cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.11307113.v1
title: Genetic polymorphisms, forensic efficiency and phylogenetic analysis of 17 autosomal STR loci in the Han population of Wuxi, Eastern China

description: The autosomal short tandem repeat (STR) plays a unique role in population comparisons, phylogenetic reconstruction and migration history tracing. This study investigated the frequencies of 17 autosomal STR loci in the Han population from Wuxi, Eastern China, with the aim of expanding the available population information in human genetic databases and for forensic DNA analysis. The genetic polymorphisms of 17 STR loci were analysed in 5358 individuals of the Han population from Wuxi, Eastern China. Population comparisons including genetic distances, the neighbour-joining tree and multidimensional scaling plot were carried out between the Wuxi Han population and different ethnic groups. A total of 777 alleles at 17 autosomal STR loci were observed, with the corresponding allelic frequencies ranging from 0.0001–0.5210. The combined power of discrimination and exclusion for the 17 autosomal STR loci were 0.0000 and 0.000, respectively. Moreover, the phylogenetic analysis was performed between the Wuxi Han population and other relevant populations. The neighbour-joining tree and multidimensional scaling plot were generated based on Nei’s standard genetic distance. Population comparisons indicated that the Wuxi Han population had the closest genetic relationship with the Hubei Han population, relative to the other populations, which mirrors the historical and geographical background of the populations compared.
DOI: 10.6084/m9.figshare.19695755
title: Additional file 2 of Geographical resistome profiling in the honeybee microbiome reveals resistance gene transfer conferred by mobilizable plasmids

description: Additional file 2: Dataset S1. List of honeybee samples in this study.
DOI: 10.6084/m9.figshare.19695755.v1
title: Additional file 2 of Geographical resistome profiling in the honeybee microbiome reveals resistance gene transfer conferred by mobilizable plasmids

description: Additional file 2: Dataset S1. List of honeybee samples in this study.
DOI: 10.6084/m9.figshare.19695758
title: Additional file 3 of Geographical resistome profiling in the honeybee microbiome reveals resistance gene transfer conferred by mobilizable plasmids

description: Additional file 3: Dataset S2. Normalized abundance of ARGs in each metagenomic sample.
DOI: 10.6084/m9.figshare.19695758.v1
title: Additional file 3 of Geographical resistome profiling in the honeybee microbiome reveals resistance gene transfer conferred by mobilizable plasmids

description: Additional file 3: Dataset S2. Normalized abundance of ARGs in each metagenomic sample.
DOI: 10.6084/m9.figshare.19695761
title: Additional file 4 of Geographical resistome profiling in the honeybee microbiome reveals resistance gene transfer conferred by mobilizable plasmids

description: Additional file 4: Dataset S3. Taxonomic assignment of ARG reads.
DOI: 10.6084/m9.figshare.19695761.v1
title: Additional file 4 of Geographical resistome profiling in the honeybee microbiome reveals resistance gene transfer conferred by mobilizable plasmids

description: Additional file 4: Dataset S3. Taxonomic assignment of ARG reads.
DOI: 10.6084/m9.figshare.19695764
title: Additional file 5 of Geographical resistome profiling in the honeybee microbiome reveals resistance gene transfer conferred by mobilizable plasmids

description: Additional file 5: Dataset S4. Taxonomic assignment of transferrable ARGs in each sample.
DOI: 10.6084/m9.figshare.19695764.v1
title: Additional file 5 of Geographical resistome profiling in the honeybee microbiome reveals resistance gene transfer conferred by mobilizable plasmids

description: Additional file 5: Dataset S4. Taxonomic assignment of transferrable ARGs in each sample.
DOI: 10.6084/m9.figshare.19695767
title: Additional file 6 of Geographical resistome profiling in the honeybee microbiome reveals resistance gene transfer conferred by mobilizable plasmids

description: Additional file 6: Dataset S5. Detailed information of antibiotic susceptibility of different honeybee gut strains.
DOI: 10.6084/m9.figshare.19695767.v1
title: Additional file 6 of Geographical resistome profiling in the honeybee microbiome reveals resistance gene transfer conferred by mobilizable plasmids

description: Additional file 6: Dataset S5. Detailed information of antibiotic susceptibility of different honeybee gut strains.
DOI: 10.6084/m9.figshare.11307188
title: DNA hydroxymethylation increases the susceptibility of reactivation of methylated <i>P16</i> alleles in cancer cells

description: It is well established that 5-methylcytosine (5mC) in genomic DNA of mammalian cells can be oxidized into 5-hydroxymethylcytosine (5hmC) and other derivates by DNA dioxygenase TETs. While conversion of 5mC to 5hmC plays an important role in active DNA demethylation through further oxidation steps, a certain proportion of 5hmCs remain in the genome. Although 5hmCs contribute to the flexibility of chromatin and protect bivalent promoters from hypermethylation, the direct effect of 5hmCs on gene transcription is unknown. In this present study, we have engineered a zinc-finger protein-based P16-specific DNA dioxygenase (P16-TET) to induce <i>P16</i> hydroxymethylation and demethylation in cancer cells. Our results demonstrate, for the first time, that although the hydroxymethylated <i>P16</i> alleles retain transcriptionally inactive, hydroxymethylation could increase the susceptibility of reactivation of methylated <i>P16</i> alleles.
DOI: 10.6084/m9.figshare.11307188.v2
title: DNA hydroxymethylation increases the susceptibility of reactivation of methylated <i>P16</i> alleles in cancer cells

description: It is well established that 5-methylcytosine (5mC) in genomic DNA of mammalian cells can be oxidized into 5-hydroxymethylcytosine (5hmC) and other derivates by DNA dioxygenase TETs. While conversion of 5mC to 5hmC plays an important role in active DNA demethylation through further oxidation steps, a certain proportion of 5hmCs remain in the genome. Although 5hmCs contribute to the flexibility of chromatin and protect bivalent promoters from hypermethylation, the direct effect of 5hmCs on gene transcription is unknown. In this present study, we have engineered a zinc-finger protein-based P16-specific DNA dioxygenase (P16-TET) to induce <i>P16</i> hydroxymethylation and demethylation in cancer cells. Our results demonstrate, for the first time, that although the hydroxymethylated <i>P16</i> alleles retain transcriptionally inactive, hydroxymethylation could increase the susceptibility of reactivation of methylated <i>P16</i> alleles.
DOI: 10.6084/m9.figshare.19695795
title: Additional file 3 of Enhancer transcription detected in the nascent transcriptomic landscape of bread wheat

description: Additional file 3: Supplementary Table S2. TSS and TC counts identified by TSScall.
DOI: 10.6084/m9.figshare.19695795.v1
title: Additional file 3 of Enhancer transcription detected in the nascent transcriptomic landscape of bread wheat

description: Additional file 3: Supplementary Table S2. TSS and TC counts identified by TSScall.
DOI: 10.6084/m9.figshare.19695792.v1
title: Additional file 2 of Enhancer transcription detected in the nascent transcriptomic landscape of bread wheat

description: Additional file 2: Supplementary Table S1. Statistics of nascent RNA sequencing data quality.
DOI: 10.6084/m9.figshare.19695792
title: Additional file 2 of Enhancer transcription detected in the nascent transcriptomic landscape of bread wheat

description: Additional file 2: Supplementary Table S1. Statistics of nascent RNA sequencing data quality.
DOI: 10.6084/m9.figshare.11307188.v1
title: DNA hydroxymethylation increases the susceptibility of reactivation of methylated <i>P16</i> alleles in cancer cells

description: It is well established that 5-methylcytosine (5mC) in genomic DNA of mammalian cells can be oxidized into 5-hydroxymethylcytosine (5hmC) and other derivates by DNA dioxygenase TETs. While conversion of 5mC to 5hmC plays an important role in active DNA demethylation through further oxidation steps, a certain proportion of 5hmCs remain in the genome. Although 5hmCs contribute to the flexibility of chromatin and protect bivalent promoters from hypermethylation, the direct effect of 5hmCs on gene transcription is unknown. In this present study, we have engineered a zinc-finger protein-based P16-specific DNA dioxygenase (P16-TET) to induce <i>P16</i> hydroxymethylation and demethylation in cancer cells. Our results demonstrate, for the first time, that although the hydroxymethylated <i>P16</i> alleles retain transcriptionally inactive, hydroxymethylation could increase the susceptibility of reactivation of methylated <i>P16</i> alleles.
DOI: 10.6084/m9.figshare.17598647
title: Additional file 1 of Transcriptome analysis reveals the molecular mechanism of Yiqi Rougan decoction in reducing CCl4-induced liver fibrosis in rats

description: Additional file 1. Detailed information of YQRG-compounds were obtained by MS/MS.
DOI: 10.6084/m9.figshare.19695798
title: Additional file 4 of Enhancer transcription detected in the nascent transcriptomic landscape of bread wheat

description: Additional file 4: Supplementary Table S3. Transcribed enhancer counts linked to homeolog pairs (pNET).
DOI: 10.6084/m9.figshare.17598647.v1
title: Additional file 1 of Transcriptome analysis reveals the molecular mechanism of Yiqi Rougan decoction in reducing CCl4-induced liver fibrosis in rats

description: Additional file 1. Detailed information of YQRG-compounds were obtained by MS/MS.
DOI: 10.6084/m9.figshare.19695798.v1
title: Additional file 4 of Enhancer transcription detected in the nascent transcriptomic landscape of bread wheat

description: Additional file 4: Supplementary Table S3. Transcribed enhancer counts linked to homeolog pairs (pNET).
DOI: 10.6084/m9.figshare.19695801
title: Additional file 5 of Enhancer transcription detected in the nascent transcriptomic landscape of bread wheat

description: Additional file 5: Supplementary Table S4. Transcribed enhancer counts linked to homeolog pairs (GRO).
DOI: 10.6084/m9.figshare.19695801.v1
title: Additional file 5 of Enhancer transcription detected in the nascent transcriptomic landscape of bread wheat

description: Additional file 5: Supplementary Table S4. Transcribed enhancer counts linked to homeolog pairs (GRO).
DOI: 10.6084/m9.figshare.19695804
title: Additional file 6 of Enhancer transcription detected in the nascent transcriptomic landscape of bread wheat

description: Additional file 6: Supplementary Table S5. Genomic positions and primers used for the reporter assay.
DOI: 10.6084/m9.figshare.19695794
title: Additional file 1 of Single-cell transcriptomics reveal a unique memory-like NK cell subset that accumulates with ageing and correlates with disease severity in COVID-19

description: Additional file 1: Table S1. Sample information. Table S2. Lymphocyte cluster marker genes. Table S3. Bulk RNA-seq DEseq normalization data in Fig. 1C. Table S4. NK1 vs NK2 DEGs in Fig. 1D. Table S5. NK1 vs NK2 GO term in Fig. 1H. Table S6. NK cell subsets marker genes in Fig. 2D. Table S7. Gene-sets of CD56bright NK cell signature genes and CD56dim NK cell signature genes. Table S8. Top50 age-related genes in Fig. 3F. Table S9. DEGs in NK2.1, NK2.2, and NK2.3 cells (Elderly vs Young). Table S10. GO term in NK2.1, NK2.2, and NK2.3 cells (Elderly vs Young). Table S11. COVID-19 patient information in Fig. 6A. Table S12. GO term of upregulated genes (Elderly COVID-19 patients vs elderly healthy controls) in Fig. 6G. Table S13. Interferon alpha/beta signaling genes.
DOI: 10.6084/m9.figshare.19695794.v1
title: Additional file 1 of Single-cell transcriptomics reveal a unique memory-like NK cell subset that accumulates with ageing and correlates with disease severity in COVID-19

description: Additional file 1: Table S1. Sample information. Table S2. Lymphocyte cluster marker genes. Table S3. Bulk RNA-seq DEseq normalization data in Fig. 1C. Table S4. NK1 vs NK2 DEGs in Fig. 1D. Table S5. NK1 vs NK2 GO term in Fig. 1H. Table S6. NK cell subsets marker genes in Fig. 2D. Table S7. Gene-sets of CD56bright NK cell signature genes and CD56dim NK cell signature genes. Table S8. Top50 age-related genes in Fig. 3F. Table S9. DEGs in NK2.1, NK2.2, and NK2.3 cells (Elderly vs Young). Table S10. GO term in NK2.1, NK2.2, and NK2.3 cells (Elderly vs Young). Table S11. COVID-19 patient information in Fig. 6A. Table S12. GO term of upregulated genes (Elderly COVID-19 patients vs elderly healthy controls) in Fig. 6G. Table S13. Interferon alpha/beta signaling genes.
DOI: 10.6084/m9.figshare.19695804.v1
title: Additional file 6 of Enhancer transcription detected in the nascent transcriptomic landscape of bread wheat

description: Additional file 6: Supplementary Table S5. Genomic positions and primers used for the reporter assay.
DOI: 10.6084/m9.figshare.19695807
title: Additional file 7 of Enhancer transcription detected in the nascent transcriptomic landscape of bread wheat

description: Additional file 7: Supplementary Table S6. Location, eRNA level, and enhancer activity of 36 putative enhancers tested in wheat protoplasts.
DOI: 10.6084/m9.figshare.19695807.v1
title: Additional file 7 of Enhancer transcription detected in the nascent transcriptomic landscape of bread wheat

description: Additional file 7: Supplementary Table S6. Location, eRNA level, and enhancer activity of 36 putative enhancers tested in wheat protoplasts.
DOI: 10.6084/m9.figshare.14752150
title: Additional file 4 of Identification of long noncoding natural antisense transcripts (lncNATs) correlated with drought stress response in wild rice (Oryza nivara)

description: Additional file 4: Table S4. Differentially expressed genes (DEGs) identified in Nip, BJ89, and BJ278 under the drought stress relative to control conditions.
DOI: 10.25919/sbrf-z111
title: Social and Economic Long Term Monitoring Program (SELTMP) for the Great Barrier Reef data, 2023

description: SELTMP is assisting Reef managers and other decision-makers within the Great Barrier Reef region to incorporate the human dimension into their planning and management. Analogous to the Australian Census, SELTMP gathers long-term data specific to Reef users, communities and industries, enabling new insights into relationships, vulnerabilities and dependencies between people and the natural resources.
DOI: 10.6084/m9.figshare.14752150.v1
title: Additional file 4 of Identification of long noncoding natural antisense transcripts (lncNATs) correlated with drought stress response in wild rice (Oryza nivara)

description: Additional file 4: Table S4. Differentially expressed genes (DEGs) identified in Nip, BJ89, and BJ278 under the drought stress relative to control conditions.
DOI: 10.25919/s2yv-kg48
title: Seaborne metadata database

description: The SEABORNE (Sustainable UsE And Benefits fOR mariNE) has consolidated and synthesised existing information about who is using the Reef, how it is being used and what the benefits are from this use. SEABORNE began in November 2021, and initially, we were provided with a list of potential datasets relevant to our project in a spreadsheet. To this, we continued to search various data portals online and find additional datasets relevant to our project, particularly focusing on the Great Barrier Reef. We recorded these initially in an Excel spreadsheet. We then transferred this to an MS Access database and developed a more user-friendly entry form. Within the MS Access database, there is one table that stores all the metadata records entered. And another table that stores the static preview images. There are 58 fields (which have been described in a data dictionary) – some of these are mandatory. At the moment there are 3 metadata records entered and we expect this to grow to 50-100 records by the completion of the project.
DOI: 10.6084/m9.figshare.19695827
title: Additional file 1 of Genome-wide identification, evolutionary and functional analyses of KFB family members in potato

description: Additional file 1 Table S1. The information of profile HMMs of F-box and Kelch domains in Pfam database. Table S2. The sequences and positions information of F-box domains in 44 StKFB members. Table S3. The sequences and positions information of Kelch motifs in 44 StKFB members. Table S4. The 20 conserved motifs in StKFB proteins identified by MEME software and motifs annotation analysis by InterProScan. Table S5. The orthologous KFB genes identified by comparison between potato and other plants. Table S6. Expression profiles of 44 StKFB genes in different potato tissues, in potato plants with different treatments and in tubers with different colors. The FPKM values of 44 StKFB genes in different potato tissues and in potato plants with different treatments were extracted from RNA-Seq Gene Expression Data: DM_RH_RNA-Seq_FPKM_expression_matrix_for_DM_v4.03_13dec2013_desc.xlsx, the excel file of FPKM values of all the representative transcripts across 40 DM and 16 RH libraries ( http://spuddb.uga.edu/pgsc_download.shtml ); the FPKM values in tubers with different colors was extracted from RNA-seq data in our lab deposited in the NCBI Sequence Read Archive under the Bioproject accession PRJNA729884. Table S7. Quality of transcriptome sequencing of potato tuber with three colors. Raw reads: Number of reads in raw data; Clean reads: Number of reads filtered from raw data; Raw bases: The number of bases in the raw data; Clean bases: The number of bases filtered from the raw data; Error rate: Error rate of data sequencing; Q20: Percentage of bases with a Phred value greater than 20; Q30: Percentage of bases with a Phred value greater than 30; GC content: The percentage of G and C in clean reads. Table S8. Sequence alignment results of reads mapped to the reference genome (DM v4.03/v4.04). Total reads: the number of clean reads used for mapping analysis; Total mapped: the number of reads that could be mapped to the reference genome; Multiple mapped: the number of reads mapped to multiple locations in the reference genome; Uniquely mapped: the number of reads mapped to single location in the reference genome; Read-1 and Read-2: the number of reads mapped to the reference genome in Read 1 and Read 2, respectively; Reads mapped to ‘+’ and Reads mapped to ‘-’: the number of reads mapped to the positive and negative strands of the reference genome, respectively; Non-splice reads: the number of reads with the entire segment mapped to exons; Splice reads: the number of segmented reads mapped on two different exons; Reads mapped in proper pairs:the number of reads paired mapped to the reference genome; Proper-paired reads map to different chrom: the number of paired reads mapped to different chromosomes in the reference genome. Table S9. All primers used in qRT-PCR. Table S10. The annotation of 44 StKFBs and their corresponding orthologous genes in Arabidopsis thaliana. The potato StKFB protein sequences were aligned with those of Arabidopsis thaliana using Blastp.
DOI: 10.6084/m9.figshare.19695827.v1
title: Additional file 1 of Genome-wide identification, evolutionary and functional analyses of KFB family members in potato

description: Additional file 1 Table S1. The information of profile HMMs of F-box and Kelch domains in Pfam database. Table S2. The sequences and positions information of F-box domains in 44 StKFB members. Table S3. The sequences and positions information of Kelch motifs in 44 StKFB members. Table S4. The 20 conserved motifs in StKFB proteins identified by MEME software and motifs annotation analysis by InterProScan. Table S5. The orthologous KFB genes identified by comparison between potato and other plants. Table S6. Expression profiles of 44 StKFB genes in different potato tissues, in potato plants with different treatments and in tubers with different colors. The FPKM values of 44 StKFB genes in different potato tissues and in potato plants with different treatments were extracted from RNA-Seq Gene Expression Data: DM_RH_RNA-Seq_FPKM_expression_matrix_for_DM_v4.03_13dec2013_desc.xlsx, the excel file of FPKM values of all the representative transcripts across 40 DM and 16 RH libraries ( http://spuddb.uga.edu/pgsc_download.shtml ); the FPKM values in tubers with different colors was extracted from RNA-seq data in our lab deposited in the NCBI Sequence Read Archive under the Bioproject accession PRJNA729884. Table S7. Quality of transcriptome sequencing of potato tuber with three colors. Raw reads: Number of reads in raw data; Clean reads: Number of reads filtered from raw data; Raw bases: The number of bases in the raw data; Clean bases: The number of bases filtered from the raw data; Error rate: Error rate of data sequencing; Q20: Percentage of bases with a Phred value greater than 20; Q30: Percentage of bases with a Phred value greater than 30; GC content: The percentage of G and C in clean reads. Table S8. Sequence alignment results of reads mapped to the reference genome (DM v4.03/v4.04). Total reads: the number of clean reads used for mapping analysis; Total mapped: the number of reads that could be mapped to the reference genome; Multiple mapped: the number of reads mapped to multiple locations in the reference genome; Uniquely mapped: the number of reads mapped to single location in the reference genome; Read-1 and Read-2: the number of reads mapped to the reference genome in Read 1 and Read 2, respectively; Reads mapped to ‘+’ and Reads mapped to ‘-’: the number of reads mapped to the positive and negative strands of the reference genome, respectively; Non-splice reads: the number of reads with the entire segment mapped to exons; Splice reads: the number of segmented reads mapped on two different exons; Reads mapped in proper pairs:the number of reads paired mapped to the reference genome; Proper-paired reads map to different chrom: the number of paired reads mapped to different chromosomes in the reference genome. Table S9. All primers used in qRT-PCR. Table S10. The annotation of 44 StKFBs and their corresponding orthologous genes in Arabidopsis thaliana. The potato StKFB protein sequences were aligned with those of Arabidopsis thaliana using Blastp.
DOI: 10.15468/dl.6rv6xp
title: Occurrence Download

description: A dataset containing 2104 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Réserves Naturelles de France (RNF) - RNF - Données de l'ONF Isère"
 ]
}

 The dataset includes 2104 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0232571-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2shjz7
title: Occurrence Download

description: A dataset containing 1606 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Anotia Kirby, 1821"
 ]
}

 The dataset includes 1606 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0313197-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ub0w8t
title: Occurrence Download

description: A dataset containing 38 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Uzbekistan",
 "TaxonKey is Cyanistes cyanus (Pallas, 1770)"
 ]
}

 The dataset includes 38 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006904-180508205500799/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.