246, COL1468, 60444, and TME3) after whitefly infestation. Table S4. log2FC and FDR values for PR genes detected in whitefly-susceptible genotypes after whitefly infestation. Table S5. Mean RPKM values of PR genes during whitefly infestation (0–22 dpi) of four whitefly-susceptible genotypes. Table S6. Read counts of PR genes during whitefly infestation (0–22 dpi) of four whitefly-susceptible genotypes. Table S7. log2FC and FDR values of DEGs in COL2246 after SA treatment. Table S8. log2FC and FDR values for PR genes detected in COL2246 after SA treatment. Table S9. Mean RPKM values for PR genes after SA treatment (0–24 h) of COL2246. Table S10. Read counts of PR genes after SA treatments (0–24 h) of COL2246. Table S11. log2FC and FDR values of DEGs in COL2246 after JA treatment. Table S12. log2FC and FDR values for PR genes detected in COL2246 after JA treatment. Table S13. Mean RPKM values for PR genes after JA treatment (0–24 h) of COL2246. Table S14. Read counts for PR genes after JA treatment (0–24 h) of COL2246.
DOI: 10.6084/m9.figshare.11769516.v1
title: Additional file 4 of Genome-wide analyses of cassava Pathogenesis-related (PR) gene families reveal core transcriptome responses to whitefly infestation, salicylic acid and jasmonic acid

description: Additional file 4 Table S15. Expression profile clusters for PR responses to whitefly feeding. Table S16. Expression profile clusters for PR responses to whitefly, SA and JA.
DOI: 10.6084/m9.figshare.11769513.v1
title: Additional file 3 of Genome-wide analyses of cassava Pathogenesis-related (PR) gene families reveal core transcriptome responses to whitefly infestation, salicylic acid and jasmonic acid

description: Additional file 3 PR gene expression after whitefly, SA and JA treatments of cassava. Table S3. log2FC and FDR values of DEGs identified in whitefly-susceptible genotypes (COL2246, COL1468, 60444, and TME3) after whitefly infestation. Table S4. log2FC and FDR values for PR genes detected in whitefly-susceptible genotypes after whitefly infestation. Table S5. Mean RPKM values of PR genes during whitefly infestation (0–22 dpi) of four whitefly-susceptible genotypes. Table S6. Read counts of PR genes during whitefly infestation (0–22 dpi) of four whitefly-susceptible genotypes. Table S7. log2FC and FDR values of DEGs in COL2246 after SA treatment. Table S8. log2FC and FDR values for PR genes detected in COL2246 after SA treatment. Table S9. Mean RPKM values for PR genes after SA treatment (0–24 h) of COL2246. Table S10. Read counts of PR genes after SA treatments (0–24 h) of COL2246. Table S11. log2FC and FDR values of DEGs in COL2246 after JA treatment. Table S12. log2FC and FDR values for PR genes detected in COL2246 after JA treatment. Table S13. Mean RPKM values for PR genes after JA treatment (0–24 h) of COL2246. Table S14. Read counts for PR genes after JA treatment (0–24 h) of COL2246.
DOI: 10.6084/m9.figshare.11769507
title: Additional file 1 of Genome-wide analyses of cassava Pathogenesis-related (PR) gene families reveal core transcriptome responses to whitefly infestation, salicylic acid and jasmonic acid

description: Additional file 1: Table S1. Cassava PR gene nomenclature. Founder protein(s) used to identify each PR family via BLASTP and HMM queries, a list of cassava PR genes and functions, and loci designations in the cassava genome are provided. E-values and % identity are also provided. Table S2. PR gene clusters in the cassava genome.
DOI: 10.6084/m9.figshare.11769507.v1
title: Additional file 1 of Genome-wide analyses of cassava Pathogenesis-related (PR) gene families reveal core transcriptome responses to whitefly infestation, salicylic acid and jasmonic acid

description: Additional file 1: Table S1. Cassava PR gene nomenclature. Founder protein(s) used to identify each PR family via BLASTP and HMM queries, a list of cassava PR genes and functions, and loci designations in the cassava genome are provided. E-values and % identity are also provided. Table S2. PR gene clusters in the cassava genome.
DOI: 10.6084/m9.figshare.11769501
title: Additional file 19 of Genome-wide analyses of cassava Pathogenesis-related (PR) gene families reveal core transcriptome responses to whitefly infestation, salicylic acid and jasmonic acid

description: Additional file 19. qRT-PCR primers.
DOI: 10.6084/m9.figshare.11769501.v1
title: Additional file 19 of Genome-wide analyses of cassava Pathogenesis-related (PR) gene families reveal core transcriptome responses to whitefly infestation, salicylic acid and jasmonic acid

description: Additional file 19. qRT-PCR primers.
DOI: 10.6084/m9.figshare.11769489
title: Additional file 17 of Genome-wide analyses of cassava Pathogenesis-related (PR) gene families reveal core transcriptome responses to whitefly infestation, salicylic acid and jasmonic acid

description: Additional file 17 PR gene expression in TME204 shoots, roots and embryonic callus. Loci (cassava genome v6), PR gene names and expression values from Wilson et al. [86] are provided. These data are used in AdditionalÂ files 12, 13, 14, 15 and 16.
DOI: 10.6084/m9.figshare.11769489.v1
title: Additional file 17 of Genome-wide analyses of cassava Pathogenesis-related (PR) gene families reveal core transcriptome responses to whitefly infestation, salicylic acid and jasmonic acid

description: Additional file 17 PR gene expression in TME204 shoots, roots and embryonic callus. Loci (cassava genome v6), PR gene names and expression values from Wilson et al. [86] are provided. These data are used in AdditionalÂ files 12, 13, 14, 15 and 16.
DOI: 10.6084/m9.figshare.11769483
title: Additional file 16 of Genome-wide analyses of cassava Pathogenesis-related (PR) gene families reveal core transcriptome responses to whitefly infestation, salicylic acid and jasmonic acid

description: Additional file 16 Table S23. PR genes associated with correlations between whitefly and bacteria and/or CBSV responses. Table S24. PR genes associated with correlation between whitefly and CMV responses.
DOI: 10.6084/m9.figshare.11769483.v1
title: Additional file 16 of Genome-wide analyses of cassava Pathogenesis-related (PR) gene families reveal core transcriptome responses to whitefly infestation, salicylic acid and jasmonic acid

description: Additional file 16 Table S23. PR genes associated with correlations between whitefly and bacteria and/or CBSV responses. Table S24. PR genes associated with correlation between whitefly and CMV responses.
DOI: 10.6084/m9.figshare.11769477
title: Additional file 15 of Genome-wide analyses of cassava Pathogenesis-related (PR) gene families reveal core transcriptome responses to whitefly infestation, salicylic acid and jasmonic acid

description: Additional file 15 Hormone regulation of stress-responsive PR genes. Numbers and percentages of stress-regulated genes belonging to each hormone-expression program are provided. Table S17. Hormone regulation of whitefly-responsive PR genes. Table S18. Hormone regulation of mealybug-responsive PR genes. Table S19. Hormone regulation of bacteria-responsive PR genes. Table S20. Hormone regulation of fungi-responsive PR genes. Table S21. Hormone regulation of CMV-responsive PR genes. Table S22. Hormone regulation of CBSV-responsive PR genes.
DOI: 10.6084/m9.figshare.11769477.v1
title: Additional file 15 of Genome-wide analyses of cassava Pathogenesis-related (PR) gene families reveal core transcriptome responses to whitefly infestation, salicylic acid and jasmonic acid

description: Additional file 15 Hormone regulation of stress-responsive PR genes. Numbers and percentages of stress-regulated genes belonging to each hormone-expression program are provided. Table S17. Hormone regulation of whitefly-responsive PR genes. Table S18. Hormone regulation of mealybug-responsive PR genes. Table S19. Hormone regulation of bacteria-responsive PR genes. Table S20. Hormone regulation of fungi-responsive PR genes. Table S21. Hormone regulation of CMV-responsive PR genes. Table S22. Hormone regulation of CBSV-responsive PR genes.
DOI: 10.6084/m9.figshare.11769387
title: Additional file 9 of A mouse ear skin model to study the dynamics of innate immune responses against Staphylococcus aureus biofilms

description: Additional file 9: Table S4. Table presenting the straightness of all cells in infected and control mice at early and late time points. Raw data extracted from Imaris software.
DOI: 10.6084/m9.figshare.11769387.v1
title: Additional file 9 of A mouse ear skin model to study the dynamics of innate immune responses against Staphylococcus aureus biofilms

description: Additional file 9: Table S4. Table presenting the straightness of all cells in infected and control mice at early and late time points. Raw data extracted from Imaris software.
DOI: 10.6084/m9.figshare.11769381
title: Additional file 8 of A mouse ear skin model to study the dynamics of innate immune responses against Staphylococcus aureus biofilms

description: Additional file 8: Table S3. Table presenting the average speed of all cells in infected and control mice at early and late time points. Raw data extracted from Imaris software.
DOI: 10.6084/m9.figshare.11769381.v1
title: Additional file 8 of A mouse ear skin model to study the dynamics of innate immune responses against Staphylococcus aureus biofilms

description: Additional file 8: Table S3. Table presenting the average speed of all cells in infected and control mice at early and late time points. Raw data extracted from Imaris software.
DOI: 10.6073/pasta/47db4ee01f516b0a47b7c585fd552645
title: SBC LTER: Reef: Long-term experiment: biomass of kelp forest species, ongoing since 2008

description: These data represent values of biomass density for more than 200 species of macroalgae, invertebrates and fish measured in fixed plots at five reefs as part of a long-term experiment designed to evaluate the effects of disturbance to giant kelp on the structure and productivity of the benthic community. Taxon-specific relationships between size and mass were applied to field measurements of species abundance to estimate biomass density of each species. The five reefs (Arroyo Quemado 34°28.048’N, 120°07.031’W; Carpinteria 34°23.474’N, 119°32.510’W; Isla Vista 34°23.275’N, 119°32.792’W; Mohawk 34°23.649’N, 119°43.762’W; and Naples 34° 25.342’N, 119° 57.102’W) ranged in depth from 5.8 m to 8.9 m (MLLW) and were chosen to represent a range of physical and biological characteristics known to influence subtidal macroalgal assemblages in the region. A common (but not always persistent) feature on these reefs was the presence of the giant kelp, which forms a dense canopy at the sea surface that suppresses recruitment and growth of understory algae below it. See Methods for more information.
DOI: 10.6084/m9.figshare.11769351
title: Additional file 3 of A mouse ear skin model to study the dynamics of innate immune responses against Staphylococcus aureus biofilms

description: Additional file 3: Table S2. Table presenting raw data used to measure the ratio of the sum of EGFP fluorescence intensities to ROI areas.
DOI: 10.6084/m9.figshare.11769351.v1
title: Additional file 3 of A mouse ear skin model to study the dynamics of innate immune responses against Staphylococcus aureus biofilms

description: Additional file 3: Table S2. Table presenting raw data used to measure the ratio of the sum of EGFP fluorescence intensities to ROI areas.
DOI: 10.6084/m9.figshare.11769345
title: Additional file 2 of A mouse ear skin model to study the dynamics of innate immune responses against Staphylococcus aureus biofilms

description: Additional file 2: Table S1. Tables presenting raw data used for the preparation of calibrated Staphylococcus aureus biofilm and planktonic inocula.
DOI: 10.6084/m9.figshare.11769345.v1
title: Additional file 2 of A mouse ear skin model to study the dynamics of innate immune responses against Staphylococcus aureus biofilms

description: Additional file 2: Table S1. Tables presenting raw data used for the preparation of calibrated Staphylococcus aureus biofilm and planktonic inocula.
DOI: 10.6084/m9.figshare.11769333
title: Additional file 13 of A mouse ear skin model to study the dynamics of innate immune responses against Staphylococcus aureus biofilms

description: Additional file 13: Table S8. Table presenting the straightness of cells in contact with bacteria or not in infected mice at late time points. Raw data extracted from Imaris software.
DOI: 10.6084/m9.figshare.11769330
title: Additional file 12 of A mouse ear skin model to study the dynamics of innate immune responses against Staphylococcus aureus biofilms

description: Additional file 12: Table S7. Table presenting the average speed of cells in contact with bacteria or not in infected mice at late time points. Raw data extracted from Imaris software.
DOI: 10.6084/m9.figshare.11769333.v1
title: Additional file 13 of A mouse ear skin model to study the dynamics of innate immune responses against Staphylococcus aureus biofilms

description: Additional file 13: Table S8. Table presenting the straightness of cells in contact with bacteria or not in infected mice at late time points. Raw data extracted from Imaris software.
DOI: 10.6084/m9.figshare.11769330.v1
title: Additional file 12 of A mouse ear skin model to study the dynamics of innate immune responses against Staphylococcus aureus biofilms

description: Additional file 12: Table S7. Table presenting the average speed of cells in contact with bacteria or not in infected mice at late time points. Raw data extracted from Imaris software.
DOI: 10.6084/m9.figshare.11769327
title: Additional file 11 of A mouse ear skin model to study the dynamics of innate immune responses against Staphylococcus aureus biofilms

description: Additional file 11: Table S6. Table presenting the straightness of cells in contact with bacteria or not in infected mice at early time points. Raw data extracted from Imaris software.
DOI: 10.6084/m9.figshare.11769324
title: Additional file 10 of A mouse ear skin model to study the dynamics of innate immune responses against Staphylococcus aureus biofilms

description: Additional file 10: Table S5. Table presenting the average speed of cells in contact with bacteria or not in infected mice at early time points. Raw data extracted from Imaris software.
DOI: 10.6084/m9.figshare.11769327.v1
title: Additional file 11 of A mouse ear skin model to study the dynamics of innate immune responses against Staphylococcus aureus biofilms

description: Additional file 11: Table S6. Table presenting the straightness of cells in contact with bacteria or not in infected mice at early time points. Raw data extracted from Imaris software.
DOI: 10.6084/m9.figshare.11769324.v1
title: Additional file 10 of A mouse ear skin model to study the dynamics of innate immune responses against Staphylococcus aureus biofilms

description: Additional file 10: Table S5. Table presenting the average speed of cells in contact with bacteria or not in infected mice at early time points. Raw data extracted from Imaris software.
DOI: 10.6084/m9.figshare.11769240
title: Additional file 4 of Case report: recurrent pituitary adenoma has increased load of somatic variants

description: Additional file 4. Excel spreadsheet with the list of genes used for targeted PA genetic marker search.
DOI: 10.6084/m9.figshare.11769240.v1
title: Additional file 4 of Case report: recurrent pituitary adenoma has increased load of somatic variants

description: Additional file 4. Excel spreadsheet with the list of genes used for targeted PA genetic marker search.
DOI: 10.6084/m9.figshare.11769219
title: Additional file 2 of Case report: recurrent pituitary adenoma has increased load of somatic variants

description: Additional file 2. Interval file of HG19 exome coordinates. This reference exome version was used to search for variants and CNVs.
DOI: 10.6084/m9.figshare.11769219.v1
title: Additional file 2 of Case report: recurrent pituitary adenoma has increased load of somatic variants

description: Additional file 2. Interval file of HG19 exome coordinates. This reference exome version was used to search for variants and CNVs.
DOI: 10.6084/m9.figshare.11769198
title: Additional file 11 of Tuberomics: a molecular profiling for the adaption of edible fungi (Tuber magnatum Pico) to different natural environments

description: Additional file 11: Data file S1. Differentially expressed genes (DEGs) data related to sample comparisons. Data sheets A) DEGs related to comparison San Miniato (SM) vs Alba (AL); B) DEGs related to comparison Isernia (IS) vs Alba (AL); C) DEGs identified in both the comparisons (SMvsAL, ISvsAL); D) DEGs identified only in San Miniato (SM) vs Alba (AL); E) DEGs identified only in Isernia (IS) vs Alba (AL); F) Gene specificty reported in TPM (transcripts per million) for each sample.
DOI: 10.6084/m9.figshare.11769198.v1
title: Additional file 11 of Tuberomics: a molecular profiling for the adaption of edible fungi (Tuber magnatum Pico) to different natural environments

description: Additional file 11: Data file S1. Differentially expressed genes (DEGs) data related to sample comparisons. Data sheets A) DEGs related to comparison San Miniato (SM) vs Alba (AL); B) DEGs related to comparison Isernia (IS) vs Alba (AL); C) DEGs identified in both the comparisons (SMvsAL, ISvsAL); D) DEGs identified only in San Miniato (SM) vs Alba (AL); E) DEGs identified only in Isernia (IS) vs Alba (AL); F) Gene specificty reported in TPM (transcripts per million) for each sample.
DOI: 10.6084/m9.figshare.11769183
title: Additional file 1 of Genome-wide identification and expression of GRAS gene family members in cassava

description: Additional file 1: Table S1. List of the GRAS protein sequences in cassava. Table S2. A catalog of MeGRAS proteins with their HMM profiles. Table S3. Protein property and subcellular localization of MeGRAS proteins. Table S4. Secondary structure of amino acid sequences in cassava. Table S5. GRAS genes used in Arabidopsis, rice, castor bean, Populus, tomato, and tea plant. Table S6. The structural features of motif 1â€“20. Table S7. The expression data of the cassava GRAS genes in different tissues. Table S8. The accession number of transcriptomic data in NCBI. Table S9. Sequences of primers used in qRT-PCR.