cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.26950089
title: Selective synergistic effects of oxalic acid and salicylic acid in enhancing amino acid levels and alleviating lead stress in <i>Zea mays</i> L

description: Lead is one of the major environmental pollutants which is highly toxic to plants and living beings. The current investigation thoroughly evaluated the synergistic effects of oxalic acid (OA) and salicylic acid (SA) on <i>Zea mays L</i>. plants subjected to varying durations (15, 30, 30, and 45 days) of lead (Pb) stress. Besides, the effects of oxalic acid (OA) combined with salicylic acid (SA) for different amino acids at various periods of Pb stress were also investigated on <i>Zea mays</i> L. The soil was treated with lead nitrate Pb (NO<sub>3</sub>)<sub>2</sub> (0.5 mM) to induce Pb stress while the stressed plants were further treated using oxalic acid (25 mg/L), salicylic acid (25 mg/L), and their combination OA + SA (25 mg/L each). Measurements of protein content, malondialdehyde (MDA) levels, guaiacol peroxidase (GPOX) activity, catalase (CAT) activity, GSH content, and Pb concentration in maize leaves were done during this study. MDA levels increased by 71% under Pb stress, while protein content decreased by 56%, GSH content by 35%, and CAT activity by 46%. After treatment with SA, OA, and OA+SA, there was a significant reversal of these damages, with the OA+SA combination showing the highest improvement. Specifically, OA+SA treatment led to a 45% increase in protein content and a 39% reduction in MDA levels compared to Pb treatment alone. Moreover, amino acid concentrations increased by 68% under the Pb+OA+SA treatment, reflecting the most significant recovery (<i>p</i> &lt; 0.0001).
DOI: 10.6084/m9.figshare.26950089.v1
title: Selective synergistic effects of oxalic acid and salicylic acid in enhancing amino acid levels and alleviating lead stress in <i>Zea mays</i> L

description: Lead is one of the major environmental pollutants which is highly toxic to plants and living beings. The current investigation thoroughly evaluated the synergistic effects of oxalic acid (OA) and salicylic acid (SA) on <i>Zea mays L</i>. plants subjected to varying durations (15, 30, 30, and 45 days) of lead (Pb) stress. Besides, the effects of oxalic acid (OA) combined with salicylic acid (SA) for different amino acids at various periods of Pb stress were also investigated on <i>Zea mays</i> L. The soil was treated with lead nitrate Pb (NO<sub>3</sub>)<sub>2</sub> (0.5 mM) to induce Pb stress while the stressed plants were further treated using oxalic acid (25 mg/L), salicylic acid (25 mg/L), and their combination OA + SA (25 mg/L each). Measurements of protein content, malondialdehyde (MDA) levels, guaiacol peroxidase (GPOX) activity, catalase (CAT) activity, GSH content, and Pb concentration in maize leaves were done during this study. MDA levels increased by 71% under Pb stress, while protein content decreased by 56%, GSH content by 35%, and CAT activity by 46%. After treatment with SA, OA, and OA+SA, there was a significant reversal of these damages, with the OA+SA combination showing the highest improvement. Specifically, OA+SA treatment led to a 45% increase in protein content and a 39% reduction in MDA levels compared to Pb treatment alone. Moreover, amino acid concentrations increased by 68% under the Pb+OA+SA treatment, reflecting the most significant recovery (<i>p</i> &lt; 0.0001).
DOI: 10.6084/m9.figshare.25474817
title: Quasi-targeted metabolomics revealed isoliquiritigenin and lauric acid associated with resistance to tobacco black shank

description: Tobacco black shank (TBS), caused by <i>Phytophthora nicotianae</i>, is a severe disease. Plant root exudates play a crucial role in mediating plant-pathogen interactions in the rhizosphere. However, the specific interaction between key secondary metabolites present in root exudates and the mechanisms of disease resistance remains poorly understood. This study conducted a comprehensive comparison via quasi-targeted metabolomic analysis on the root exudate metabolites from the tobacco cultivar Yunyan87 and K326, both before and after inoculation with <i>P. nicotianae</i>. The results showed that the root exudate metabolites changed after <i>P. nicotianae</i> inoculation, and the root exudate metabolites of different tobacco cultivar was significantly different. Furthermore, homovanillic acid, lauric acid, and isoliquiritigenin were identified as potential key compounds for TBS resistance based on their impact on the mycelium growth of the pathogens. The pot experiment showed that isoliquiritigenin reduced the incidence by 55.2%, while lauric acid reduced it by 45.8%. This suggests that isoliquiritigenin and lauric acid have potential applications in the management of TBS. In summary, this study revealed the possible resistance mechanisms of differential metabolites in resistance of commercial tobacco cultivar, and for the first time discovered the inhibitory effects of isoliquiritigenin and homovanillic acid on <i>P. nictianae</i>, and attempt to use plants secondary metabolites of for plant protection.
DOI: 10.6084/m9.figshare.25474817.v1
title: Quasi-targeted metabolomics revealed isoliquiritigenin and lauric acid associated with resistance to tobacco black shank

description: Tobacco black shank (TBS), caused by <i>Phytophthora nicotianae</i>, is a severe disease. Plant root exudates play a crucial role in mediating plant-pathogen interactions in the rhizosphere. However, the specific interaction between key secondary metabolites present in root exudates and the mechanisms of disease resistance remains poorly understood. This study conducted a comprehensive comparison via quasi-targeted metabolomic analysis on the root exudate metabolites from the tobacco cultivar Yunyan87 and K326, both before and after inoculation with <i>P. nicotianae</i>. The results showed that the root exudate metabolites changed after <i>P. nicotianae</i> inoculation, and the root exudate metabolites of different tobacco cultivar was significantly different. Furthermore, homovanillic acid, lauric acid, and isoliquiritigenin were identified as potential key compounds for TBS resistance based on their impact on the mycelium growth of the pathogens. The pot experiment showed that isoliquiritigenin reduced the incidence by 55.2%, while lauric acid reduced it by 45.8%. This suggests that isoliquiritigenin and lauric acid have potential applications in the management of TBS. In summary, this study revealed the possible resistance mechanisms of differential metabolites in resistance of commercial tobacco cultivar, and for the first time discovered the inhibitory effects of isoliquiritigenin and homovanillic acid on <i>P. nictianae</i>, and attempt to use plants secondary metabolites of for plant protection.
DOI: 10.6084/m9.figshare.25250085
title: MsMYB62-like as a negative regulator of anthocyanin biosynthesis in <i>Malus spectabilis</i>

description: Crabapple is a valuable tree species in gardens due to its captivating array of flower and leaf colors, rendering it a favored choice in landscaping. The economic and ornamental values of <i>Malus</i> crabapple are closely associated with the biosynthesis of anthocyanin, a pigment responsible for its vibrant hues. The intricate regulation of anthocyanin biosynthesis involves the concerted activity of various genes. However, the specific mechanism governing this process in crabapple warrants in-depth exploration. In this study, we explored the inhibitory role of MsMYB62-like in anthocyanin biosynthesis. We identified <i>MsDFR</i> and <i>MsANS</i> as two downstream target genes of MsMYB62-like. These genes encode enzymes integral to the anthocyanin biosynthetic pathway. The findings demonstrate that MsMYB62-like directly binds to the promoters of <i>MsDFR</i> and <i>MsANS</i>, resulting in the downregulation of their expression levels. Additionally, our observations indicate that the plant hormone cytokinins exert a suppressive effect on the expression levels of <i>MsMYB62-like</i>, while concurrently upregulating <i>MsDFR</i> and <i>MsANS</i>. This study reveals that the MsMYB62-like-<i>MsDFR</i>/<i>MsANS</i> module plays an important role in governing anthocyanin levels in <i>Malus</i> crabapple. Notably, the regulatory interplay is modulated by the plant hormone cytokinins.
DOI: 10.6084/m9.figshare.25250085.v1
title: MsMYB62-like as a negative regulator of anthocyanin biosynthesis in <i>Malus spectabilis</i>

description: Crabapple is a valuable tree species in gardens due to its captivating array of flower and leaf colors, rendering it a favored choice in landscaping. The economic and ornamental values of <i>Malus</i> crabapple are closely associated with the biosynthesis of anthocyanin, a pigment responsible for its vibrant hues. The intricate regulation of anthocyanin biosynthesis involves the concerted activity of various genes. However, the specific mechanism governing this process in crabapple warrants in-depth exploration. In this study, we explored the inhibitory role of MsMYB62-like in anthocyanin biosynthesis. We identified <i>MsDFR</i> and <i>MsANS</i> as two downstream target genes of MsMYB62-like. These genes encode enzymes integral to the anthocyanin biosynthetic pathway. The findings demonstrate that MsMYB62-like directly binds to the promoters of <i>MsDFR</i> and <i>MsANS</i>, resulting in the downregulation of their expression levels. Additionally, our observations indicate that the plant hormone cytokinins exert a suppressive effect on the expression levels of <i>MsMYB62-like</i>, while concurrently upregulating <i>MsDFR</i> and <i>MsANS</i>. This study reveals that the MsMYB62-like-<i>MsDFR</i>/<i>MsANS</i> module plays an important role in governing anthocyanin levels in <i>Malus</i> crabapple. Notably, the regulatory interplay is modulated by the plant hormone cytokinins.
DOI: 10.57841/casdc.0004239
title: 小麦TaMYB7分子调控网络论文及数据集
DOI: 10.6084/m9.figshare.c.3637118_d4.v1
title: Additional file 3: Table S2. of Functionally conserved enhancers with divergent sequences in distant vertebrates

description: Zebrafish CNSs that did not drive expression activity in the zebrafish transgenic assay. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.c.3637118_d5.v1
title: Additional file 4: Table S3. of Functionally conserved enhancers with divergent sequences in distant vertebrates

description: Conserved transcription factor binding motifs in the five zebrafish/mouse syntenic enhancers. Identical n-mers (n â Ľ 7) identified in the zebrafish, mouse, and human sequences of the five syntenic CNS were examined for the presence of transcription factor binding motifs; only motifs with E-value E â ¤ 0.1 are shown. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.c.3637118_d3.v1
title: Additional file 2: Table S1. of Functionally conserved enhancers with divergent sequences in distant vertebrates

description: Number of fish expressing a construct in a given tissue, reported as the proportion of fish alive at the experimental time point. The first worksheet shows the fish counts for the CNSs obtained from the zebrafish genome, and the second worksheet shows the fish counts for the CNSs obtained from the mouse genome. Ectopic expression counts driven by the enhancerless (labeled “empty”) vector are shown in the first row of each worksheet and are subtracted from the counts obtained with the vector with enhancer (labeled “insert”) to obtain the correct counts for each construct (labeled “insert-empty”). (XLSX 41 kb)
DOI: 10.6084/m9.figshare.c.3637118_d1.v1
title: Additional file 5: Table S4. of Functionally conserved enhancers with divergent sequences in distant vertebrates

description: List of primers used in the cloning of the reporter vectors. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.c.3637100_d5.v1
title: Additional file 5: Table S4. of PIM-1 contributes to the malignancy of pancreatic cancer and displays diagnostic and prognostic value

description: Univariate and multivariable analyses of factors predictive of poor overall survival in patients with pancreatic cancer (plasma). (XLSX 12 kb)
DOI: 10.15468/dl.xr9pxz
title: Occurrence Download

description: A dataset containing 14 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Myoxocephalus jaok (Cuvier, 1829)",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 14 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035624-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.c.3636890_d1.v1
title: MOESM1 of Designing and conducting a cluster-randomized trial of ICU admission for the elderly patients: the ICE-CUB 2 study

description: Additional file 1. Members of the ICE-CUB 2 study network.
DOI: 10.6084/m9.figshare.c.3636791_d23.v1
title: Additional file 16: Table S14. of Exploring the rice dispensable genome using a metagenome-like assembly strategy

description: Sheet 1 shows contigs of the indica dispensable genome that were composed by reads mainly from a subgroup. Sheet 2 shows contigs of the japonica dispensable genome that were composed by reads mainly from a subgroup. Columns 2â  4 show the percentage of reads mapped to the contig that belong to each subgroup. (XLS 1556Â kb)
DOI: 10.6084/m9.figshare.c.3636791_d20.v1
title: Additional file 10: Table S9. of Exploring the rice dispensable genome using a metagenome-like assembly strategy

description: RNA sequencing data used in the expression profiling of predicted genes of the dispensable genome. (XLS 10Â kb)
DOI: 10.6084/m9.figshare.c.3636791_d21.v1
title: Additional file 4: Table S3. of Exploring the rice dispensable genome using a metagenome-like assembly strategy

description: Alignment of contigs of the indica dispensable genome to different sequenced genomes of the Oryza genus. (XLS 8272Â kb)
DOI: 10.6084/m9.figshare.c.3636791_d19.v1
title: Additional file 6: Table S5. of Exploring the rice dispensable genome using a metagenome-like assembly strategy

description: The alignment of genes in the sequenced region of Kasalath that harbors PSTOL1 to the dispensable genome. (XLS 17Â kb)
DOI: 10.6084/m9.figshare.c.3636791_d17.v1
title: Additional file 20: Table S18. of Exploring the rice dispensable genome using a metagenome-like assembly strategy

description: LTR retrotransposons found within the dispensable genome. (XLS 2869Â kb)
DOI: 10.6084/m9.figshare.c.3636791_d18.v1
title: Additional file 2: Table S2. of Exploring the rice dispensable genome using a metagenome-like assembly strategy

description: Mapping rate of sequencing reads aligned to the Nipponbare genome of different accessions. (XLS 107Â kb)
DOI: 10.6084/m9.figshare.c.3636791_d16.v1
title: Additional file 14: Table S12. of Exploring the rice dispensable genome using a metagenome-like assembly strategy

description: The genomic positions relative to the Nipponbare genome of overlapping contigs of the indica and japonica dispensable genomes. Genomic positions were determined using an integration approach based on alignment and linkage disequilibrium for 7820 indica contigs corresponding to 7689 japonica contigs which were found to have reciprocal coordinate overlap of more than 60 % (identity ≥90 %). (XLS 1582 kb)
DOI: 10.6084/m9.figshare.c.3636791_d14.v1
title: Additional file 5: Table S4. of Exploring the rice dispensable genome using a metagenome-like assembly strategy

description: PCR validation of 43 DNA fragments from 30 randomly selected contigs. Primer position is the position of a primer in the sequence of the contig. (XLS 19Â kb)
DOI: 10.6084/m9.figshare.c.3636791_d15.v1
title: Additional file 11: Table S10. of Exploring the rice dispensable genome using a metagenome-like assembly strategy

description: Sheet 1 shows the transposon annotation results of the indica dispensable genome given by Censor. Sheet 2 is the transposon annotation results of the japonica dispensable genome given by Censor. (XLS 5583Â kb)
DOI: 10.6084/m9.figshare.c.3636791_d13.v1
title: Additional file 8: Table S7.  of Exploring the rice dispensable genome using a metagenome-like assembly strategy

description: The alignment of predicted proteins of the indica dispensable genome to proteins coded by cloned genes of the Nipponbare genome using Blastp. (XLS 33Â kb)
DOI: 10.6084/m9.figshare.c.3636791_d11.v1
title: Additional file 21: Table S19. of Exploring the rice dispensable genome using a metagenome-like assembly strategy

description: Pack-MULEs found within the indica dispensable genome. (XLS 15Â kb)
DOI: 10.6084/m9.figshare.c.3636791_d12.v1
title: Additional file 15: Table S13. of Exploring the rice dispensable genome using a metagenome-like assembly strategy

description: Identified chromosome insertion hotspots. (XLS 51Â kb)
DOI: 10.6084/m9.figshare.c.3636791_d7.v1
title: Additional file 22: Table S20. of Exploring the rice dispensable genome using a metagenome-like assembly strategy

description: Association mapping results of metabolic traits using whole genome SNPs or depth polymorphisms of the dispensable genome. Lead_SNP is the SNP with the most significant association signal for a specific metabolic trait. Chromosome is the chromosome position of Lead_SNP. Position is the chromosome position of Lead_SNP. P value is the association P value for Lead_SNP. Close_DP is the associated depth polymorphism closest to Lead_SNP. Close_DP_P value is the association P value for close_DP. Close_DP_Position is the genomic position of Close_DP relative to the Nipponbare genome. Close_DP_Distance is the distance (kb) between the Lead_SNP and the Close_DP. Lead_CDP is the continuous depth polymorphism with the most significant association signal for a specific metabolic trait. Lead_CDP_P value is the association P value for Lead_CDP. Lead_CDP_Pfam is the Pfam prediction result for Lead_CDP. Lead_BDP is the Boolean depth polymorphism with the most significant association signal for a specific metabolic trait. Lead_BDP_P value is the association P value for Lead_BDP. Lead_BDP_Pfam is the Pfam prediction result for Lead_BDP. (XLS 496Â kb)
DOI: 10.6084/m9.figshare.c.3636791_d5.v1
title: Additional file 9: Table S8. of Exploring the rice dispensable genome using a metagenome-like assembly strategy

description: The Pfam annotation results of the predicted proteins of the indica dispensable genome. See the Pfam website [81] for more details. (XLS 222Â kb)
DOI: 10.6084/m9.figshare.c.3636791_d6.v1
title: Additional file 19: Table S17. of Exploring the rice dispensable genome using a metagenome-like assembly strategy

description: Sheet 1 shows the transposon clusters found within the indica dispensable genome. Sheet 2 shows the transposon clusters found within the japonica dispensable genome. The second to sixth columns show the percentage of query coverage of the alignment of the contig to different sequenced Oryza genome. (XLS 323Â kb)
DOI: 10.6084/m9.figshare.c.3636791_d3.v1
title: Additional file 13: Table S11. of Exploring the rice dispensable genome using a metagenome-like assembly strategy

description: Sheet 1 shows the genomic position relative to the Nipponbare genome for contigs of the indica dispensable genome. Sheet 2 shows the genomic position relative to the Nipponbare genome for contigs of the japonica dispensable genome. (XLS 22307Â kb)
DOI: 10.6084/m9.figshare.c.3636791_d1.v1
title: Additional file 23: Table S21. of Exploring the rice dispensable genome using a metagenome-like assembly strategy

description: The rice accessions were classified into six groups (groups Aâ  F) to do local reassembly for contigs which could not be assigned genomic positions relative to the reference genome. (XLS 86Â kb)
DOI: 10.15468/dl.9acvm6
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cottus jaok Cuvier, 1829",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035625-241126133413365/datasets/export for details.
DOI: 10.6084/m9.figshare.c.3636644_d3.v1
title: Additional file 8: File S1. of ChiLin: a comprehensive ChIP-seq and DNase-seq quality control and analysis pipeline

description: H3K27me3 data QC report from ChiLin. The sequencing reads had been mapped to the mm10 genome build for BWA and Bowtie. File S2. Second H3K27me3 data QC report from ChiLin. The sequencing reads had been mapped to the hg38 genome build for BWA and Bowtie. File S3. H3K4me3 data QC report from ChiLin. The sequencing reads had been mapped to the mm10 genome build for BWA and Bowtie. File S4. Second H3K4me3 data QC report from ChiLin. The sequencing reads had been mapped to the mm10 genome build for BWA and Bowtie. File S5. H2A.Z data QC report from ChiLin. The sequencing reads had been mapped to the mm10 genome build for BWA and Bowtie. File S6. TRRAP data QC report from ChiLin. The sequencing reads had been mapped to the hg38 genome build for BWA and Bowtie. File S7. FOXA1 data QC report from ChiLin. The sequencing reads had been mapped to the hg38 genome build for BWA and Bowtie. File S8. STAT6 data QC report from ChiLin. The sequencing reads had been mapped to the mm10 genome build for BWA and Bowtie. File S9. AR data QC report from ChiLin. This report includes two immunoprecipitated and two input samples. The sequencing reads had been mapped to the hg38 genome build for BWA and Bowtie. File S10. RAD21 paired end data QC report from ChiLin. The sequencing reads had been mapped to the mm10 genome build for BWA and Bowtie. File S11. RAG2 data QC report from ChiLin. The sequencing reads had been mapped to the mm10 genome build for BWA and Bowtie. File S12. CHD7 data QC report from ChiLin. The sequencing reads had been mapped to the mm10 genome build for BWA and Bowtie. File S13. DNase-seq QC report from ChiLin. The sequencing reads had been mapped to the hg38 genome build for BWA and Bowtie. (GZ 9019Â kb)
DOI: 10.6084/m9.figshare.c.3636617_d1.v1
title: Additional file 1: Supplement T1. of Development of a D genome specific marker resource for diploid and hexaploid wheat

description: Comparison of NimbleGen mapping data with the previous wheat EST deletion bin map. (XLSX 20Â kb)
DOI: 10.6084/m9.figshare.c.3636584_d12.v1
title: Additional file 7: of Transcriptome sequencing reveals thousands of novel long non-coding RNAs in B cell lymphoma

description: List of protein-coding genes correlated with lncRNAs. Each protein-coding gene co-expressed with a novel lncRNA, with spearman correlation value, P value, and adjusted P value, respectively. The list includes most significantly positively correlated genes per lncRNA. (XLSX 23304 kb)
DOI: 10.6084/m9.figshare.c.3636584_d11.v1
title: Additional file 2: of Transcriptome sequencing reveals thousands of novel long non-coding RNAs in B cell lymphoma

description: Genomic coordinates of lncRNAs. Data include genomic coordinates of the 2,632 lncRNAs with start, end coord, and IDs. Also consists of multiple sheets with additional information on mutation hotspots, genomic coordinates, and IDs for the 45 highly expressed lncRNAs and the divergent lncRNAs. (XLSX 896 kb)
DOI: 10.6084/m9.figshare.c.3636584_d9.v1
title: Additional file 1: of Transcriptome sequencing reveals thousands of novel long non-coding RNAs in B cell lymphoma

description: List of cell lines. Data include list of DLBCL cell line names used in the analysis. (XLSX 38 kb)
DOI: 10.6084/m9.figshare.c.3636584_d4.v1
title: Additional file 14: of Transcriptome sequencing reveals thousands of novel long non-coding RNAs in B cell lymphoma

description: lncRNAs overlapping and correlated with known datasets. Data showing results for each lncRNA analyzed. Information included for each lncRNA, showing number of isoforms, lncRNA present in cell lines, normal B cell samples, near enriched ChIPSeq peaks, DLBCL super enhancers, PacBio data. Also, lncRNAs significantly co-expressed with known DLBCL target genes such as EZH2, BCL6. (XLSX 170 kb)