cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1319614.v2
title: De-regulated expression of the BRG1 chromatin remodeling factor in bone marrow mesenchymal stromal cells induces senescence associated with the silencing of NANOG and changes in the levels of chromatin proteins

description: Stem cells have a peculiar chromatin architecture that contributes to their unique properties, including uncommitted status, multi/pluripotency and self-renewal. We analyzed the effect of the de-regulation of the SWI/SNF chromatin remodeling complex in mesenchymal stromal cells (MSC) through the silencing and up-regulation of BRG1, which is the ATPase subunit of the complex. The altered expression of BRG1 promoted the senescence of MSC with suppression of the NANOG transcription, which is part of the transcriptional circuitry governing stem cell functions. To gain insight on the way NANOG was silenced, we evaluated how the de-regulated BRG1 expression affect the binding of activators and repressors on the NANOG promoter. We found 4 E2F binding motifs on NANOG promoter, which can be occupied by RB1 and RB2/P130. These are members of the retinoblastoma gene family. In MSC with a silenced BRG1, the relative binding of the 2 retinoblastoma proteins increased, and this was associated with the recruitment of DNMT1. This induced the methylation of CpG on the NANOG promoter. Opposingly, when a high level of BRG1 was present, the same E2F binding motifs were docking sites for BRG1, which induced chromatin compaction without CpG methylation but with increased histone deacetylation, associated with the presence of HDAC1 on E2F binding sites. Besides the sharp regulation of the NANOG expression, we evidenced, through proteomic analysis, that the de-regulation of the SWI/SNF function affected the expression of histones and other nuclear proteins involved in “nuclear architecture,” suggesting that BRG1 may act as global regulator of gene expression.
DOI: 10.6084/m9.figshare.1319583.v1
title: Gaussian Job Archive for BrH9O4

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1319565
title: Gaussian Job Archive for FH7O3

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1319565.v1
title: Gaussian Job Archive for FH7O3

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1319614.v3
title: De-regulated expression of the BRG1 chromatin remodeling factor in bone marrow mesenchymal stromal cells induces senescence associated with the silencing of NANOG and changes in the levels of chromatin proteins

description: Stem cells have a peculiar chromatin architecture that contributes to their unique properties, including uncommitted status, multi/pluripotency and self-renewal. We analyzed the effect of the de-regulation of the SWI/SNF chromatin remodeling complex in mesenchymal stromal cells (MSC) through the silencing and up-regulation of BRG1, which is the ATPase subunit of the complex. The altered expression of BRG1 promoted the senescence of MSC with suppression of the NANOG transcription, which is part of the transcriptional circuitry governing stem cell functions. To gain insight on the way NANOG was silenced, we evaluated how the de-regulated BRG1 expression affect the binding of activators and repressors on the NANOG promoter. We found 4 E2F binding motifs on NANOG promoter, which can be occupied by RB1 and RB2/P130. These are members of the retinoblastoma gene family. In MSC with a silenced BRG1, the relative binding of the 2 retinoblastoma proteins increased, and this was associated with the recruitment of DNMT1. This induced the methylation of CpG on the NANOG promoter. Opposingly, when a high level of BRG1 was present, the same E2F binding motifs were docking sites for BRG1, which induced chromatin compaction without CpG methylation but with increased histone deacetylation, associated with the presence of HDAC1 on E2F binding sites. Besides the sharp regulation of the NANOG expression, we evidenced, through proteomic analysis, that the de-regulation of the SWI/SNF function affected the expression of histones and other nuclear proteins involved in “nuclear architecture,” suggesting that BRG1 may act as global regulator of gene expression.
DOI: 10.6084/m9.figshare.1319550
title: Gaussian Job Archive for BrH5O2

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1319582.v1
title: Biogeography of Termites in Brazilian Amazonia

description: Fucnctions and datasets used in manuscript about termite biogeography in Amazonia
DOI: 10.6084/m9.figshare.1319551
title: Gaussian Job Archive for BrH7O3

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1319548
title: Gaussian Job Archive for FH3O

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1319549
title: Gaussian Job Archive for FH5O2

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1319614.v4
title: De-regulated expression of the BRG1 chromatin remodeling factor in bone marrow mesenchymal stromal cells induces senescence associated with the silencing of NANOG and changes in the levels of chromatin proteins

description: Stem cells have a peculiar chromatin architecture that contributes to their unique properties, including uncommitted status, multi/pluripotency and self-renewal. We analyzed the effect of the de-regulation of the SWI/SNF chromatin remodeling complex in mesenchymal stromal cells (MSC) through the silencing and up-regulation of BRG1, which is the ATPase subunit of the complex. The altered expression of BRG1 promoted the senescence of MSC with suppression of the NANOG transcription, which is part of the transcriptional circuitry governing stem cell functions. To gain insight on the way NANOG was silenced, we evaluated how the de-regulated BRG1 expression affect the binding of activators and repressors on the NANOG promoter. We found 4 E2F binding motifs on NANOG promoter, which can be occupied by RB1 and RB2/P130. These are members of the retinoblastoma gene family. In MSC with a silenced BRG1, the relative binding of the 2 retinoblastoma proteins increased, and this was associated with the recruitment of DNMT1. This induced the methylation of CpG on the NANOG promoter. Opposingly, when a high level of BRG1 was present, the same E2F binding motifs were docking sites for BRG1, which induced chromatin compaction without CpG methylation but with increased histone deacetylation, associated with the presence of HDAC1 on E2F binding sites. Besides the sharp regulation of the NANOG expression, we evidenced, through proteomic analysis, that the de-regulation of the SWI/SNF function affected the expression of histones and other nuclear proteins involved in “nuclear architecture,” suggesting that BRG1 may act as global regulator of gene expression.
DOI: 10.6084/m9.figshare.1319549.v1
title: Gaussian Job Archive for FH5O2

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1319551.v1
title: Gaussian Job Archive for BrH7O3

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1319548.v1
title: Gaussian Job Archive for FH3O

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1319582.v2
title: Biogeography of Termites in Brazilian Amazonia

description: Fucnctions and datasets used in manuscript about termite biogeography in Amazonia
DOI: 10.6084/m9.figshare.1319614.v6
title: De-regulated expression of the BRG1 chromatin remodeling factor in bone marrow mesenchymal stromal cells induces senescence associated with the silencing of NANOG and changes in the levels of chromatin proteins

description: Stem cells have a peculiar chromatin architecture that contributes to their unique properties, including uncommitted status, multi/pluripotency and self-renewal. We analyzed the effect of the de-regulation of the SWI/SNF chromatin remodeling complex in mesenchymal stromal cells (MSC) through the silencing and up-regulation of BRG1, which is the ATPase subunit of the complex. The altered expression of BRG1 promoted the senescence of MSC with suppression of the NANOG transcription, which is part of the transcriptional circuitry governing stem cell functions. To gain insight on the way NANOG was silenced, we evaluated how the de-regulated BRG1 expression affect the binding of activators and repressors on the NANOG promoter. We found 4 E2F binding motifs on NANOG promoter, which can be occupied by RB1 and RB2/P130. These are members of the retinoblastoma gene family. In MSC with a silenced BRG1, the relative binding of the 2 retinoblastoma proteins increased, and this was associated with the recruitment of DNMT1. This induced the methylation of CpG on the NANOG promoter. Opposingly, when a high level of BRG1 was present, the same E2F binding motifs were docking sites for BRG1, which induced chromatin compaction without CpG methylation but with increased histone deacetylation, associated with the presence of HDAC1 on E2F binding sites. Besides the sharp regulation of the NANOG expression, we evidenced, through proteomic analysis, that the de-regulation of the SWI/SNF function affected the expression of histones and other nuclear proteins involved in “nuclear architecture,” suggesting that BRG1 may act as global regulator of gene expression.
DOI: 10.6084/m9.figshare.1319614.v5
title: De-regulated expression of the BRG1 chromatin remodeling factor in bone marrow mesenchymal stromal cells induces senescence associated with the silencing of NANOG and changes in the levels of chromatin proteins

description: Stem cells have a peculiar chromatin architecture that contributes to their unique properties, including uncommitted status, multi/pluripotency and self-renewal. We analyzed the effect of the de-regulation of the SWI/SNF chromatin remodeling complex in mesenchymal stromal cells (MSC) through the silencing and up-regulation of BRG1, which is the ATPase subunit of the complex. The altered expression of BRG1 promoted the senescence of MSC with suppression of the NANOG transcription, which is part of the transcriptional circuitry governing stem cell functions. To gain insight on the way NANOG was silenced, we evaluated how the de-regulated BRG1 expression affect the binding of activators and repressors on the NANOG promoter. We found 4 E2F binding motifs on NANOG promoter, which can be occupied by RB1 and RB2/P130. These are members of the retinoblastoma gene family. In MSC with a silenced BRG1, the relative binding of the 2 retinoblastoma proteins increased, and this was associated with the recruitment of DNMT1. This induced the methylation of CpG on the NANOG promoter. Opposingly, when a high level of BRG1 was present, the same E2F binding motifs were docking sites for BRG1, which induced chromatin compaction without CpG methylation but with increased histone deacetylation, associated with the presence of HDAC1 on E2F binding sites. Besides the sharp regulation of the NANOG expression, we evidenced, through proteomic analysis, that the de-regulation of the SWI/SNF function affected the expression of histones and other nuclear proteins involved in “nuclear architecture,” suggesting that BRG1 may act as global regulator of gene expression.
DOI: 10.6084/m9.figshare.1319544
title: Gaussian Job Archive for BrH3O

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1319544.v1
title: Gaussian Job Archive for BrH3O

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1319582.v3
title: Biogeography of Termites in Brazilian Amazonia

description: Fucnctions and datasets used in manuscript about termite biogeography in Amazonia
DOI: 10.6084/m9.figshare.1319506
title: Scientific Data Management (1.8) Pitch - Sandpit1

description: Scientific Data Management (1.8) Pitch - Sandpit1
DOI: 10.6084/m9.figshare.1319582.v4
title: Data associated with the study entitled "Biogeography of Termites in Brazilian Amazonia"

description: Fucnctions and datasets used in manuscript about termite biogeography in Amazonia
DOI: 10.6084/m9.figshare.1319582.v5
title: Data associated with the study entitled "Biogeography of Termites in Brazilian Amazonia"

description: Fucnctions and datasets used in manuscript about termite biogeography in Amazonia
DOI: 10.6084/m9.figshare.1319506.v1
title: Scientific Data Management (1.8) Pitch - Sandpit1

description: Scientific Data Management (1.8) Pitch - Sandpit1
DOI: 10.6084/m9.figshare.1319503
title: JISC Research Data Spring Project 3.8 (AMASED)

description: Summary, project plan and costings for project 3.8 of Jisc Research Data Spring. AMASED: Access Methods for Analysing SEnsitive Data.
DOI: 10.6084/m9.figshare.1319505
title: Project Plan DRAFT 1 - after sandpit1

description: Project Plan DRAFT 1 - after sandpit1
DOI: 10.6084/m9.figshare.1319500
title: Developing cost-effective field assessments of carbon-stocks in human-modified tropical forests

description: Dataset used to develop cost-effective guidance on how to conduct cost-effective field carbon assessmens in tropical forests.
DOI: 10.6084/m9.figshare.1319505.v1
title: Project Plan DRAFT 1 - after sandpit1

description: Project Plan DRAFT 1 - after sandpit1
DOI: 10.6084/m9.figshare.1319582.v6
title: Data associated with the study entitled "Biogeography of Termites in Brazilian Amazonia"

description: Fucnctions and datasets used in manuscript about termite biogeography in Amazonia
DOI: 10.6084/m9.figshare.1319500.v1
title: Developing cost-effective field assessments of carbon-stocks in human-modified tropical forests

description: Dataset used to develop cost-effective guidance on how to conduct cost-effective field carbon assessmens in tropical forests.
DOI: 10.6084/m9.figshare.1319484
title: Detrital zircon ages of Cambrian and Devonian sandstones from Estonia, central Baltica: a possible link to Avalonia during the Late Neoproterozoic

description: Detrital zircon U–Pb ages of Lower Cambrian and Middle Devonian have been determined for sandstone in Estonia through LA-ICP-MS (Nu instruments, Wrexham, UK). Both sandstones have a similar zircon age spectrum with distinct age clusters that reflect the basement geology of Baltica, i.e. 2800–2700 Ma (Kola–Karelia), 1900–1700 Ma (Svecofennian), 1600–1500 Ma (Rapakivi) and 1200–1000 Ma (Sveconorwegian). Noteworthy is a cluster at 750–550 Ma, because rocks of such age are absent within the core of Baltica. The present results suggest a possible link between Baltica and Avalonia/Cadomia during the Late Neoproterozoic.
DOI: 10.6084/m9.figshare.1319484.v1
title: Detrital zircon ages of Cambrian and Devonian sandstones from Estonia, central Baltica: a possible link to Avalonia during the Late Neoproterozoic

description: Detrital zircon U–Pb ages of Lower Cambrian and Middle Devonian have been determined for sandstone in Estonia through LA-ICP-MS (Nu instruments, Wrexham, UK). Both sandstones have a similar zircon age spectrum with distinct age clusters that reflect the basement geology of Baltica, i.e. 2800–2700 Ma (Kola–Karelia), 1900–1700 Ma (Svecofennian), 1600–1500 Ma (Rapakivi) and 1200–1000 Ma (Sveconorwegian). Noteworthy is a cluster at 750–550 Ma, because rocks of such age are absent within the core of Baltica. The present results suggest a possible link between Baltica and Avalonia/Cadomia during the Late Neoproterozoic.
DOI: 10.6084/m9.figshare.1319582.v7
title: Data associated with the study entitled "Biogeography of Termites in Brazilian Amazonia"

description: Fucnctions and datasets used in manuscript about termite biogeography in Amazonia
DOI: 10.6084/m9.figshare.1319503.v2
title: JISC Research Data Spring Project 3.8

description: Summary, project plan and costings for project 3.8 of Jisc Research Data Spring.
DOI: 10.6084/m9.figshare.1319479
title: Centra Germany Dataset Metadata

description: Metadata describing the Centra Germany dataset shapefile
DOI: 10.6084/m9.figshare.1319503.v4
title: JISC Research Data Spring Project 3.8 (AMASED)

description: Summary, project plan and costings for project 3.8 of Jisc Research Data Spring. AMASED: Access Methods for Analysing SEnsitive Data.
DOI: 10.6084/m9.figshare.1319582.v8
title: Data associated with the study entitled "Biogeography of Termites in Brazilian Amazonia"

description: Fucnctions and datasets used in manuscript about termite biogeography in Amazonia
DOI: 10.6084/m9.figshare.1319503.v3
title: JISC Research Data Spring Project 3.8

description: Summary, project plan and costings for project 3.8 of Jisc Research Data Spring.
DOI: 10.6084/m9.figshare.1319582.v10
title: Data associated with the study entitled "Isolation by distance, not rivers, control the distribution of termite species in the Amazonian rain forest"

description: Fucnctions and datasets used in manuscript about termite biogeography in Amazonia
DOI: 10.6084/m9.figshare.1319582.v9
title: Data associated with the study entitled "Biogeography of Termites in Brazilian Amazonia"

description: Fucnctions and datasets used in manuscript about termite biogeography in Amazonia
DOI: 10.6084/m9.figshare.1319443
title: Scoring sheet for judges at research data spring

description: These are the rough scoring criteria for the judges at research data spring sandpit 1.
DOI: 10.6084/m9.figshare.1319470.v3
title: Best RDM practice is standard

description: Project Pitch
DOI: 10.6084/m9.figshare.1319443.v2
title: Scoring sheet for judges at research data spring

description: These are the rough scoring criteria for the judges at research data spring sandpit 1.
DOI: 10.6084/m9.figshare.1319441
title: Time-lapse videos of groundwater seepage, pressurized groundwater outbursts and crater-lake overflow in flume experiments

description: Time-lapse videos of flume experiments on groundwater seepage, pressurized groundwater outflow and crater-lake overflow. Goal of this work is to understand erosion processes from different sources of water on ancient Mars. Full description of the experiment is published in: Marra, W.A., L. Braat, A.W. Baar & M.G. Kleinhans, <em></em>2014<em>, </em><em>Valley formation by groundwater seepage, pressurized groundwater outbursts and crater-lake overflow in flume experiments with implications for Mars</em>, Icarus 232, p 97-117, <strong>doi:10.1016/j.icarus.2013.12.026.</strong> Which is part of: Marra, W.A. Martian groundwater outflow processes and morphology, reconstruction of paleohydrology using landscape evolution experiments, 2015, PhD Thesis, Universiteit Utrecht, The Netherlands.
DOI: 10.6084/m9.figshare.1319470.v4
title: Best RDM practice is standard

description: Project Pitch
DOI: 10.6084/m9.figshare.1319441.v1
title: Time-lapse videos of groundwater seepage, pressurized groundwater outbursts and crater-lake overflow in flume experiments

description: Time-lapse videos of flume experiments on groundwater seepage, pressurized groundwater outflow and crater-lake overflow. Goal of this work is to understand erosion processes from different sources of water on ancient Mars. Full description of the experiment is published in: Marra, W.A., L. Braat, A.W. Baar & M.G. Kleinhans, <em></em>2014<em>, </em><em>Valley formation by groundwater seepage, pressurized groundwater outbursts and crater-lake overflow in flume experiments with implications for Mars</em>, Icarus 232, p 97-117, <strong>doi:10.1016/j.icarus.2013.12.026.</strong> Which is part of: Marra, W.A. Martian groundwater outflow processes and morphology, reconstruction of paleohydrology using landscape evolution experiments, 2015, PhD Thesis, Universiteit Utrecht, The Netherlands.
DOI: 10.6084/m9.figshare.1319443.v1
title: Scoring sheet for judges at research data spring

description: These are the rough scoring criteria for the judges at research data spring sandpit 1.
DOI: 10.6084/m9.figshare.1319413
title: Reactivity of sorbose dehydrogenase from <i>Sinorhizobium</i> sp. 97507 for 1,5-anhydro-d-glucitol

description: Purified recombinant sorbose dehydrogenase from <i>Sinorhizobium</i> sp. 97507 exhibited high reactivity for 1,5-anhydro-d-glucitol (1,5-AG) and l-sorbose, but little activity for the other sugars or sugar alcohols tested. Kinetic analysis revealed that its catalytic efficiency (<i>k</i><sub>cat</sub><i>/K</i><sub>m</sub>) for l-sorbose and 1,5-AG is 1.8 × 10<sup>2</sup> and 1.5 × 10<sup>2</sup> s<sup>−1</sup>·M<sup>−1</sup>, respectively.
DOI: 10.6084/m9.figshare.1319413.v1
title: Reactivity of sorbose dehydrogenase from <i>Sinorhizobium</i> sp. 97507 for 1,5-anhydro-d-glucitol

description: Purified recombinant sorbose dehydrogenase from <i>Sinorhizobium</i> sp. 97507 exhibited high reactivity for 1,5-anhydro-d-glucitol (1,5-AG) and l-sorbose, but little activity for the other sugars or sugar alcohols tested. Kinetic analysis revealed that its catalytic efficiency (<i>K</i><sub>cat</sub><i>/K</i><sub>m</sub>) for l-sorbose and 1,5-AG is 1.8 × 10<sup>2</sup> and 1.5 × 10<sup>2</sup> s<sup>−1</sup>·M<sup>−1</sup>, respectively.
DOI: 10.6084/m9.figshare.1319413.v3
title: Reactivity of sorbose dehydrogenase from <i>Sinorhizobium</i> sp. 97507 for 1,5-anhydro-d-glucitol

description: Purified recombinant sorbose dehydrogenase from <i>Sinorhizobium</i> sp. 97507 exhibited high reactivity for 1,5-anhydro-d-glucitol (1,5-AG) and l-sorbose, but little activity for the other sugars or sugar alcohols tested. Kinetic analysis revealed that its catalytic efficiency (<i>k</i><sub>cat</sub><i>/K</i><sub>m</sub>) for l-sorbose and 1,5-AG is 1.8 × 10<sup>2</sup> and 1.5 × 10<sup>2</sup> s<sup>−1</sup>·M<sup>−1</sup>, respectively.
DOI: 10.6084/m9.figshare.1319413.v2
title: Reactivity of sorbose dehydrogenase from <i>Sinorhizobium</i> sp. 97507 for 1,5-anhydro-d-glucitol

description: Purified recombinant sorbose dehydrogenase from <i>Sinorhizobium</i> sp. 97507 exhibited high reactivity for 1,5-anhydro-d-glucitol (1,5-AG) and l-sorbose, but little activity for the other sugars or sugar alcohols tested. Kinetic analysis revealed that its catalytic efficiency (<i>k</i><sub>cat</sub><i>/K</i><sub>m</sub>) for l-sorbose and 1,5-AG is 1.8 × 10<sup>2</sup> and 1.5 × 10<sup>2</sup> s<sup>−1</sup>·M<sup>−1</sup>, respectively.