cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8024846
title: Whole genome bisulfite sequencing of Down syndrome brain reveals regional DNA hypermethylation and novel disorder insights

description: Down Syndrome (DS) is the most common genetic cause of intellectual disability, in which an extra copy of human chromosome 21 (HSA21) affects regional DNA methylation profiles across the genome. Although DNA methylation has been previously examined at select regulatory regions across the genome in a variety of DS tissues and cells, differentially methylated regions (DMRs) have yet to be examined in an unbiased sequencing-based approach. Here, we present the first analysis of DMRs from whole genome bisulfite sequencing (WGBS) data of human DS and matched control brain, specifically frontal cortex. While no global differences in DNA methylation were observed, we identified 3,152 DS-DMRs across the entire genome, the majority of which were hypermethylated in DS. DS-DMRs were significantly enriched at CpG islands and de-enriched at specific gene body and regulatory regions. Functionally, the hypermethylated DS-DMRs were enriched for one-carbon metabolism, membrane transport, and glutamatergic synaptic signalling, while the hypomethylated DMRs were enriched for proline isomerization, glial immune response, and apoptosis. Furthermore, in a cross-tissue comparison to previous studies of DNA methylation from diverse DS tissues and reference epigenomes, hypermethylated DS-DMRs showed a strong cross-tissue concordance, while a more tissue-specific pattern was observed for the hypomethylated DS-DMRs. Overall, this approach highlights that low-coverage WGBS of clinical samples can identify epigenetic alterations to known biological pathways, which are potentially relevant to therapeutic treatments and include metabolic pathways. These results also provide new insights into the genome-wide effects of genetic alterations on DNA methylation profiles indicative of altered neurodevelopment and brain function.
DOI: 10.6084/m9.figshare.8024846.v2
title: Whole genome bisulfite sequencing of Down syndrome brain reveals regional DNA hypermethylation and novel disorder insights

description: Down Syndrome (DS) is the most common genetic cause of intellectual disability, in which an extra copy of human chromosome 21 (HSA21) affects regional DNA methylation profiles across the genome. Although DNA methylation has been previously examined at select regulatory regions across the genome in a variety of DS tissues and cells, differentially methylated regions (DMRs) have yet to be examined in an unbiased sequencing-based approach. Here, we present the first analysis of DMRs from whole genome bisulfite sequencing (WGBS) data of human DS and matched control brain, specifically frontal cortex. While no global differences in DNA methylation were observed, we identified 3,152 DS-DMRs across the entire genome, the majority of which were hypermethylated in DS. DS-DMRs were significantly enriched at CpG islands and de-enriched at specific gene body and regulatory regions. Functionally, the hypermethylated DS-DMRs were enriched for one-carbon metabolism, membrane transport, and glutamatergic synaptic signalling, while the hypomethylated DMRs were enriched for proline isomerization, glial immune response, and apoptosis. Furthermore, in a cross-tissue comparison to previous studies of DNA methylation from diverse DS tissues and reference epigenomes, hypermethylated DS-DMRs showed a strong cross-tissue concordance, while a more tissue-specific pattern was observed for the hypomethylated DS-DMRs. Overall, this approach highlights that low-coverage WGBS of clinical samples can identify epigenetic alterations to known biological pathways, which are potentially relevant to therapeutic treatments and include metabolic pathways. These results also provide new insights into the genome-wide effects of genetic alterations on DNA methylation profiles indicative of altered neurodevelopment and brain function.
DOI: 10.6084/m9.figshare.8024846.v1
title: Whole genome bisulfite sequencing of Down syndrome brain reveals regional DNA hypermethylation and novel disorder insights

description: Down Syndrome (DS) is the most common genetic cause of intellectual disability, in which an extra copy of human chromosome 21 (HSA21) affects regional DNA methylation profiles across the genome. Although DNA methylation has been previously examined at select regulatory regions across the genome in a variety of DS tissues and cells, differentially methylated regions (DMRs) have yet to be examined in an unbiased sequencing-based approach. Here, we present the first analysis of DMRs from whole genome bisulfite sequencing (WGBS) data of human DS and matched control brain, specifically frontal cortex. While no global differences in DNA methylation were observed, we identified 3,152 DS-DMRs across the entire genome, the majority of which were hypermethylated in DS. DS-DMRs were significantly enriched at CpG islands and de-enriched at specific gene body and regulatory regions. Functionally, the hypermethylated DS-DMRs were enriched for one-carbon metabolism, membrane transport, and glutamatergic synaptic signalling, while the hypomethylated DMRs were enriched for proline isomerization, glial immune response, and apoptosis. Furthermore, in a cross-tissue comparison to previous studies of DNA methylation from diverse DS tissues and reference epigenomes, hypermethylated DS-DMRs showed a strong cross-tissue concordance, while a more tissue-specific pattern was observed for the hypomethylated DS-DMRs. Overall, this approach highlights that low-coverage WGBS of clinical samples can identify epigenetic alterations to known biological pathways, which are potentially relevant to therapeutic treatments and include metabolic pathways. These results also provide new insights into the genome-wide effects of genetic alterations on DNA methylation profiles indicative of altered neurodevelopment and brain function.
DOI: 10.6084/m9.figshare.8024858.v1
title: Hi-C genome scaffolds

description: Genome assemblies of the softshell turtle based on Hi-C scaffolding. The genomic DNA was prepared from the liver tissue and the blood cells, and crosslinked DNA molecules were digested with restriction enzymes. These assemblies were produced by 3d-dna and SALSA2 scaffolding software. The scaffold names contained in the files are not named in order of length. See the "Assembly_ID.xlsx" for details of the combinations of tissue, enzyme, software and parameters, and the number of input read pairs.
DOI: 10.6084/m9.figshare.8024549
title: Additional file 2: of Myostatin gene promoter: structure, conservation and importance as a target for muscle modulation

description: Table S2. Percent identity matrix of MSTN promoter sequences for all the vertebrate species analysed in this review. Multiple sequence alignment was used to calculate the %Â id matrix in BioEdit [113]. (XLS 189 kb)
DOI: 10.6084/m9.figshare.8024549.v1
title: Additional file 2: of Myostatin gene promoter: structure, conservation and importance as a target for muscle modulation

description: Table S2. Percent identity matrix of MSTN promoter sequences for all the vertebrate species analysed in this review. Multiple sequence alignment was used to calculate the %Â id matrix in BioEdit [113]. (XLS 189 kb)
DOI: 10.6084/m9.figshare.8024534
title: Additional file 1: of Myostatin gene promoter: structure, conservation and importance as a target for muscle modulation

description: Table S1. Summarized information on the different MSTN promoters analysed in this review. Information includes accession numbers, number of E-boxes and presence (x) or absence of TFBS in each species. TFBS or sequences identified independently by our group are indicated by a red asterisk (*) [119]. (XLS 239 kb)
DOI: 10.6084/m9.figshare.8024534.v1
title: Additional file 1: of Myostatin gene promoter: structure, conservation and importance as a target for muscle modulation

description: Table S1. Summarized information on the different MSTN promoters analysed in this review. Information includes accession numbers, number of E-boxes and presence (x) or absence of TFBS in each species. TFBS or sequences identified independently by our group are indicated by a red asterisk (*) [119]. (XLS 239 kb)
DOI: 10.6084/m9.figshare.8024096
title: SNAPP files for Eudyptes penguins

description: Files used (.xml and .txt) and output files (.log and .trees) for the SNAPP analyses.<br>Macaroni indicates the file is for <i>Eudyptes chrysolophus chrysolophus</i> and <i>Eudyptes chrysolophus schlegeli</i>, Rockhopper indicates the file is for <i>Eudyptes moseleyi</i>, <i>Eudyptes chrysocome</i> and <i>Eudyptes filholi</i> and Tawaki indicates that the file is for <i>Eudyptes pachyrhynchus</i> and <i>Eudyptes robustus</i>.
DOI: 10.6084/m9.figshare.8024081
title: CCDB_4097.jpg

description: Computed slice through a tomographic volume of isolated mitochondria from mouse liver after treatment with the BH3 peptide domain from Bid.
DOI: 10.6084/m9.figshare.8024084
title: CCDB_4098.jpg

description: Computed slice through an electron tomographic volume of mitochondria isolated from mouse liver and treated with both the protease inhibitor MG132 and BH3 peptide from Bid.
DOI: 10.6084/m9.figshare.8024084.v1
title: CCDB_4098.jpg

description: Computed slice through an electron tomographic volume of mitochondria isolated from mouse liver and treated with both the protease inhibitor MG132 and BH3 peptide from Bid.
DOI: 10.6084/m9.figshare.8024096.v1
title: SNAPP files for Eudyptes penguins

description: Files used (.xml and .txt) and output files (.log and .trees) for the SNAPP analyses.<br>Macaroni indicates the file is for <i>Eudyptes chrysolophus chrysolophus</i> and <i>Eudyptes chrysolophus schlegeli</i>, Rockhopper indicates the file is for <i>Eudyptes moseleyi</i>, <i>Eudyptes chrysocome</i> and <i>Eudyptes filholi</i> and Tawaki indicates that the file is for <i>Eudyptes pachyrhynchus</i> and <i>Eudyptes robustus</i>.
DOI: 10.6084/m9.figshare.8024081.v1
title: CCDB_4097.jpg

description: Computed slice through a tomographic volume of isolated mitochondria from mouse liver after treatment with the BH3 peptide domain from Bid.
DOI: 10.6084/m9.figshare.8024060
title: CCDB_4096.jpg

description: Computed slice through an electron tomographic volume of mitochondriaisolated from mouse liver and treated with the serine protease inhibitor MG132.
DOI: 10.6084/m9.figshare.8023991
title: Dataset for: The comparative biogeography of Philippine geckos challenges predictions from a paradigm of climate-driven vicariant diversification across an island archipelago

description: A primary goal of biogeography is to understand how large-scale environmental processes, like climate change, affect diversification. One often-invoked but seldom tested process is the so-called ''species-pump'' model, in which repeated bouts of co-speciation is driven by oscillating climate-induced habitat connectivity cycles. For example, over the past three million years, the landscape of the Philippine Islands has repeatedly coalesced and fragmented due to sea-level changes associated with the glacial cycles. This repeated climate-driven vicariance has been proposed as a model of speciation across evolutionary lineages codistributed throughout the islands. This model predicts speciation times that are temporally clustered around the times when interglacial rises in sea level fragmented the islands. Given the significance and conceptual impact the model has shown, surprisingly few tests of this prediction have been provided. We collected comparative genomic data from 16 pairs of insular gecko populations to test the prediction of temporally clustered divergences. Specifically, we analyze these data in a full-likelihood, Bayesian model-choice framework to test for shared divergence times among the pairs. Our results provide support against the species-pump model prediction in favor of an alternative interpretation, namely that each pair of gecko populations diverged independently. These results suggest the repeated bouts of climate-driven landscape fragmentation has not been an important mechanism of speciation for gekkonid lizards on the Philippine Islands. Interpretations of shared mechanisms of diversification historically have been pervasive in biogeography, often advanced on the basis of taxonomy-based depictions of species distributions. Our results call for possible re-evaluation of other, classic co-diversification studies in a variety of geographic systems.
DOI: 10.6084/m9.figshare.8024060.v1
title: CCDB_4096.jpg

description: Computed slice through an electron tomographic volume of mitochondriaisolated from mouse liver and treated with the serine protease inhibitor MG132.
DOI: 10.6084/m9.figshare.8023991.v1
title: Dataset for: The comparative biogeography of Philippine geckos challenges predictions from a paradigm of climate-driven vicariant diversification across an island archipelago

description: A primary goal of biogeography is to understand how large-scale environmental processes, like climate change, affect diversification. One often-invoked but seldom tested process is the so-called ''species-pump'' model, in which repeated bouts of co-speciation is driven by oscillating climate-induced habitat connectivity cycles. For example, over the past three million years, the landscape of the Philippine Islands has repeatedly coalesced and fragmented due to sea-level changes associated with the glacial cycles. This repeated climate-driven vicariance has been proposed as a model of speciation across evolutionary lineages codistributed throughout the islands. This model predicts speciation times that are temporally clustered around the times when interglacial rises in sea level fragmented the islands. Given the significance and conceptual impact the model has shown, surprisingly few tests of this prediction have been provided. We collected comparative genomic data from 16 pairs of insular gecko populations to test the prediction of temporally clustered divergences. Specifically, we analyze these data in a full-likelihood, Bayesian model-choice framework to test for shared divergence times among the pairs. Our results provide support against the species-pump model prediction in favor of an alternative interpretation, namely that each pair of gecko populations diverged independently. These results suggest the repeated bouts of climate-driven landscape fragmentation has not been an important mechanism of speciation for gekkonid lizards on the Philippine Islands. Interpretations of shared mechanisms of diversification historically have been pervasive in biogeography, often advanced on the basis of taxonomy-based depictions of species distributions. Our results call for possible re-evaluation of other, classic co-diversification studies in a variety of geographic systems.
DOI: 10.6084/m9.figshare.8023820
title: CCDB_4074.jpg

description: Triple labeled confocal image of the dentate gyrus of a transgenic mouse engineered to overexpress alpha synuclein under the Thy-1 promotor, immunolabeled for mGluR5 (red), alpha synuclein (green) and counterstained with DAPI (blue) to reveal cell nuclei. A second image through cerebellar cortex may be viewed by downloading the 2D Image zip file associated with this record.
DOI: 10.6084/m9.figshare.8023823
title: CCDB_4075.jpg

description: Triple labeled confocal image of the neostriatum of a transgenic mouse engineered to overexpress alpha synuclein under the Thy-1 promotor, immunolabeled for mGluR5 (red), alpha synuclein (green) and counterstained with DAPI (blue) to reveal cell nuclei.
DOI: 10.6084/m9.figshare.8023814
title: CCDB_4073.jpg

description: Triple labeled confocal image of the cerebral cortex of a transgenic mouse engineered to overexpress alpha synuclein under the Thy-1 promotor, immunolabeled for mGluR5 (red), alpha synuclein (green) and counterstained with DAPI (blue) to reveal cell nuclei.
DOI: 10.6084/m9.figshare.8023820.v1
title: CCDB_4074.jpg

description: Triple labeled confocal image of the dentate gyrus of a transgenic mouse engineered to overexpress alpha synuclein under the Thy-1 promotor, immunolabeled for mGluR5 (red), alpha synuclein (green) and counterstained with DAPI (blue) to reveal cell nuclei. A second image through cerebellar cortex may be viewed by downloading the 2D Image zip file associated with this record.
DOI: 10.6084/m9.figshare.8023823.v1
title: CCDB_4075.jpg

description: Triple labeled confocal image of the neostriatum of a transgenic mouse engineered to overexpress alpha synuclein under the Thy-1 promotor, immunolabeled for mGluR5 (red), alpha synuclein (green) and counterstained with DAPI (blue) to reveal cell nuclei.
DOI: 10.6084/m9.figshare.8023811
title: CCDB_4072.jpg

description: Triple labeled confocal image of hippocampal area CA3 of a transgenic mouse engineered to overexpress alpha synuclein under the Thy-1 promotor, immunolabeled for mGluR5 (red), alpha synuclein (green) and counterstained with DAPI (blue) to reveal cell nuclei.
DOI: 10.6084/m9.figshare.8023814.v1
title: CCDB_4073.jpg

description: Triple labeled confocal image of the cerebral cortex of a transgenic mouse engineered to overexpress alpha synuclein under the Thy-1 promotor, immunolabeled for mGluR5 (red), alpha synuclein (green) and counterstained with DAPI (blue) to reveal cell nuclei.
DOI: 10.6084/m9.figshare.8023802
title: CCDB_4070.jpg

description: Triple labeled confocal image of the dentate gyrus of a transgenic mouse engineered to overexpress alpha synuclein under the Thy-1 promotor, immunolabeled for mGluR5 (red), alpha synuclein (green) and counterstained with DAPI (blue) to reveal cell nuclei.
DOI: 10.6084/m9.figshare.8023805
title: CCDB_4071.jpg

description: Triple labeled confocal image of hippocampal area CA1 of a transgenic mouse engineered to overexpress alpha synuclein under the Thy-1 promotor, immunolabeled for mGluR5 (red), alpha synuclein (green) and counterstained with DAPI (blue) to reveal cell nuclei.
DOI: 10.6084/m9.figshare.8023790
title: CCDB_4069.jpg

description: Triple labeled confocal image of the neostriatum of a transgenic mouse engineered to overexpress alpha synuclein under the Thy-1 promotor, immunolabeled for mGluR5 (red), alpha synuclein (green) and counterstained with DAPI (blue) to reveal cell nuclei.
DOI: 10.6084/m9.figshare.8023802.v1
title: CCDB_4070.jpg

description: Triple labeled confocal image of the dentate gyrus of a transgenic mouse engineered to overexpress alpha synuclein under the Thy-1 promotor, immunolabeled for mGluR5 (red), alpha synuclein (green) and counterstained with DAPI (blue) to reveal cell nuclei.
DOI: 10.6084/m9.figshare.8023811.v1
title: CCDB_4072.jpg

description: Triple labeled confocal image of hippocampal area CA3 of a transgenic mouse engineered to overexpress alpha synuclein under the Thy-1 promotor, immunolabeled for mGluR5 (red), alpha synuclein (green) and counterstained with DAPI (blue) to reveal cell nuclei.
DOI: 10.6084/m9.figshare.8023784
title: 2019 Wikimedia Commons Digital Cultural Media Analysis

description: March-April 2019 data collection of digital cultural heritage media found on Wikimedia Commons and then searched in Google Images for reuse on the internet
DOI: 10.6084/m9.figshare.8023805.v1
title: CCDB_4071.jpg

description: Triple labeled confocal image of hippocampal area CA1 of a transgenic mouse engineered to overexpress alpha synuclein under the Thy-1 promotor, immunolabeled for mGluR5 (red), alpha synuclein (green) and counterstained with DAPI (blue) to reveal cell nuclei.
DOI: 10.6084/m9.figshare.8023781
title: CCDB_4068.jpg

description: Triple labeled confocal image of the cerebellar cortex of a transgenic mouse engineered to overexpress alpha synuclein under the Thy-1 promotor, immunolabeled for mGluR5 (red), alpha synuclein (green) and counterstained with DAPI (blue) to reveal cell nuclei.
DOI: 10.6084/m9.figshare.8023790.v1
title: CCDB_4069.jpg

description: Triple labeled confocal image of the neostriatum of a transgenic mouse engineered to overexpress alpha synuclein under the Thy-1 promotor, immunolabeled for mGluR5 (red), alpha synuclein (green) and counterstained with DAPI (blue) to reveal cell nuclei.
DOI: 10.6084/m9.figshare.8023775
title: CCDB_4066.jpg

description: Triple labeled confocal image of hippocampal area CA3 of a transgenic mouse engineered to overexpress alpha synuclein under the Thy-1 promotor, immunolabeled for mGluR5 (red), alpha synuclein (green) and counterstained with DAPI (blue) to reveal cell nuclei.
DOI: 10.6084/m9.figshare.8023778
title: CCDB_4067.jpg

description: Triple labeled confocal image of the cerebral cortex of a transgenic mouse engineered to overexpress alpha synuclein under the Thy-1 promotor, immunolabeled for mGluR5 (red), alpha synuclein (green) and counterstained with DAPI (blue) to reveal cell nuclei. An image of a no primary control is available for download; some light non-specific labeling was visible in the red and green channels.
DOI: 10.6084/m9.figshare.8023778.v1
title: CCDB_4067.jpg

description: Triple labeled confocal image of the cerebral cortex of a transgenic mouse engineered to overexpress alpha synuclein under the Thy-1 promotor, immunolabeled for mGluR5 (red), alpha synuclein (green) and counterstained with DAPI (blue) to reveal cell nuclei. An image of a no primary control is available for download; some light non-specific labeling was visible in the red and green channels.
DOI: 10.6084/m9.figshare.8023781.v1
title: CCDB_4068.jpg

description: Triple labeled confocal image of the cerebellar cortex of a transgenic mouse engineered to overexpress alpha synuclein under the Thy-1 promotor, immunolabeled for mGluR5 (red), alpha synuclein (green) and counterstained with DAPI (blue) to reveal cell nuclei.
DOI: 10.6084/m9.figshare.8023766
title: CCDB_4064.jpg

description: Triple labeled confocal image of the dentate gyrus of a transgenic mouse engineered to overexpress alpha synuclein under the Thy-1 promotor, immunolabeled for mGluR5 (red), alpha synuclein (green) and counterstained with DAPI (blue) to reveal cell nuclei.
DOI: 10.6084/m9.figshare.8023769
title: CCDB_4065.jpg

description: Triple labeled confocal image of hippocampal area CA1 of a transgenic mouse engineered to overexpress alpha synuclein under the Thy-1 promotor, immunolabeled for mGluR5 (red), alpha synuclein (green) and counterstained with DAPI (blue) to reveal cell nuclei.
DOI: 10.6084/m9.figshare.8023775.v1
title: CCDB_4066.jpg

description: Triple labeled confocal image of hippocampal area CA3 of a transgenic mouse engineered to overexpress alpha synuclein under the Thy-1 promotor, immunolabeled for mGluR5 (red), alpha synuclein (green) and counterstained with DAPI (blue) to reveal cell nuclei.
DOI: 10.6084/m9.figshare.8023763
title: CCDB_4063.jpg

description: Triple labeled confocal image of the neostriatum of a transgenic mouse engineered to overexpress alpha synuclein under the Thy-1 promotor, immunolabeled for mGluR5 (red), alpha synuclein (green) and counterstained with DAPI (blue) to reveal nuclei.
DOI: 10.6084/m9.figshare.8023766.v1
title: CCDB_4064.jpg

description: Triple labeled confocal image of the dentate gyrus of a transgenic mouse engineered to overexpress alpha synuclein under the Thy-1 promotor, immunolabeled for mGluR5 (red), alpha synuclein (green) and counterstained with DAPI (blue) to reveal cell nuclei.
DOI: 10.6084/m9.figshare.8023760
title: CCDB_4062.jpg

description: Triple labeled confocal image of the cerebellar cortex of a transgenic mouse engineered to overexpress alpha synuclein under the Thy-1 promotor, immunolabeled for mGluR5 (red), alpha synuclein (green) and counterstained with DAPI (blue) to reveal cell nuclei.
DOI: 10.6084/m9.figshare.8023769.v1
title: CCDB_4065.jpg

description: Triple labeled confocal image of hippocampal area CA1 of a transgenic mouse engineered to overexpress alpha synuclein under the Thy-1 promotor, immunolabeled for mGluR5 (red), alpha synuclein (green) and counterstained with DAPI (blue) to reveal cell nuclei.