cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7204793
title: table S1.doc from DNA methylation subpatterns at distinct regulatory regions in human early embryos

description: DNA methylation has been investigated for many years, but recent technologies have allowed for single-cell and single-base resolution DNA methylation datasets and more accurate assessment of DNA methylation dynamics at the key genomic regions that regulate gene expression in human early embryonic development. In this study, the region staring from upstream 20 kb to downstream 20 kb of RefSeq gene was selected and divided into 12 distinct regions (up20, up10, up5, up2, 5'UTR, exon, intron, 3'UTR, down2, down5, down10 and down20). The candidate promoter region (TSS ± 2 kb) was further divided into 20 consecutive subregions, which were termed bins. The DNA methylation dynamics of these regions were systematically analysed along with their effects on gene expression in human early embryos. The dynamic DNA methylation subpatterns at the distinct genomic regions with a focus on promoter regions were mapped. For the 12 distinct genomic regions, up2 and 5'UTR had the lowest DNA methylation levels and their methylation dynamics were different with other regions. The region 3'UTR had the highest DNA methylation levels, and the correlation analysis with gene expression proved that it was a feature of transcribed genes. For the 20 bins in promoter region, the CpG densities showed a normal distribution pattern, and the trend of the methylated CpG counts was inverse with the DNA methylation levels, especially for the bin 1 (downstream 200 bp of the TSS). Through the correlation analysis between DNA methylation and gene expression, current study finally revealed that, the region bin −4 to 6 (800 bp upstream to 1200 bp downstream of the TSS) was the best candidate for the promoter region in human early embryos, and bin 1 was the putative key regulator of gene activity. This study provided a global and high-resolution view of DNA methylation subpatterns at the distinct genomic regions in human early embryos.
DOI: 10.5281/zenodo.6904218
title: Terminus Traces for publication 'Ocean-forcing and glacier-specific factors drive differing glacier response across the 69 oN boundary, east Greenland' (Version 1)

description: Dataset supporting publication 'Brough, S., Carr, J.R., Ross, N., Lea, J.M. (2023) Ocean-forcing and glacier-specific factors drive differing glacier response across the 69 oN boundary, east Greenland. J. Geophys. Res. Earth Surf. https://doi.org/10.1029/2022JF006857.'

This dataset provides GIS ready shapefiles of mapped terminus traces for 24 east Greenland glaciers between 2013 and 2020 for the aforementioned publication. Data are provided in both geographic (EPSG: 4326; WGS84) and projected (EPSG:3413; NSIDC Sea Ice Polar Stereographic North) coordinate systems. As each terminus trace has metadata appended, including the unique path identifier, it is possible to directly and easily identify the original image used in the mapping process. Both shapefiles are compatible for ingestion into the Google Earth Digitisation Tool (GEEDiT) Reviewer (https://liverpoolgee.wordpress.com/) for reviewing and sub-setting the dataset (see Lea, J.M. [2018] Earth Surf. Dynam. 6, 551–561. https://doi.org/10.5194/esurf-6-551-2018).

 

When using this data product in a publication, please include the following citations:

Brough, S., Carr, J.R., Ross, N., Lea, J.M. (2023). Terminus Traces for publication 'Ocean-forcing and glacier-specific factors drive differing glacier response across the 69 oN boundary, east Greenland' (Version 1) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.6904219.

Brough, S., Carr, J.R., Ross, N., Lea, J.M. (2023) Ocean-forcing and glacier-specific factors drive differing glacier response across the 69 oN boundary, east Greenland.  J. Geophys. Res. Earth Surf. https://doi.org/10.1029/2022JF006857.
DOI: 10.5281/zenodo.6904219
title: Terminus Traces for publication 'Ocean-forcing and glacier-specific factors drive differing glacier response across the 69 oN boundary, east Greenland' (Version 1)

description: Dataset supporting publication 'Brough, S., Carr, J.R., Ross, N., Lea, J.M. (2023) Ocean-forcing and glacier-specific factors drive differing glacier response across the 69 oN boundary, east Greenland. J. Geophys. Res. Earth Surf. https://doi.org/10.1029/2022JF006857.'

This dataset provides GIS ready shapefiles of mapped terminus traces for 24 east Greenland glaciers between 2013 and 2020 for the aforementioned publication. Data are provided in both geographic (EPSG: 4326; WGS84) and projected (EPSG:3413; NSIDC Sea Ice Polar Stereographic North) coordinate systems. As each terminus trace has metadata appended, including the unique path identifier, it is possible to directly and easily identify the original image used in the mapping process. Both shapefiles are compatible for ingestion into the Google Earth Digitisation Tool (GEEDiT) Reviewer (https://liverpoolgee.wordpress.com/) for reviewing and sub-setting the dataset (see Lea, J.M. [2018] Earth Surf. Dynam. 6, 551–561. https://doi.org/10.5194/esurf-6-551-2018).

 

When using this data product in a publication, please include the following citations:

Brough, S., Carr, J.R., Ross, N., Lea, J.M. (2023). Terminus Traces for publication 'Ocean-forcing and glacier-specific factors drive differing glacier response across the 69 oN boundary, east Greenland' (Version 1) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.6904219.

Brough, S., Carr, J.R., Ross, N., Lea, J.M. (2023) Ocean-forcing and glacier-specific factors drive differing glacier response across the 69 oN boundary, east Greenland.  J. Geophys. Res. Earth Surf. https://doi.org/10.1029/2022JF006857.
DOI: 10.6084/m9.figshare.14544735.v1
title: Additional file 7 of MYOD1 inhibits avian adipocyte differentiation via miRNA-206/KLF4 axis

description: Additional file 7: Table S6. A list of the expression fold changes of known lipid biosynthesis genes in MYOD1KO, MYOD1NC and MYOD1OE cells. (Genes are selected from genecards database: Pathcards: Fatty Acyl-CoA Biosynthesis & Triglyceride Biosynthesis).
DOI: 10.6084/m9.figshare.14544738
title: Additional file 8 of MYOD1 inhibits avian adipocyte differentiation via miRNA-206/KLF4 axis

description: Additional file 8: Table S7. Binding sites of MYOD1 in the 2000 bp upstream region of gga-miR-206.
DOI: 10.6084/m9.figshare.14544729.v1
title: Additional file 5 of MYOD1 inhibits avian adipocyte differentiation via miRNA-206/KLF4 axis

description: Additional file 5: Table S4. List of all DEGs before (day 0) and after adipogenic differentiation (day 5) in MYOD1KO, MYOD1NC and MYOD1OE cells.
DOI: 10.6084/m9.figshare.7204778
title: table S2.doc from DNA methylation subpatterns at distinct regulatory regions in human early embryos

description: DNA methylation has been investigated for many years, but recent technologies have allowed for single-cell and single-base resolution DNA methylation datasets and more accurate assessment of DNA methylation dynamics at the key genomic regions that regulate gene expression in human early embryonic development. In this study, the region staring from upstream 20 kb to downstream 20 kb of RefSeq gene was selected and divided into 12 distinct regions (up20, up10, up5, up2, 5'UTR, exon, intron, 3'UTR, down2, down5, down10 and down20). The candidate promoter region (TSS ± 2 kb) was further divided into 20 consecutive subregions, which were termed bins. The DNA methylation dynamics of these regions were systematically analysed along with their effects on gene expression in human early embryos. The dynamic DNA methylation subpatterns at the distinct genomic regions with a focus on promoter regions were mapped. For the 12 distinct genomic regions, up2 and 5'UTR had the lowest DNA methylation levels and their methylation dynamics were different with other regions. The region 3'UTR had the highest DNA methylation levels, and the correlation analysis with gene expression proved that it was a feature of transcribed genes. For the 20 bins in promoter region, the CpG densities showed a normal distribution pattern, and the trend of the methylated CpG counts was inverse with the DNA methylation levels, especially for the bin 1 (downstream 200 bp of the TSS). Through the correlation analysis between DNA methylation and gene expression, current study finally revealed that, the region bin −4 to 6 (800 bp upstream to 1200 bp downstream of the TSS) was the best candidate for the promoter region in human early embryos, and bin 1 was the putative key regulator of gene activity. This study provided a global and high-resolution view of DNA methylation subpatterns at the distinct genomic regions in human early embryos.
DOI: 10.6084/m9.figshare.7204793.v1
title: table S1.doc from DNA methylation subpatterns at distinct regulatory regions in human early embryos

description: DNA methylation has been investigated for many years, but recent technologies have allowed for single-cell and single-base resolution DNA methylation datasets and more accurate assessment of DNA methylation dynamics at the key genomic regions that regulate gene expression in human early embryonic development. In this study, the region staring from upstream 20 kb to downstream 20 kb of RefSeq gene was selected and divided into 12 distinct regions (up20, up10, up5, up2, 5'UTR, exon, intron, 3'UTR, down2, down5, down10 and down20). The candidate promoter region (TSS ± 2 kb) was further divided into 20 consecutive subregions, which were termed bins. The DNA methylation dynamics of these regions were systematically analysed along with their effects on gene expression in human early embryos. The dynamic DNA methylation subpatterns at the distinct genomic regions with a focus on promoter regions were mapped. For the 12 distinct genomic regions, up2 and 5'UTR had the lowest DNA methylation levels and their methylation dynamics were different with other regions. The region 3'UTR had the highest DNA methylation levels, and the correlation analysis with gene expression proved that it was a feature of transcribed genes. For the 20 bins in promoter region, the CpG densities showed a normal distribution pattern, and the trend of the methylated CpG counts was inverse with the DNA methylation levels, especially for the bin 1 (downstream 200 bp of the TSS). Through the correlation analysis between DNA methylation and gene expression, current study finally revealed that, the region bin −4 to 6 (800 bp upstream to 1200 bp downstream of the TSS) was the best candidate for the promoter region in human early embryos, and bin 1 was the putative key regulator of gene activity. This study provided a global and high-resolution view of DNA methylation subpatterns at the distinct genomic regions in human early embryos.
DOI: 10.25545/xwgrbp/jyt6oy
title: MSI_heterozygosity_vcf

description: Filtered SNP dataset (in VCF format) with only individuals from the MSI breeding colony. Data was used to estimate colony-specific heterozygosity and inbreeding.
DOI: 10.6084/m9.figshare.14544822
title: Additional file 2 of DeepNetBim: deep learning model for predicting HLA-epitope interactions based on network analysis by harnessing binding and immunogenicity information

description: Additional file 2: Table S1. Chi-square test on network metrics features on positive and negative datasets of binding and immunogenic model.
DOI: 10.6084/m9.figshare.14544822.v1
title: Additional file 2 of DeepNetBim: deep learning model for predicting HLA-epitope interactions based on network analysis by harnessing binding and immunogenicity information

description: Additional file 2: Table S1. Chi-square test on network metrics features on positive and negative datasets of binding and immunogenic model.
DOI: 10.6084/m9.figshare.14544819.v1
title: Additional file 1 of DeepNetBim: deep learning model for predicting HLA-epitope interactions based on network analysis by harnessing binding and immunogenicity information

description: Additional file 1: Figure S1. The correlation of network metrics. The correlation among network metrics was higher amongst HLA attributes and amongst peptide attributes than between attributes of these two distinct groups. Figure S2. Density distribution of network metrics. Density distribution of HLA (a) and peptides (b) in the binding model and in the immunogenic model (c-d) where positives refer to binding/immunogenic and negatives refer to non-binding/non-immunogenic. Figure S3. Performance comparison between the original model and the submodels. The comparison between the original model and its submodels (each time dropping one of the network metrics from the full model) in the binding model (a) and the immunogenic model (b). Figure S4. The illustration of network construction. Each HLA and peptide was taken as a node. The network weight was assigned by the transformed affinity (in the binding model) or immunogenic binary category (in the immunogenic model).
DOI: 10.25545/xwgrbp/brdlhl
title: ATPU_rmOutliers_rmRelated_fam

description: Plink files used for Admixture analysis. Chromosomes were renamed numerically, individual SampleIDs were renamed, removing the species. Related individuals and outlier SNPs were removed from the dataset.
DOI: 10.25545/xwgrbp/scm5g4
title: ATPU_SNPs_rmOutliers_rmRelated_structure

description: SNP data (with outlier SNPs and related individuals removed) in Structure format. Populations are formatted as numbers
DOI: 10.25545/xwgrbp/75eoth
title: UnknownIndividuals_MSI_WB_genepop

description: Individuals withheld from testing and training datasets in assignment tests, using the package assignPOP. Individuals were assigned to one of two genetic clusters (MSI vs. 'Northern' colonies). However, models were built only using only individuals from MSI and WB, with WB individuals representing the 'Northern' cluster. Data is in genepop format. This dataset was used to test the accuracy of the model built using the 'known individuals' dataset.
DOI: 10.25545/xwgrbp/ei1dlx
title: ATPU_rmOutliers_rmRelated_ped

description: Plink files used for Admixture analysis. Chromosomes were renamed numerically, individual SampleIDs were renamed, removing the species. Related individuals and outlier SNPs were removed from the dataset.
DOI: 10.25545/xwgrbp/mm79tv
title: KnownIndividuals_MSI_WB_genepop

description: Individuals used in testing and training datasets in assignment tests, using the package assignPOP. Individuals were assigned to one of two genetic clusters (MSI vs. 'Northern' colonies). However, models were built only using only individuals from MSI and WB, with WB individuals representing the 'Northern' cluster.
DOI: 10.6084/m9.figshare.15063301.v1
title: Additional file 2 of Prognosis and treatment of 46 Chinese pediatric cystic fibrosis patients

description: Additional file 2: Table S2. Clinical data of 46 Chinese CF patients.
DOI: 10.25545/xwgrbp/fzl3ld
title: KnownIndividuals_2Clusters_200snps_genepop

description: Individuals used in testing and training datasets in assignment tests, using the package assignPOP. Individuals were assigned to one of two genetic clusters (MSI vs. 'Northern' colonies) using a subset of the 200 highest-Fst SNPs. Data is in genepop format.
DOI: 10.25545/xwgrbp/cdrudz
title: WB_heterozygosity_vcf

description: Filtered SNP dataset (in VCF format) with only individuals from the QC breeding colony. Data was used to estimate colony-specific heterozygosity and inbreeding
DOI: 10.25545/xwgrbp/t0gmnz
title: JI_heterozygosity_vcf

description: Filtered SNP dataset (in VCF format) with only individuals from the JI breeding colony. Data was used to estimate colony-specific heterozygosity and inbreeding.
DOI: 10.25545/xwgrbp/w9monj
title: UnknownIndividuals_2Clusters_200snps_genepop

description: Individuals withheld from testing and training datasets in assignment tests, using the package assignPOP. Individuals were assigned to one of two genetic clusters (MSI vs. 'Northern' colonies) using a subset of the 200 highest-Fst SNPs. Data is in genepop format. This dataset was used to test the accuracy of the model built using the 'known individuals' dataset.
DOI: 10.25545/xwgrbp/fgo78y
title: UnknownIndividuals_2Clusters_genepop

description: Individuals withheld from testing and training datasets in assignment tests, using the package assignPOP. Individuals were assigned to one of two genetic clusters (MSI vs. 'Northern' colonies). Data is in genepop format. This dataset was used to test the accuracy of the model built using the 'known individuals' dataset.
DOI: 10.6084/m9.figshare.12972213
title: Additional file 2 of Genetic profiling of primary and secondary tumors from patients with lung adenocarcinoma and bone metastases reveals targeted therapy options

description: Additional file 2.
DOI: 10.6084/m9.figshare.15063553.v1
title: Additional file 1 of Genome of the pincer wasp Gonatopus flavifemur reveals unique venom evolution and a dual adaptation to parasitism and predation

description: Additional file 1: Supplementary Table 1. Statistics of Nanopore sequencing. Supplementary Table 2. Statistics of Illumina sequencing. Supplementary Table 3. Statistics of Gonatopus flavifemur genome assembly by Nanopore reads. Supplementary Table 4. Statistics of Gonatopus flavifemur genome assembly after error-corrected by Illumina and Nanopore reads. Supplementary Table 5. Genome size of G. flavifemur estimated by flow cytometry and 17-mer analysis. Supplementary Table 6. The mapping rate with short sequencing reads of Gonatopus flavifemur genome. Supplementary Table 7. Genes in detoxification system and chemoreception system in 13 hymenopterans. Supplementary Table 8. TE sequences in Gonatopus flavifemur and other surveyed species. Supplementary Table 9. Characteristics of DNA TEs in Gonatopus flavifemur. Supplementary Table 10. GO enrichment analysis of Aculeate-specific genes, Biological Process category (padj &lt; 0.05). Supplementary Table 11. GO enrichment analysis of Gonatopus flavifemur special genes. (padj &lt; 0.05). Supplementary Table 12. Genes under positive selection in Gonatopus flavifemur detected by both aBSREL model in HyPhy and branch-site model in PAML. Supplementary Table 13. GO enrichment analysis of Gonatopus flavifemur expanded gene families, Biological Process category (padj &lt; 0.05). Supplementary Table 14. Venom gland-associated genes (VGGs) in Gonatopus flavifemur. Supplementary Table 15. GO enrichment analysis of VGGs in Gonatopus flavifemur, Biological Process category (padj &lt; 0.05). Supplementary Table 16. Chitinase-like genes in Gonatopus flavifemur and other species. Supplementary Table 17. Neprilysin-like genes in Gonatopus flavifemur and other Hymenoptera genomes. Supplementary Table 18. Upregulated genes in the prey-feeding female transcriptomes compared to the sucrose-feeding female transcriptomes. Supplementary Table 19. Yellow genes and expression level in Gonatopus flavifemur. Supplementary Table 20. Downregulated genes in the prey-feeding female transcriptomes compared to the sucrose-feeding female transcriptomes. Supplementary Table 21. GO enrichment analysis of extremely female-biased genes in Gonatopus flavifemur. Biological Process category (padj &lt; 0.05). Supplementary Table 22. GO enrichment analysis of extremely male-biased genes in Gonatopus flavifemur. Biological Process category (padj &lt; 0.05). Supplementary Table 23. Extremely male-biased genes in Gonatopus flavifemur. Supplementary Table 24. Sample information for sequencing used in this study.
DOI: 10.25545/xwgrbp/bfuhtv
title: KnownIndividuals_4populations_genepop.txt

description: Individuals used in testing and training datasets in assignment tests, using the package assignPOP. Individuals were assigned to one of four populations, corresponding to their breeding colony. Data is in genepop format.
DOI: 10.6084/m9.figshare.18739285
title: Additional file 10 of Characterization and regulation mechanism analysis of ubiquitin-conjugating family genes in strawberry reveals a potential role in fruit ripening

description: Additional file 10: Table S9. Expression of FaUBC genes and expression clusters.
DOI: 10.6084/m9.figshare.18739312
title: Additional file 8 of Characterization and regulation mechanism analysis of ubiquitin-conjugating family genes in strawberry reveals a potential role in fruit ripening

description: Additional file 8: Table S7. KEGG function classification of FaUBC genes.
DOI: 10.6084/m9.figshare.18739285.v1
title: Additional file 10 of Characterization and regulation mechanism analysis of ubiquitin-conjugating family genes in strawberry reveals a potential role in fruit ripening

description: Additional file 10: Table S9. Expression of FaUBC genes and expression clusters.
DOI: 10.6084/m9.figshare.18739309.v1
title: Additional file 7 of Characterization and regulation mechanism analysis of ubiquitin-conjugating family genes in strawberry reveals a potential role in fruit ripening

description: Additional file 7: Table S6. GO categories and distribution of FaUBC genes.
DOI: 10.6084/m9.figshare.14545026
title: Additional file 5 of Proteomic analysis of human frontal and temporal cortex using iTRAQ-based 2D LC-MS/MS

description: Additional file 5: Supplemental Table 3. Proteins involved in neurological disease. The function annotation, p value and molecules were displayed.
DOI: 10.6084/m9.figshare.18739300
title: Additional file 4 of Characterization and regulation mechanism analysis of ubiquitin-conjugating family genes in strawberry reveals a potential role in fruit ripening

description: Additional file 4: Table S3. Ka, Ks and Ka/Ks of paralogous gene pairs of FaUBC genes.
DOI: 10.6084/m9.figshare.14545017
title: Additional file 2 of Proteomic analysis of human frontal and temporal cortex using iTRAQ-based 2D LC-MS/MS

description: Additional file 2: Supplemental Table 2. Protein identification and quantification data in both frontal and temporal lobe. A. Protein identification and quantification data in both frontal and temporal lobe. B. Quantified proteins with calculation of p-value and fold change. C. Unchanged proteins. D. Differentially expressed proteins. E. up-regulated and down-regulated proteins.
DOI: 10.6084/m9.figshare.18739303
title: Additional file 5 of Characterization and regulation mechanism analysis of ubiquitin-conjugating family genes in strawberry reveals a potential role in fruit ripening

description: Additional file 5: Table S4. Ka, Ks and Ka/Ks of paralogous gene pairs of UBC genes among three Rosaceae species.
DOI: 10.15468/dl.bxerwv
title: Occurrence Download

description: A dataset containing 1410 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Neopelma chrysocephalum (Pelzeln, 1868))",
 "DecimalLatitude is greater than or equal to -20.85",
 "DecimalLatitude is less than or equal to 2.46666666666667",
 "DecimalLongitude is greater than or equal to -83.8333333333333",
 "DecimalLongitude is less than or equal to -66.15"
 ]
}

 The dataset includes 1410 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0324081-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vstkgt
title: Occurrence Download

description: A dataset containing 7 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Allantophomopsis lycopodina (Höhn.) Carris",
 {
 "or" : [
 "Country is United States of America",
 "Country is Canada"
 ]
 },
 {
 "not" : {
 "DatasetKey" : [
 "is Global database of alien macrofungi"
 ]
 }
 }
 ]
}

 The dataset includes 7 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0100793-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/pcra-c14-57262
title: Redemption tidings, vol. 38, nos. 1-52, 5 Jan. - 28 Dec. 1962

description: [description english/roman)] Issued weekly. "A full gospel magazine" -- subtitle.