cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8298875
title: EZH2 upregulates the PI3K/AKT pathway through IGF1R and MYC in clinically aggressive chronic lymphocytic leukaemia

description: EZH2 is overexpressed in poor-prognostic chronic lymphocytic leukaemia (CLL) cases, acting as an oncogene; however, thus far, the EZH2 target genes in CLL have not been disclosed. In this study, using ChIP-sequencing, we identified EZH2 and H3K27me3 target genes in two prognostic subgroups of CLL with distinct prognosis and outcome, i.e., cases with unmutated (U-CLL, n = 6) or mutated IGHV genes (M-CLL, n = 6). While the majority of oncogenic pathways were equally enriched for EZH2 target genes in both prognostic subgroups, PI3K pathway genes were differentially bound by EZH2 in U-CLL versus M-CLL. The occupancy of EZH2 for selected PI3K pathway target genes was validated in additional CLL samples (n = 16) and CLL cell lines using siRNA-mediated EZH2 downregulation and ChIP assays. Intriguingly, we found that EZH2 directly binds to the <i>IGF1R</i> promoter along with MYC and upregulates IGF1R expression in U-CLL, leading to downstream PI3K activation. By investigating an independent CLL cohort (n = 96), a positive correlation was observed between <i>EZH2</i> and <i>IGF1R</i> expression with higher levels in U-CLL compared to M-CLL. Accordingly, siRNA-mediated downregulation of either <i>EZH2, MYC</i> or <i>IGF1R</i> and treatment with EZH2 and MYC pharmacological inhibitors in the HG3 CLL cell line induced a significant reduction in PI3K pathway activation. In conclusion, we characterize for the first time EZH2 target genes in CLL revealing a hitherto unknown implication of EZH2 in modulating the PI3K pathway in a non-canonical, PRC2-independent way, with potential therapeutic implications considering that PI3K inhibitors are effective therapeutic agents for CLL.
DOI: 10.6084/m9.figshare.8298872
title: The histone lysine demethylase <i>KDM7A</i> is required for normal development and first cell lineage specification in porcine embryos

description: There is growing evidence that histone lysine demethylases (KDMs) play critical roles in the regulation of embryo development. This study investigated if KDM7A, a lysine demethylase known to act on mono-(me1) and di-(me2) methylation of H3K9 and H3K27, participates in the regulation of early embryo development. Knockdown of <i>KDM7A</i> mRNA reduced blastocyst formation by 69.2% in <i>in vitro</i> fertilized (IVF), 48.4% in parthenogenetically activated (PA), and 48.1% in somatic cell nuclear transfer (SCNT) embryos compared to controls. Global immunofluorescence (IF) signal in <i>KDM7A</i> knockdown compared to control embryos was increased for H3K27me1 on D7, for H3K27me2 on D3 and D5, for H3K9me1 on D5 and D7, and for H3K9me2 on D5 embryos, but decreased for H3K9me1, me2 and me3 on D3. Moreover, <i>KDM7A</i> knockdown altered mRNA expression, including the downregulation of <i>KDM3C</i> on D3, <i>NANOG</i> on D5 and D7, and <i>OCT4</i> on D7 embryos, and the upregulation of <i>CDX2, KDM4B</i> and <i>KDM6B</i> on D5 embryos. On D3 and D5 embryos, total cell number and mRNA expression of embryo genome activation (EGA) markers (<i>EIF1AX</i> and <i>PPP1R15B</i>) were not affected by <i>KDM7A</i> knockdown. However, the ratio of inner cell mass (ICM)/total number of cells in D7 blastocysts was reduced by 45.5% in <i>KDM7A</i> knockdown compared to control embryos. These findings support a critical role for KDM7A in the regulation of early development and cell lineage specification in porcine embryos, which is likely mediated through the modulation of H3K9me1/me2 and H3K27me1/me2 levels, and changes in the expression of other KDMs and pluripotency genes.
DOI: 10.6084/m9.figshare.8298875.v2
title: EZH2 upregulates the PI3K/AKT pathway through IGF1R and MYC in clinically aggressive chronic lymphocytic leukaemia

description: EZH2 is overexpressed in poor-prognostic chronic lymphocytic leukaemia (CLL) cases, acting as an oncogene; however, thus far, the EZH2 target genes in CLL have not been disclosed. In this study, using ChIP-sequencing, we identified EZH2 and H3K27me3 target genes in two prognostic subgroups of CLL with distinct prognosis and outcome, i.e., cases with unmutated (U-CLL, n = 6) or mutated IGHV genes (M-CLL, n = 6). While the majority of oncogenic pathways were equally enriched for EZH2 target genes in both prognostic subgroups, PI3K pathway genes were differentially bound by EZH2 in U-CLL versus M-CLL. The occupancy of EZH2 for selected PI3K pathway target genes was validated in additional CLL samples (n = 16) and CLL cell lines using siRNA-mediated EZH2 downregulation and ChIP assays. Intriguingly, we found that EZH2 directly binds to the <i>IGF1R</i> promoter along with MYC and upregulates IGF1R expression in U-CLL, leading to downstream PI3K activation. By investigating an independent CLL cohort (n = 96), a positive correlation was observed between <i>EZH2</i> and <i>IGF1R</i> expression with higher levels in U-CLL compared to M-CLL. Accordingly, siRNA-mediated downregulation of either <i>EZH2, MYC</i> or <i>IGF1R</i> and treatment with EZH2 and MYC pharmacological inhibitors in the HG3 CLL cell line induced a significant reduction in PI3K pathway activation. In conclusion, we characterize for the first time EZH2 target genes in CLL revealing a hitherto unknown implication of EZH2 in modulating the PI3K pathway in a non-canonical, PRC2-independent way, with potential therapeutic implications considering that PI3K inhibitors are effective therapeutic agents for CLL.
DOI: 10.6084/m9.figshare.8298872.v2
title: The histone lysine demethylase <i>KDM7A</i> is required for normal development and first cell lineage specification in porcine embryos

description: There is growing evidence that histone lysine demethylases (KDMs) play critical roles in the regulation of embryo development. This study investigated if KDM7A, a lysine demethylase known to act on mono-(me1) and di-(me2) methylation of H3K9 and H3K27, participates in the regulation of early embryo development. Knockdown of <i>KDM7A</i> mRNA reduced blastocyst formation by 69.2% in <i>in vitro</i> fertilized (IVF), 48.4% in parthenogenetically activated (PA), and 48.1% in somatic cell nuclear transfer (SCNT) embryos compared to controls. Global immunofluorescence (IF) signal in <i>KDM7A</i> knockdown compared to control embryos was increased for H3K27me1 on D7, for H3K27me2 on D3 and D5, for H3K9me1 on D5 and D7, and for H3K9me2 on D5 embryos, but decreased for H3K9me1, me2 and me3 on D3. Moreover, <i>KDM7A</i> knockdown altered mRNA expression, including the downregulation of <i>KDM3C</i> on D3, <i>NANOG</i> on D5 and D7, and <i>OCT4</i> on D7 embryos, and the upregulation of <i>CDX2, KDM4B</i> and <i>KDM6B</i> on D5 embryos. On D3 and D5 embryos, total cell number and mRNA expression of embryo genome activation (EGA) markers (<i>EIF1AX</i> and <i>PPP1R15B</i>) were not affected by <i>KDM7A</i> knockdown. However, the ratio of inner cell mass (ICM)/total number of cells in D7 blastocysts was reduced by 45.5% in <i>KDM7A</i> knockdown compared to control embryos. These findings support a critical role for KDM7A in the regulation of early development and cell lineage specification in porcine embryos, which is likely mediated through the modulation of H3K9me1/me2 and H3K27me1/me2 levels, and changes in the expression of other KDMs and pluripotency genes.
DOI: 10.6084/m9.figshare.8298875.v1
title: EZH2 upregulates the PI3K/AKT pathway through IGF1R and MYC in clinically aggressive chronic lymphocytic leukemia

description: EZH2 is overexpressed in poor-prognostic chronic lymphocytic leukemia (CLL) cases, acting as an oncogene; however, thus far, the EZH2 target genes in CLL have not been disclosed. In this study, using ChIP-sequencing, we identified EZH2 and H3K27me3 target genes in two prognostic subgroups of CLL with distinct prognosis and outcome, i.e. cases with unmutated (U-CLL, n=6) or mutated IGHV genes (M-CLL, n=6). While the majority of oncogenic pathways were equally enriched for EZH2 target genes in both prognostic subgroups, PI3K pathway genes were differentially bound by EZH2 in U-CLL versus M-CLL. The occupancy of EZH2 for selected PI3K pathway target genes was validated in additional CLL samples (n=16) and CLL cell lines using siRNA-mediated EZH2 downregulation and ChIP assays. Intriguingly, we found that EZH2 directly binds to the <i>IGF1R</i> promoter along with MYC and upregulates IGF1R expression in U-CLL, leading to downstream PI3K activation. By investigating an independent CLL cohort (n=96), a positive correlation was observed between <i>EZH2</i> and <i>IGF1R</i> expression with higher levels in U-CLL compared to M-CLL. Accordingly, siRNA-mediated downregulation of either <i>EZH2, MYC</i> or <i>IGF1R</i> and treatment with EZH2 and MYC pharmacological inhibitors in the HG3 CLL cell line induced significant reduction in PI3K pathway activation. In conclusion, we characterize for the first time EZH2 target genes in CLL revealing a hitherto unknown implication of EZH2 in modulating the PI3K pathway in a non-cannonical, PRC2-independent way, with potential therapeutic implications considering that PI3K inhibitors are effective therapeutic agents for CLL.
DOI: 10.6084/m9.figshare.8298872.v1
title: The histone lysine demethylase <i>KDM7A</i> is required for normal development and first cell lineage specification in porcine embryos

description: There is growing evidence that histone lysine demethylases (KDMs) play critical roles in the regulation of embryo development. This study investigated if <i>KDM7A</i>, a lysine demethylase known to act on mono-(me1) and di-(me2) methylation of H3K9 and H3K27, participates in the regulation of early embryo development. Knockdown of <i>KDM7A</i> mRNA significantly reduced blastocyst formation by 69.2% in <i>in vitro</i> fertilized (IVF), 48.4% in parthenogenetically activated (PA), and 48.1% in somatic cell nuclear transfer (SCNT) embryos compared to controls. Global immunofluorescence (IF) signal in <i>KDM7A</i> knockdown compared to control embryos was increased for H3K27me1 on D7, for H3K27me2 on D3 and D5, for H3K9me1 on D5 and D7, and for H3K9me2 on D5 embryos, but decreased for H3K9me1, me2 and me3 on D3. Moreover, <i>KDM7A</i> knockdown altered mRNA expression, including the downregulation of <i>KDM3C</i> on D3, <i>NANOG</i> on D5 and D7, and <i>OCT4</i> on D7 embryos, and the upregulation of <i>CDX2, KDM4B</i> and <i>KDM6B</i> on D5 embryos. On D3 and D5 embryos, total cell number and mRNA expression of embryo genome activation (EGA) markers (<i>EIF1AX</i> and <i>PPP1R15B</i>) were not affected by <i>KDM7A</i> knockdown. However, the ratio of inner cell mass (ICM)/total number of cells in D7 blastocysts was reduced by 45.5% in <i>KDM7A</i> knockdown compared to control embryos. These findings support a critical role for <i>KDM7A</i> in the regulation of early development and cell lineage specification in porcine embryos, which is likely mediated through the modulation of H3K9me1/me2 and H3K27me1/me2 levels, and changes in the expression of other KDMs and pluripotency genes.
DOI: 10.6084/m9.figshare.8298860
title: Data from: Hydrodynamics of metachronal paddling: effects of varying Reynolds number and phase lag

description: Data used in the paper by Ford et al. (2019). Readme.txt within every folder/subfolder contains information on data formatting.
DOI: 10.6084/m9.figshare.8298860.v1
title: Hydrodynamics of metachronal paddling: effects of varying Reynolds number and phase lag

description: Data used in the paper by Ford et al. (2019). Readme.txt within every folder/subfolder contains information on data formatting.
DOI: 10.6084/m9.figshare.8298845
title: Measuring the survival of White Peach Scale (<i>Pseudaulacaspis pentagona</i>) on kiwifruit (<i>Actinidia chinensis</i> var. <i>deliciosa</i> ‘Hayward’) in coolstorage in Italy

description: The survival of overwintering adult White Peach Scale (WPS) (<i>Pseudaulacaspis pentagona</i>) on kiwifruit (<i>Actinidia chinensis</i> var. <i>deliciosa</i> ‘Hayward’) in a commercial coolstore in Italy was measured using a biochemical live/dead test. Fruit infested with adult female (overwintering) WPS were collected from two Italian kiwifruit orchards at harvest in October 2016 and stored in a commercial coolstore at 0–1°C. The time required to kill 99% of the WPS on the fruit was 203 days (95% CI 199–208 days). Insect mortality did not rise above background rates until after 80 days in coolstorage. Mature WPS adults on fruit removed from the coolstore after 128 days were able to mature eggs normally, and subsequent crawler settlement was observed after 22 days out of coolstore at 20°C. Italian kiwifruit infested with WPS is imported into New Zealand during January and February each year, after a coolstore duration of 60–130 days. Most of the mature WPS will be alive and viable in terms of egg development and crawler production.
DOI: 10.6084/m9.figshare.8298689
title: Questionnaire-sleep and health behavior among diabetes

description: Questionnaire used to survey sleep and other health behaviors of diabetic patient and non-diabetics.
DOI: 10.6084/m9.figshare.8298845.v2
title: Measuring the survival of White Peach Scale (<i>Pseudaulacaspis pentagona</i>) on kiwifruit (<i>Actinidia chinensis</i> var. <i>deliciosa</i> ‘Hayward’) in coolstorage in Italy

description: The survival of overwintering adult White Peach Scale (WPS) (<i>Pseudaulacaspis pentagona</i>) on kiwifruit (<i>Actinidia chinensis</i> var. <i>deliciosa</i> ‘Hayward’) in a commercial coolstore in Italy was measured using a biochemical live/dead test. Fruit infested with adult female (overwintering) WPS were collected from two Italian kiwifruit orchards at harvest in October 2016 and stored in a commercial coolstore at 0–1°C. The time required to kill 99% of the WPS on the fruit was 203 days (95% CI 199–208 days). Insect mortality did not rise above background rates until after 80 days in coolstorage. Mature WPS adults on fruit removed from the coolstore after 128 days were able to mature eggs normally, and subsequent crawler settlement was observed after 22 days out of coolstore at 20°C. Italian kiwifruit infested with WPS is imported into New Zealand during January and February each year, after a coolstore duration of 60–130 days. Most of the mature WPS will be alive and viable in terms of egg development and crawler production.
DOI: 10.6084/m9.figshare.8298845.v1
title: Measuring the survival of White Peach Scale (<i>Pseudaulacaspis pentagona</i>) on kiwifruit (<i>Actinidia chinensis</i> var. <i>deliciosa</i> ‘Hayward’) in coolstorage in Italy

description: The survival of overwintering adult White Peach Scale (WPS) (<i>Pseudaulacaspis pentagona</i>) on kiwifruit (<i>Actinidia chinensis</i> var. <i>deliciosa</i> ‘Hayward’) in a commercial coolstore in Italy was measured using a biochemical live/dead test. Fruit infested with adult female (overwintering) WPS were collected from two Italian kiwifruit orchards at harvest in October 2016 and stored in a commercial coolstore at 0–1°C. The time required to kill 99% of the WPS on the fruit was 203 days (95% CI 199–208 days). Insect mortality did not rise above background rates until after 80 days in coolstorage. Mature WPS adults on fruit removed from the coolstore after 128 days were able to mature eggs normally, and subsequent crawler settlement was observed after 22 days out of coolstore at 20°C. Italian kiwifruit infested with WPS is imported into New Zealand during January and February each year, after a coolstore duration of 60–130 days. Most of the mature WPS will be alive and viable in terms of egg development and crawler production.
DOI: 10.6084/m9.figshare.8298686
title: GAD67 abutments overall spreadsheet

description: GAD67 abutments overall spreadsheet 2019 paper
DOI: 10.6084/m9.figshare.8298689.v1
title: Questionnaire-sleep and health behavior among diabetes

description: Questionnaire used to survey sleep and other health behaviors of diabetic patient and non-diabetics.
DOI: 10.6084/m9.figshare.8298686.v1
title: GAD67 abutments overall spreadsheet

description: GAD67 abutments overall spreadsheet 2019 paper
DOI: 10.6084/m9.figshare.8298674
title: Limousin (including F94L variant) SNP data & Phenotypes

description: This data set includes SNP genotyping and phenotypes in Limousin.
DOI: 10.6084/m9.figshare.8298482
title: Figure 6 "Rapid fabrication of reinforced and cell-laden vascular grafts structurally inspired by human coronary arteries"

description: This data set corresponds to the raw data displayed as graphs in figure 6 of the paper entitled "<b>Rapid fabrication of reinforced and cell-laden vascular grafts structurally inspired by human coronary arteries". </b>The excel file contains 5 sheets. The first sheet contains the longitudinal stress-strain data collected for 5 replicates of fabricated small diameter vascular grafts (SDVGs) and displayed as an average graph in figure 6a. The second sheet contains the circumferential stress-strain data collected for 5 replicates of fabricated SDVGs and displayed as an average graph in figure 6b. The third, fourth and fifth sheet contain different data of diameter change ratio (D/D<sub>0</sub>) as function of luminal pressure applied to 5 replicates of fabricated SDVG. SDVG replicates mounted on the pressurized system were pre-stretched longitudinally at 10, 20 and 25% strain and the average D/D<sub>0</sub> v/s luminal pressure displayed as graph in figure 6d, 6e and 6f, respectively.
DOI: 10.6084/m9.figshare.8298449
title: Figure 5 Rapid fabrication of reinforced and cell-laden vascular grafts structurally inspired by human coronary arteries.

description: This data set corresponds to the raw data displayed as graphs in figure 5 of the paper titled "<b>Rapid fabrication of reinforced and cell-laden vascular grafts structurally inspired by human coronary arteries". </b>The excel file contains 4 sheets. The first sheet contains the longitudinal stress-strain data collected for 3 replicates of fabricated outer graft layer of the small diameter vascular graft (SDVGs) and displayed as an average graph in figure 5b. The second sheet contains the circumferential stress-strain data collected for 3 replicates of fabricated outer graft layer of the small diameter vascular graft (SDVGs) and displayed as an average graph in figure 5c. The third sheet contains the longitudinal stress-strain data collected for 3 replicates of fabricated middle graft layer of the small diameter vascular graft (SDVGs) and displayed as an average graph in figure 5d. Finally, the fourth sheet contains the circumferential stress-strain data collected for 3 replicates of fabricated middle graft layer of the small diameter vascular graft (SDVGs) and displayed as an average graph in figure 5e.
DOI: 10.6084/m9.figshare.8298482.v1
title: Figure 6 "Rapid fabrication of reinforced and cell-laden vascular grafts structurally inspired by human coronary arteries"

description: This data set corresponds to the raw data displayed as graphs in figure 6 of the paper entitled "<b>Rapid fabrication of reinforced and cell-laden vascular grafts structurally inspired by human coronary arteries". </b>The excel file contains 5 sheets. The first sheet contains the longitudinal stress-strain data collected for 5 replicates of fabricated small diameter vascular grafts (SDVGs) and displayed as an average graph in figure 6a. The second sheet contains the circumferential stress-strain data collected for 5 replicates of fabricated SDVGs and displayed as an average graph in figure 6b. The third, fourth and fifth sheet contain different data of diameter change ratio (D/D<sub>0</sub>) as function of luminal pressure applied to 5 replicates of fabricated SDVG. SDVG replicates mounted on the pressurized system were pre-stretched longitudinally at 10, 20 and 25% strain and the average D/D<sub>0</sub> v/s luminal pressure displayed as graph in figure 6d, 6e and 6f, respectively.
DOI: 10.6084/m9.figshare.8298359
title: Dataset for: Vection in Virtual Reality Modulates Vestibular-Evoked Myogenic Potentials

description: The popularity of Virtual Reality (VR) has increased rapidly in recent years. While significant technological advancements are apparent, a troublesome problem with VR is that between 20% and 80% of users will experience unpleasant side-effects such as nausea, disorientation, blurred vision, and headaches – a malady known as Cybersickness. Cybersickness may be caused by a conflict between sensory signals for self-motion: while vision signals that the user is moving in a certain direction with certain acceleration, the vestibular organs provide no corroborating information. To resolve the sensory conflict vestibular cues may be down-weighted leading to an alteration of how the brain interprets actual vestibular information. This may account for the frequently reported after-effects of VR exposure. Here we investigated whether exposure to vection in VR modulates vestibular processing. We measured vestibular-evoked myogenic potentials (VEMPs) during brief immersion in a vection-inducing VR environment presented via head-mounted display. We found changes in VEMPs asymmetry ratio, with a substantial increase in VEMPs amplitude recorded on the left sternocleidomastoid muscle following just one minute of exposure to vection in VR. Our results suggest that exposure to vection in VR modulates vestibular processing, which may explain common after-effects of VR.
DOI: 10.6084/m9.figshare.8298332
title: Schifanella SHIVC All Data.xlsx

description: Complete Dataset for Schifanella Manuscript<br>
DOI: 10.6084/m9.figshare.8298449.v1
title: Figure 5 Rapid fabrication of reinforced and cell-laden vascular grafts structurally inspired by human coronary arteries.

description: This data set corresponds to the raw data displayed as graphs in figure 5 of the paper titled "<b>Rapid fabrication of reinforced and cell-laden vascular grafts structurally inspired by human coronary arteries". </b>The excel file contains 4 sheets. The first sheet contains the longitudinal stress-strain data collected for 3 replicates of fabricated outer graft layer of the small diameter vascular graft (SDVGs) and displayed as an average graph in figure 5b. The second sheet contains the circumferential stress-strain data collected for 3 replicates of fabricated outer graft layer of the small diameter vascular graft (SDVGs) and displayed as an average graph in figure 5c. The third sheet contains the longitudinal stress-strain data collected for 3 replicates of fabricated middle graft layer of the small diameter vascular graft (SDVGs) and displayed as an average graph in figure 5d. Finally, the fourth sheet contains the circumferential stress-strain data collected for 3 replicates of fabricated middle graft layer of the small diameter vascular graft (SDVGs) and displayed as an average graph in figure 5e.
DOI: 10.6084/m9.figshare.8298161
title: SI DeepSeqData for Fine Epitope Mapping of the CD19 Extracellular Domain Promotes Design

description: SI DeepSeqData for Fine Epitope Mapping of the CD19 Extracellular Domain Promotes Design<br>Justin R. Klesmith, Lan Wu, Roy R. Lobb, Paul D. Rennert, Benjamin J. Hackel<br>Includes:Raw FASTQ filesProtein Analysis and Classifier Toolkit exported files