cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.11448024.v2
title: Supplementary Table from KAP1 targets actively transcribed genomic loci to exert pleomorphic effects on RNA polymerase II activity.

description: KAP1 (KRAB-associated protein 1) is best known as a co-repressor responsible for inducing heterochromatin formation notably at transposable elements. However, it has also been observed to bind the transcription start site of actively expressed genes. To address this paradox, we characterized the protein interactome of KAP1 in the human K562 erythro-leukaemia cell line. We found that the regulator can associate with a wide range of nucleic acid binding proteins, nucleosome remodellers, chromatin modifiers and other transcription modulators. We further determined that KAP1 is recruited at actively transcribed polymerase II promoters, where its depletion resulted in pleomorphic effects, whether expression of these genes was normally constitutive or inducible, consistent with the breadth of possible KAP1 interactors.This article is part of the discussion meeting issue ‘Crossroads between transposons and gene regulation’.
DOI: 10.6084/m9.figshare.12672881.v2
title: Data_Source_SCNGS_WGAN

description: "DSCN-WGAN.csv" contains 9824 samples, the original sample data set without feature extraction and data processing."DSCN-WGANLine1.csv" contains 3472 samples, which is the synthetic sample data of the first feeder."DSCN-WGANLine2.csv" contains 1806 samples, which is the synthetic sample data of the second feeder.<br>"DSCN-WGANLine3.csv" contains 1722 samples, which is the synthetic sample data of the third feeder.<br>
DOI: 10.6084/m9.figshare.11448024.v1
title: Supplementary Table from KAP1 targets actively transcribed genomic loci to exert pleomorphic effects on RNA polymerase II activity

description: KAP1 (KRAB-associated protein 1) is best known as a co-repressor responsible for inducing heterochromatin formation notably at transposable elements. However, it has also been observed to bind the transcription start site of actively expressed genes. To address this paradox, we characterized the protein interactome of KAP1 in the human K562 erythro-leukaemia cell line. We found that the regulator can associate with a wide range of nucleic acid binding proteins, nucleosome remodellers, chromatin modifiers and other transcription modulators. We further determined that KAP1 is recruited at actively transcribed polymerase II promoters, where its depletion resulted in pleomorphic effects, whether expression of these genes was normally constitutive or inducible, consistent with the breadth of possible KAP1 interactors.This article is part of the discussion meeting issue ‘Crossroads between transposons and gene regulation’.
DOI: 10.6084/m9.figshare.11449845
title: Scrambled AluYa5 sequence from Contribution of unfixed transposable element insertions to human regulatory variation.

description: Fasta sequence of the scrambled AluYa5 insertion in the 3'-UTR of HSD17B12
DOI: 10.6084/m9.figshare.12672881.v1
title: Data_Source_SCNGS_WGAN

description: "DSCN-WGAN.csv" contains 9824 samples, the original sample data set without feature extraction and data processing."DSCN-WGANLine1.csv" contains 3472 samples, which is the synthetic sample data of the first feeder."DSCN-WGANLine2.csv" contains 1806 samples, which is the synthetic sample data of the second feeder.<br>"DSCN-WGANLine3.csv" contains 1722 samples, which is the synthetic sample data of the third feeder.<br>
DOI: 10.6084/m9.figshare.11449842
title: TE-QTL results in LCL and iPSC from Contribution of unfixed transposable element insertions to human regulatory variation.

description: e- and ca-QTL lists for LCL and iPSC
DOI: 10.6084/m9.figshare.11449845.v2
title: Scrambled AluYa5 sequence from Contribution of unfixed transposable element insertions to human regulatory variation.

description: Fasta sequence of the scrambled AluYa5 insertion in the 3'-UTR of HSD17B12
DOI: 10.6084/m9.figshare.11449842.v2
title: TE-QTL results in LCL and iPSC from Contribution of unfixed transposable element insertions to human regulatory variation.

description: e- and ca-QTL lists for LCL and iPSC
DOI: 10.6084/m9.figshare.11449845.v1
title: Scrambled AluYa5 sequence from Contribution of unfixed transposable element insertions to human regulatory variation

description: Fasta sequence of the scrambled AluYa5 insertion in the 3'-UTR of HSD17B12
DOI: 10.6084/m9.figshare.11449842.v1
title: TE-QTL results in LCL and iPSC from Contribution of unfixed transposable element insertions to human regulatory variation

description: e- and ca-QTL lists for LCL and iPSC
DOI: 10.6084/m9.figshare.11449959
title: DOC analysis from Construction and characterization of a knock-down RNA interference line of <i>OsNRPD1</i> in rice (<i>Oryza sativa</i> ssp <i>japonica</i> cv Nipponbare).

description: In plants, RNA-directed DNA methylation (RdDM) is a silencing mechanism relying on the production of 24-nt small interfering RNAs (siRNAs) by RNA POLYMERASE IV (Pol IV) to trigger methylation and inactivation of transposable elements (TEs). We present the construction and characterization of <i>osnrpd1</i>, a knock-down RNA interference line of <i>OsNRPD1</i> gene that encodes the largest subunit of Pol IV in rice (<i>Oryza sativa</i> ssp <i>japonica</i> cv Nipponbare). We show that <i>osnrpd1</i> displays a lower accumulation of <i>OsNRPD1</i> transcripts, associated with an overall reduction of 24-nt siRNAs and DNA methylation level in all three contexts, CG, CHG and CHH. We uncovered new insertions of known active TEs, the LTR retrotransposons <i>Tos17</i> and <i>Lullaby</i> and the long interspersed nuclear element-type retrotransposon <i>Karma.</i> However, we did not observe any clear developmental phenotype, contrary to what was expected for a mutant severely affected in RdDM. In addition, despite the presence of many putatively functional TEs in the rice genome, we found no evidence of <i>in planta</i> global reactivation of transposition. This knock-down of <i>OsNRPD1</i> likely led to a weakly affected line, with no effect on development and a limited effect on transposition. We discuss the possibility that a knock-out mutation of <i>OsNRPD1</i> would cause sterility in rice.This article is part of the discussion meeting issue ‘Crossroads between transposons and gene regulation’.
DOI: 10.6084/m9.figshare.11449959.v2
title: DOC analysis from Construction and characterization of a knock-down RNA interference line of <i>OsNRPD1</i> in rice (<i>Oryza sativa</i> ssp <i>japonica</i> cv Nipponbare).

description: In plants, RNA-directed DNA methylation (RdDM) is a silencing mechanism relying on the production of 24-nt small interfering RNAs (siRNAs) by RNA POLYMERASE IV (Pol IV) to trigger methylation and inactivation of transposable elements (TEs). We present the construction and characterization of <i>osnrpd1</i>, a knock-down RNA interference line of <i>OsNRPD1</i> gene that encodes the largest subunit of Pol IV in rice (<i>Oryza sativa</i> ssp <i>japonica</i> cv Nipponbare). We show that <i>osnrpd1</i> displays a lower accumulation of <i>OsNRPD1</i> transcripts, associated with an overall reduction of 24-nt siRNAs and DNA methylation level in all three contexts, CG, CHG and CHH. We uncovered new insertions of known active TEs, the LTR retrotransposons <i>Tos17</i> and <i>Lullaby</i> and the long interspersed nuclear element-type retrotransposon <i>Karma.</i> However, we did not observe any clear developmental phenotype, contrary to what was expected for a mutant severely affected in RdDM. In addition, despite the presence of many putatively functional TEs in the rice genome, we found no evidence of <i>in planta</i> global reactivation of transposition. This knock-down of <i>OsNRPD1</i> likely led to a weakly affected line, with no effect on development and a limited effect on transposition. We discuss the possibility that a knock-out mutation of <i>OsNRPD1</i> would cause sterility in rice.This article is part of the discussion meeting issue ‘Crossroads between transposons and gene regulation’.
DOI: 10.6084/m9.figshare.11449959.v1
title: DOC analysis from Construction and characterization of a knock-down RNA interference line of <i>OsNRPD1</i> in rice (<i>Oryza sativa</i> ssp <i>japonica</i> cv Nipponbare)

description: In plants, RNA-directed DNA methylation (RdDM) is a silencing mechanism relying on the production of 24-nt small interfering RNAs (siRNAs) by RNA POLYMERASE IV (Pol IV) to trigger methylation and inactivation of transposable elements (TEs). We present the construction and characterization of <i>osnrpd1</i>, a knock-down RNA interference line of <i>OsNRPD1</i> gene that encodes the largest subunit of Pol IV in rice (<i>Oryza sativa</i> ssp <i>japonica</i> cv Nipponbare). We show that <i>osnrpd1</i> displays a lower accumulation of <i>OsNRPD1</i> transcripts, associated with an overall reduction of 24-nt siRNAs and DNA methylation level in all three contexts, CG, CHG and CHH. We uncovered new insertions of known active TEs, the LTR retrotransposons <i>Tos17</i> and <i>Lullaby</i> and the long interspersed nuclear element-type retrotransposon <i>Karma.</i> However, we did not observe any clear developmental phenotype, contrary to what was expected for a mutant severely affected in RdDM. In addition, despite the presence of many putatively functional TEs in the rice genome, we found no evidence of <i>in planta</i> global reactivation of transposition. This knock-down of <i>OsNRPD1</i> likely led to a weakly affected line, with no effect on development and a limited effect on transposition. We discuss the possibility that a knock-out mutation of <i>OsNRPD1</i> would cause sterility in rice.This article is part of the discussion meeting issue ‘Crossroads between transposons and gene regulation’.
DOI: 10.6084/m9.figshare.11533302
title: Dataset from What makes a pair bond in a Neotropical primate: female and male contributions.

description: Focal observations dataset
DOI: 10.6084/m9.figshare.11533302.v2
title: Dataset from What makes a pair bond in a Neotropical primate: female and male contributions.

description: Focal observations dataset
DOI: 10.6084/m9.figshare.11533302.v1
title: Dataset from What makes a pair bond in a Neotropical primate: female and male contributions

description: Focal observations dataset
DOI: 10.6084/m9.figshare.11547060
title: Table S9 from Recurrent mutualism breakdown events in a legume rhizobia metapopulation.

description: Bradyrhizobium strains from other host species that are closely related to isolates in the current study (See Figures S5,S6,S8,S9)
DOI: 10.6084/m9.figshare.11547060.v2
title: Table S9 from Recurrent mutualism breakdown events in a legume rhizobia metapopulation.

description: Bradyrhizobium strains from other host species that are closely related to isolates in the current study (See Figures S5,S6,S8,S9)
DOI: 10.6084/m9.figshare.11547078
title: Table S1. Summary of isolate information from Recurrent mutualism breakdown events in a legume rhizobia metapopulation.

description: Summary of isolate information including isolate type, isolate code, field collection site, species, genotype, and statistics supporting binary categories of symbiosis traits.
DOI: 10.6084/m9.figshare.11547060.v1
title: Table S9 from Recurrent mutualism breakdown events in a legume rhizobia metapopulation

description: Bradyrhizobium strains from other host species that are closely related to isolates in the current study (See Figures S5,S6,S8,S9)
DOI: 10.6084/m9.figshare.11547078.v2
title: Table S1. Summary of isolate information from Recurrent mutualism breakdown events in a legume rhizobia metapopulation.

description: Summary of isolate information including isolate type, isolate code, field collection site, species, genotype, and statistics supporting binary categories of symbiosis traits.
DOI: 10.6084/m9.figshare.11547078.v1
title: Table S1. Summary of isolate information from Recurrent mutualism breakdown events in a legume rhizobia metapopulation

description: Summary of isolate information including isolate type, isolate code, field collection site, species, genotype, and statistics supporting binary categories of symbiosis traits.
DOI: 10.6084/m9.figshare.11547066
title: Table S13 from Recurrent mutualism breakdown events in a legume rhizobia metapopulation.

description: Variation in symbiotic traits within sampled populations
DOI: 10.6084/m9.figshare.11547048
title: Table S12 from Recurrent mutualism breakdown events in a legume rhizobia metapopulation.

description: Genetic distrances between ineffective strains and closest relatives analyzed separately for each locus
DOI: 10.6084/m9.figshare.11547066.v2
title: Table S13 from Recurrent mutualism breakdown events in a legume rhizobia metapopulation.

description: Variation in symbiotic traits within sampled populations
DOI: 10.6084/m9.figshare.11547048.v2
title: Table S12 from Recurrent mutualism breakdown events in a legume rhizobia metapopulation.

description: Genetic distrances between ineffective strains and closest relatives analyzed separately for each locus
DOI: 10.6084/m9.figshare.11547066.v1
title: Table S13 from Recurrent mutualism breakdown events in a legume rhizobia metapopulation

description: Variation in symbiotic traits within sampled populations
DOI: 10.6084/m9.figshare.11547048.v1
title: Table S12 from Recurrent mutualism breakdown events in a legume rhizobia metapopulation

description: Genetic distrances between ineffective strains and closest relatives analyzed separately for each locus
DOI: 10.6084/m9.figshare.11547069
title: Table S3. Ancestral node support and ancestral state inferences from Recurrent mutualism breakdown events in a legume rhizobia metapopulation.

description: Ancestral node support and ancestral state inferences. Data are presented for well-supported nodes of the Bradyrhizobium CHR and SI phylogenies.
DOI: 10.6084/m9.figshare.11547069.v2
title: Table S3. Ancestral node support and ancestral state inferences from Recurrent mutualism breakdown events in a legume rhizobia metapopulation.

description: Ancestral node support and ancestral state inferences. Data are presented for well-supported nodes of the Bradyrhizobium CHR and SI phylogenies.
DOI: 10.6084/m9.figshare.11547069.v1
title: Table S3. Ancestral node support and ancestral state inferences from Recurrent mutualism breakdown events in a legume rhizobia metapopulation

description: Ancestral node support and ancestral state inferences. Data are presented for well-supported nodes of the Bradyrhizobium CHR and SI phylogenies.
DOI: 10.6084/m9.figshare.11575530
title: Supplementary Table from Wetter climates select for higher immune gene diversity in resident, but not migratory, songbirds.

description: Tables containing details of all species used, raw data and the full results of all statistical analyses performed.
DOI: 10.6084/m9.figshare.11575530.v2
title: Supplementary Table from Wetter climates select for higher immune gene diversity in resident, but not migratory, songbirds.

description: Tables containing details of all species used, raw data and the full results of all statistical analyses performed.
DOI: 10.6084/m9.figshare.11575530.v1
title: Supplementary Table from Wetter climates select for higher immune gene diversity in resident, but not migratory, songbirds

description: Tables containing details of all species used, raw data and the full results of all statistical analyses performed.
DOI: 10.6084/m9.figshare.11665629
title: Figure 1- CA Substrate Droplet Spread Comparison_11222016.xlsx from The moth specialist spider <i>Cyrtarachne akirai</i> uses prey scales to increase adhesion.

description: Data used to create Figure 1 CA Substrate Droplet Spread Comparison
DOI: 10.6084/m9.figshare.11665614
title: Figure 4 – Species Comparison_MothSurfaces_Final6152017.xlsx from The moth specialist spider <i>Cyrtarachne akirai</i> uses prey scales to increase adhesion.

description: Data used to create Figure 4 – species comparison of adhesion to moth surfaces
DOI: 10.6084/m9.figshare.11665629.v2
title: Figure 1- CA Substrate Droplet Spread Comparison_11222016.xlsx from The moth specialist spider <i>Cyrtarachne akirai</i> uses prey scales to increase adhesion.

description: Data used to create Figure 1 CA Substrate Droplet Spread Comparison
DOI: 10.6084/m9.figshare.11665629.v1
title: Figure 1- CA Substrate Droplet Spread Comparison_11222016.xlsx from The moth specialist spider <i>Cyrtarachne akirai</i> uses prey scales to increase adhesion

description: Data used to create Figure 1 CA Substrate Droplet Spread Comparison
DOI: 10.6084/m9.figshare.11665617
title: Figure 5 and Supplementary Ratio Comparison 5282019.xls from The moth specialist spider <i>Cyrtarachne akirai</i> uses prey scales to increase adhesion.

description: Data used to create supplementary table 1 and figure 5
DOI: 10.6084/m9.figshare.11665614.v1
title: Figure 4 – Species Comparison_MothSurfaces_Final6152017.xlsx from The moth specialist spider <i>Cyrtarachne akirai</i> uses prey scales to increase adhesion

description: Data used to create Figure 4 – species comparison of adhesion to moth surfaces
DOI: 10.6084/m9.figshare.11665617.v2
title: Figure 5 and Supplementary Ratio Comparison 5282019.xls from The moth specialist spider <i>Cyrtarachne akirai</i> uses prey scales to increase adhesion.

description: Data used to create supplementary table 1 and figure 5
DOI: 10.6084/m9.figshare.11665617.v1
title: Figure 5 and Supplementary Ratio Comparison 5282019.xls from The moth specialist spider <i>Cyrtarachne akirai</i> uses prey scales to increase adhesion

description: Data used to create supplementary table 1 and figure 5
DOI: 10.6084/m9.figshare.13095638
title: Data and scripts to run the models of the paper "Projected effects of ocean warming on an iconic pelagic fish and its fishery."

description: These files are part of the supplementary material to the document entitled “Projected effects of ocean warming on an iconic pelagic fish and its fishery.” There are 4 files, including data and scripts in R format, needed to run the models presented in the paper. The file named “input_growth.RData” contains a list of dolphinfish (<i>Coryphaena</i> <i>hippurus</i>) otolith readings used to set up, calibrate and validate the growth model developed. The file named “growth_model.R” is the script with the parameterization of the growth model (biochronology) that calls the input file and that must be executed directly in R. The file named “input_IBM” contains the results of the ecological models used to set the basis of the IBM (see the corresponding section in the main document), and the environmental parameters of the future thermal regimes and marine heatwaves simulations to carry out the projections of growth under these climate scenarios. The file named “dolphinfish_IBM” is the script with the model parameterization to perform these growth simulations under the different environmental/climate scenarios.
DOI: 10.6084/m9.figshare.13095638.v1
title: Data and scripts to run the models of the paper "Projected effects of ocean warming on an iconic pelagic fish and its fishery."

description: These files are part of the supplementary material to the document entitled “Projected effects of ocean warming on an iconic pelagic fish and its fishery.” There are 4 files, including data and scripts in R format, needed to run the models presented in the paper. The file named “input_growth.RData” contains a list of dolphinfish (<i>Coryphaena</i> <i>hippurus</i>) otolith readings used to set up, calibrate and validate the growth model developed. The file named “growth_model.R” is the script with the parameterization of the growth model (biochronology) that calls the input file and that must be executed directly in R. The file named “input_IBM” contains the results of the ecological models used to set the basis of the IBM (see the corresponding section in the main document), and the environmental parameters of the future thermal regimes and marine heatwaves simulations to carry out the projections of growth under these climate scenarios. The file named “dolphinfish_IBM” is the script with the model parameterization to perform these growth simulations under the different environmental/climate scenarios.
DOI: 10.21227/y90t-xk47
title: A Multispectral Light Field Dataset for Light Field Deep Learning

description: Deep learning undoubtedly has had a huge impact on the computer vision community in recent years. In light field imaging, machine learning-based applications have significantly outperformed their conventional counterparts. Furthermore, multi- and hyperspectral light fields have shown promising results in light field-related applications such as disparity or shape estimation. Yet, a multispectral light field data\-set, enabling data-driven approaches, is missing. Therefore, we propose a new synthetic multispectral light field dataset with depth and disparity ground truth. The dataset consists of a training, validation and test dataset, containing light fields of randomly generated scenes, as well as a challenge dataset rendered from hand-crafted scenes enabling detailed performance assessment.
DOI: 10.21227/kydt-1m80
title: A Multispectral Light Field Dataset for Light Field Deep Learning

description: Deep learning undoubtedly has had a huge impact on the computer vision community in recent years. In light field imaging, machine learning-based applications have significantly outperformed their conventional counterparts. Furthermore, multi- and hyperspectral light fields have shown promising results in light field-related applications such as disparity or shape estimation. Yet, a multispectral light field data\-set, enabling data-driven approaches, is missing. Therefore, we propose a new synthetic multispectral light field dataset with depth and disparity ground truth. The dataset consists of a training, validation and test dataset, containing light fields of randomly generated scenes, as well as a challenge dataset rendered from hand-crafted scenes enabling detailed performance assessment.
DOI: 10.21227/hhma-m635
title: A Multispectral Light Field Dataset for Light Field Deep Learning

description: Deep learning undoubtedly has had a huge impact on the computer vision community in recent years. In light field imaging, machine learning-based applications have significantly outperformed their conventional counterparts. Furthermore, multi- and hyperspectral light fields have shown promising results in light field-related applications such as disparity or shape estimation. Yet, a multispectral light field data\-set, enabling data-driven approaches, is missing. Therefore, we propose a new synthetic multispectral light field dataset with depth and disparity ground truth. The dataset consists of a training, validation and test dataset, containing light fields of randomly generated scenes, as well as a challenge dataset rendered from hand-crafted scenes enabling detailed performance assessment.
DOI: 10.5517/ccdc.csd.cc1pk85p
title: CCDC 1565722: Experimental Crystal Structure Determination

description: Related Article: Chengri Wang, Xiaoping Yang, Shiqing Wang, Desmond Schipper, Richard A. Jones|2019|Cryst.Growth Des.|19|2149|doi:10.1021/acs.cgd.8b01766
DOI: 10.5517/ccdc.csd.cc1pk86q
title: CCDC 1565723: Experimental Crystal Structure Determination

description: Related Article: Chengri Wang, Xiaoping Yang, Shiqing Wang, Desmond Schipper, Richard A. Jones|2019|Cryst.Growth Des.|19|2149|doi:10.1021/acs.cgd.8b01766
DOI: 10.5517/ccdc.csd.cc1z5r41
title: CCDC 1822773: Experimental Crystal Structure Determination

description: Related Article: Songlin Xue, Daiki Kuzuhara, Naoki Aratani, Hiroko Yamada|2019|Org.Lett.|21|2069|doi:10.1021/acs.orglett.9b00329
DOI: 10.5517/ccdc.csd.cc1zp9cb
title: CCDC 1837722: Experimental Crystal Structure Determination

description: Related Article: Yun-Si Hong, Fan Li, Shuang-Li Sun, Qian Sun, Ming Ye|2019|J.Solid State Chem.|274|315|doi:10.1016/j.jssc.2019.03.048
DOI: 10.6084/m9.figshare.13095695
title: 1_RawData and 2_HQData

description: SNP analysis, haplotype analysis and population genetic diversity analysis based on population evolution