cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.6865120
title: DNA curtain assay for dCas12a/CS10B colocalization

description: A self-assembling polypeptide (C-S<sub>10</sub>-B, labeled in green) binds to a DNA that has been pre-decorated with CRISPR-dCas12a (labeled in magenta) via multiple CRISPR-RNAs (crRNAs). C-S<sub>10</sub>-B binds and diffuses along DNA but cannot move beyond stably bound dCas12a. During self-assembly, large clusters of C-S<sub>10</sub>-B commonly form and colocalize with dCas12a. Bacteriophage λ DNA (λDNA) (NEB, N3011S) was mixed in T4 DNA ligase (NEB, M0202S) reaction buffer with biotinylated oligos complementary to λDNA cohesive ends, for 15 min at 70°C, followed by a cool down to 15 °C for over 2 h. Ligation took place overnight at room temperature. After T4 DNA ligase inactivation with 2 M NaCl, the biotinylated DNA was purified on a Sephacryl S-1000 size exclusion column (GE Healthcare). Using a lipid solution (1.954% DOPC, 0.04% DOPE-mPEG2k and 0.006% DOPE-biotin) in buffer (10 mM Tris-HCL pH 8, 100 mM NaCl), the flowcell was passivated at room temperature for 30 min. Next, BSA buffer (40 mM Tris-HCl pH 8, 2 mM MgCl<sub>2</sub>, 0.2 mg/mL BSA) was used to wash the flowcell, followed by incubation for 10 min. BSA buffer containing biotinylated DNA was injected into the flowcell, before washing out all the non-tethered DNA material. Imaging was done in BSA buffer supplemented with 100 mM NaCl, 5 mM MgCl<sub>2</sub>, 2 mM DTT. dCas12a was mixed with the crRNA pool at a 1:10 molar ratio in buffer (20 mM Tris-HCl pH 8.0, 100 mM NaCl, 5 mM MgCl<sub>2</sub>, 2% glycerol, 2 mM DTT) for 30 min at 37°C. The formed ribonucleoprotein particle complexes (10 nM) were injected into the flowcell to induce DNA binding for 30 min at room temperature. Monoclonal ANTI-FLAG ® BioM2-Biotin (Sigma-Aldrich, F9291) conjugated to quantum dots (Thermo, Q21361MP) were used to label dCas12a. C-S<sub>10</sub>-B was labeled at a single N-terminal cysteine with maleimide-Alexa-488. Imaging was carried out in an inverted Nikon Ti-E microscope at 60X magnification. Excitation of the sample was provided by a 488 nm laser. Emission light was split with a 638 nm dichroic beam splitter (Chroma) and registered by two EM-CCD cameras (Andor iXon DU897). Image processing was done in FIJI.
DOI: 10.5281/zenodo.6865119
title: DNA curtain assay for dCas12a/CS10B colocalization

description: A self-assembling polypeptide (C-S<sub>10</sub>-B, labeled in green) binds to a DNA that has been pre-decorated with CRISPR-dCas12a (labeled in magenta) via multiple CRISPR-RNAs (crRNAs). C-S<sub>10</sub>-B binds and diffuses along DNA but cannot move beyond stably bound dCas12a. During self-assembly, large clusters of C-S<sub>10</sub>-B commonly form and colocalize with dCas12a. Bacteriophage λ DNA (λDNA) (NEB, N3011S) was mixed in T4 DNA ligase (NEB, M0202S) reaction buffer with biotinylated oligos complementary to λDNA cohesive ends, for 15 min at 70°C, followed by a cool down to 15 °C for over 2 h. Ligation took place overnight at room temperature. After T4 DNA ligase inactivation with 2 M NaCl, the biotinylated DNA was purified on a Sephacryl S-1000 size exclusion column (GE Healthcare). Using a lipid solution (1.954% DOPC, 0.04% DOPE-mPEG2k and 0.006% DOPE-biotin) in buffer (10 mM Tris-HCL pH 8, 100 mM NaCl), the flowcell was passivated at room temperature for 30 min. Next, BSA buffer (40 mM Tris-HCl pH 8, 2 mM MgCl<sub>2</sub>, 0.2 mg/mL BSA) was used to wash the flowcell, followed by incubation for 10 min. BSA buffer containing biotinylated DNA was injected into the flowcell, before washing out all the non-tethered DNA material. Imaging was done in BSA buffer supplemented with 100 mM NaCl, 5 mM MgCl<sub>2</sub>, 2 mM DTT. dCas12a was mixed with the crRNA pool at a 1:10 molar ratio in buffer (20 mM Tris-HCl pH 8.0, 100 mM NaCl, 5 mM MgCl<sub>2</sub>, 2% glycerol, 2 mM DTT) for 30 min at 37°C. The formed ribonucleoprotein particle complexes (10 nM) were injected into the flowcell to induce DNA binding for 30 min at room temperature. Monoclonal ANTI-FLAG ® BioM2-Biotin (Sigma-Aldrich, F9291) conjugated to quantum dots (Thermo, Q21361MP) were used to label dCas12a. C-S<sub>10</sub>-B was labeled at a single N-terminal cysteine with maleimide-Alexa-488. Imaging was carried out in an inverted Nikon Ti-E microscope at 60X magnification. Excitation of the sample was provided by a 488 nm laser. Emission light was split with a 638 nm dichroic beam splitter (Chroma) and registered by two EM-CCD cameras (Andor iXon DU897). Image processing was done in FIJI.
DOI: 10.5281/zenodo.6865066
title: Volumetric imaging of fluorescently labeled BPAE cells

description: Using the Nanoimager-S microscope (ONI, Oxford Nanoimaging) with a sCMOS sensor (Hamamatsu, ORCA-Flash4.0 V2), FluoCells™ Prepared Slide #1 (Thermo, #F36924) were imaged with a 100X, 1.4 NA, oil-immersion objective (Olympus). DAPI, Alexa-488 and MitoTracker™ Red excitation was delivered by 405 nm, 473 nm and 561 nm lasers, respectively. Light was collected while using two emission filters (1: 525/50; 2: Band 1 575-616.5) and a Channel Splitter dichroic 561 LP. A 3D Z-stack of the sample was acquired for each channel. 22 frames were generated, each separated 50 nm from each other in Z.
DOI: 10.5281/zenodo.6865065
title: Volumetric imaging of fluorescently labeled BPAE cells

description: Using the Nanoimager-S microscope (ONI, Oxford Nanoimaging) with a sCMOS sensor (Hamamatsu, ORCA-Flash4.0 V2), FluoCells™ Prepared Slide #1 (Thermo, #F36924) were imaged with a 100X, 1.4 NA, oil-immersion objective (Olympus). DAPI, Alexa-488 and MitoTracker™ Red excitation was delivered by 405 nm, 473 nm and 561 nm lasers, respectively. Light was collected while using two emission filters (1: 525/50; 2: Band 1 575-616.5) and a Channel Splitter dichroic 561 LP. A 3D Z-stack of the sample was acquired for each channel. 22 frames were generated, each separated 50 nm from each other in Z.
DOI: 10.5281/zenodo.6972455
title: Erythroxylum dillonii zanfona 1

description: .
DOI: 10.5281/zenodo.6972454
title: Erythroxylum dillonii zanfona 1

description: .
DOI: 10.5281/zenodo.5657032
title: Stress analysis and Q-factor of free-standing (La,Sr)MnO3 oxide resonators (Dataset)

description: Datafiles of the article "Stress analysis and Q-factor of free-standing (La,Sr)MnO3 oxide resonators"
DOI: 10.34740/kaggle/dsv/4041593
title: Tales from the Pizza Guy
DOI: 10.5281/zenodo.6972478
title: Datawarrior and SwissADME physicochemical parameters.

description: Data table.
DOI: 10.5281/zenodo.6972477
title: Datawarrior and SwissADME physicochemical parameters.

description: Data table.
DOI: 10.5281/zenodo.6972479
title: Stress analysis and Q-factor of free-standing (La,Sr)MnO3 oxide resonators (Dataset)

description: Datafiles of the article "Stress analysis and Q-factor of free-standing (La,Sr)MnO3 oxide resonators"
DOI: 10.5281/zenodo.5657031
title: Stress analysis and Q-factor of free-standing (La,Sr)MnO3 oxide resonators (Dataset)

description: Datafiles of the article "Stress analysis and Q-factor of free-standing (La,Sr)MnO3 oxide resonators"
DOI: 10.5281/zenodo.6972481
title: Erythroxylum glaucum zanfona 1

description: .
DOI: 10.5281/zenodo.6972480
title: Erythroxylum glaucum zanfona 1

description: .
DOI: 10.6084/m9.figshare.20445645
title: Table S1. Features detected in methanolic extracts of marine invertebrates.

description: Features detected in methanolic extracts of marine invertebrates.
DOI: 10.6084/m9.figshare.20445645.v1
title: Table S1. Features detected in methanolic extracts of marine invertebrates.

description: Features detected in methanolic extracts of marine invertebrates.
DOI: 10.5281/zenodo.6972490
title: Bacterial genera producing compounds related to marine invertebrate-derived compounds.

description: Data table.
DOI: 10.5281/zenodo.6972489
title: Bacterial genera producing compounds related to marine invertebrate-derived compounds.

description: Data table.
DOI: 10.26186/147119
title: Exploring for the Future program Showcase 2022 - Day 1 Overview

description: The Exploring for the Future program Showcase 2022 was held on 8-10 August 2022. Day 1 (8th August) included a talk on: - Exploring for the Future - The value of precompetitive geoscience - Dr Andrew Heap
DOI: 10.5281/zenodo.6972492
title: Features detected in methanolic extracts of marine invertebrates.

description: Data table.
DOI: 10.5281/zenodo.6972491
title: Features detected in methanolic extracts of marine invertebrates.

description: Data table.
DOI: 10.5281/zenodo.6972496
title: ASVs detected in the microbiome of marine invertebrates.

description: Data table.
DOI: 10.5281/zenodo.6972495
title: ASVs detected in the microbiome of marine invertebrates.

description: Data table.
DOI: 10.6084/m9.figshare.20444748
title: Chronic pain neuroscience and psychoanalytic theory a narrative review

description: Chronic pain is felt in the body and in the mind. S. Freud, J. Lacan, neurophysiologists, and societies for the study of pain have each explained it to us independently with little success when facing the complexity of this condition by patients and health personnel who care for them, but there are these theories, and you must begin to take them all into account to understand pain in its entirety.
DOI: 10.17632/wgsjz42pg8.1
title: Supplementary data for genome-wide DNA methylation and gene expression analysis of human blood in patients with metabolic syndrome

description: These supplementary data, associated with Baek et al.[1], comprise the raw data, and the analyzed and filtered epigenetic biomarker data, for patients with MetS and controls. Raw data (GEO accession: GSE181647) included RNA sequence (fastq) and methylation array (idat) data for 20 participants. Patient characteristics are listed in Table S1. Table S2 lists the differentially methylated probes (DMPs), comparing patients with MetS and controls. Table S3 describes the functional enrichment of genes under hyper- and hypomethylation. Table S4 presents the differentially expressed genes (DEGs). Table S5 describes the functional enrichment of the DEGs, using the DisGeNET gene sets. Table S6 lists the genes with significant correlations between their expression and DNA methylation. Table S7 describes the integrated functional network genes and pathways. 
List of Tables
Table S1. Demographics and characteristics of study population
Table S2. List of differentially methylated probes (DMPs) in MetS compared to control
Table S3. List of functional enrichment analysis of genes with hyper/hypo methylated in MetS compared to control. 
Table S4. List of differentially expressed genes (DEGs) in MetS compared to control.
Table S5. List of functional enrichment analysis of DEGs using DisGeNET gene sets.
Table S6. List of significantly correlated genes between DNA methylation and gene expression. 
Table S7. List of integrated functional network genes and pathways.
DOI: 10.26188/20335203
title: Analysis data for BLAZE

description: Processed analysis data for BLAZE paper
DOI: 10.26188/20335203.v1
title: Analysis data for BLAZE

description: Processed analysis data for BLAZE paper
DOI: 10.5281/zenodo.6850637
title: CRISPR-PAINT nanorulers

description: The GATTA-PAINT 40 RG nanoruler (GATTAquant, DNA nanotechnologies) consists of three fluorophores (ATTO 655/ATTO 542) separated 40 nm from each other. Imaging of the sample was performed on an Olympus IX-81 inverted microscope equipped with an Olympus UApo N 100X/1.49 NA, oil-immersion objective in TIRF illumination mode (Olympus, cellTIRF Illuminator) with ~200 nm evanescence field depth. Sample excitation was provided by 488 nm and 561 nm lasers at 23.1 mW laser power. 300 total images were collected with an EM-CCD sensor (Andor iXon 897), exposure time set to 50 ms per frame and a pixel size of 160 nm.
DOI: 10.5281/zenodo.6850636
title: CRISPR-PAINT nanorulers

description: The GATTA-PAINT 40 RG nanoruler (GATTAquant, DNA nanotechnologies) consists of three fluorophores (ATTO 655/ATTO 542) separated 40 nm from each other. Imaging of the sample was performed on an Olympus IX-81 inverted microscope equipped with an Olympus UApo N 100X/1.49 NA, oil-immersion objective in TIRF illumination mode (Olympus, cellTIRF Illuminator) with ~200 nm evanescence field depth. Sample excitation was provided by 488 nm and 561 nm lasers at 23.1 mW laser power. 300 total images were collected with an EM-CCD sensor (Andor iXon 897), exposure time set to 50 ms per frame and a pixel size of 160 nm.
DOI: 10.5281/zenodo.6850745
title: Volumetric imaging of Arabidopsis thaliana root cells

description: <em>Arabidopsis thaliana</em> seeds were surface sterilized, germinated and grown in Murashigue and Skoog medium at pH 5.7 and supplemented with vitamins (0.1 mg l-1 pyridoxine, 0.1 mg l-1 nicotinic acid), 0.8% agar, and 1% sucrose. Plants were grown at 21°C, 16/8-hour light/dark periods at 105 µmol/m<sup>2</sup>s<sup>2</sup> light intensity. Using a Zeiss Axiovert 200M microscope and a C-APO 63X, 1.2NA objective (Oberkochen, Germany), confocal volumetric imaging of the plant material was performed, with a pixel size of 404 nm and Z step size of 500 nm. Excitation of the sample was provided by a 488 nm laser, and a filter cube with 525/45 nm and 630/92 nm bandpass filters was used for yellow and red emission light collection, respectively. An inverted Olympus FV1000-IX81 confocal microscope equipped with a LUMFLN×60, 1.3NA S objective was used for root cell nuclear imaging. Sample excitation was achieved with a 543 nm laser and a BA560-660 filter was used for emission light collection. Pixel size was 41 nm, with a Z step size of 100 nm. A custom-built selective plane illumination microscopy (SPIM) system was used for imaging of primary root cells expressing p35s:H2B-R-RF. Sample excitation was achieved with a 561 nm laser using stroboscopic illumination. Emission was filtered via a multi-bandpass emission filter (Semrock, FF01-446/523/600/677-25 BrightLine). Volumetric imaging was done by mounting the sample on a four dimensional (XYZ, and Y rotation) motorized stage (Picard Industries). A sCMOS sensor (Hamamatsu, ORCA-Flash4.0 V2) was used for signal recording. The OpenSPIM plugin of µmanager (v.1.4 for windows) was used for control of acquisition parameters, sample translation and stroboscopic illumination. Collected images had a pixel size of 0.325µm, Z step size of 100 nm and a Y rotation step of 1.8°. Experimental procedures were approved by the Bioethics Committee of the Biotechnology Institute of the National Autonomous University of Mexico.
description: {"references": ["Federici, F., Dupuy, L., Laplaze, L., Heisler, M., and Haseloff, J. Integrated genetic and computation methods for in planta cytometry, Nat. Methods 9, 483\u2013485 (2012).", "Geldner, N., D\u00e9nervaud-Tendon, V., Hyman, D. L., Mayer, U., Stierhof, Y.-D. and Chory, J. Rapid, combinatorial analysis of membrane compartments in intact plants with a multicolor marker set, The Plant J. 59, 169\u2013178 (2009).", "Schindelin, J. et al. Fiji: an open-source platform for biological-image analysis. Nat. Methods 9, 676\u2013682, (2012).", "Pitrone, P., Schindelin, J., Stuyvenberg, L. et al. OpenSPIM: an open-access light-sheet microscopy platform, Nat Methods 10, 598\u2013599 (2013).", "\"Download micro-manager latest release:\" https://micro-manager.org/Download_Micro-Manager_Latest_Release."]}
DOI: 10.5281/zenodo.6850744
title: Volumetric imaging of Arabidopsis thaliana root cells

description: <em>Arabidopsis thaliana</em> seeds were surface sterilized, germinated and grown in Murashigue and Skoog medium at pH 5.7 and supplemented with vitamins (0.1 mg l-1 pyridoxine, 0.1 mg l-1 nicotinic acid), 0.8% agar, and 1% sucrose. Plants were grown at 21°C, 16/8-hour light/dark periods at 105 µmol/m<sup>2</sup>s<sup>2</sup> light intensity. Using a Zeiss Axiovert 200M microscope and a C-APO 63X, 1.2NA objective (Oberkochen, Germany), confocal volumetric imaging of the plant material was performed, with a pixel size of 404 nm and Z step size of 500 nm. Excitation of the sample was provided by a 488 nm laser, and a filter cube with 525/45 nm and 630/92 nm bandpass filters was used for yellow and red emission light collection, respectively. An inverted Olympus FV1000-IX81 confocal microscope equipped with a LUMFLN×60, 1.3NA S objective was used for root cell nuclear imaging. Sample excitation was achieved with a 543 nm laser and a BA560-660 filter was used for emission light collection. Pixel size was 41 nm, with a Z step size of 100 nm. A custom-built selective plane illumination microscopy (SPIM) system was used for imaging of primary root cells expressing p35s:H2B-R-RF. Sample excitation was achieved with a 561 nm laser using stroboscopic illumination. Emission was filtered via a multi-bandpass emission filter (Semrock, FF01-446/523/600/677-25 BrightLine). Volumetric imaging was done by mounting the sample on a four dimensional (XYZ, and Y rotation) motorized stage (Picard Industries). A sCMOS sensor (Hamamatsu, ORCA-Flash4.0 V2) was used for signal recording. The OpenSPIM plugin of µmanager (v.1.4 for windows) was used for control of acquisition parameters, sample translation and stroboscopic illumination. Collected images had a pixel size of 0.325µm, Z step size of 100 nm and a Y rotation step of 1.8°. Experimental procedures were approved by the Bioethics Committee of the Biotechnology Institute of the National Autonomous University of Mexico.
description: {"references": ["Federici, F., Dupuy, L., Laplaze, L., Heisler, M., and Haseloff, J. Integrated genetic and computation methods for in planta cytometry, Nat. Methods 9, 483\u2013485 (2012).", "Geldner, N., D\u00e9nervaud-Tendon, V., Hyman, D. L., Mayer, U., Stierhof, Y.-D. and Chory, J. Rapid, combinatorial analysis of membrane compartments in intact plants with a multicolor marker set, The Plant J. 59, 169\u2013178 (2009).", "Schindelin, J. et al. Fiji: an open-source platform for biological-image analysis. Nat. Methods 9, 676\u2013682, (2012).", "Pitrone, P., Schindelin, J., Stuyvenberg, L. et al. OpenSPIM: an open-access light-sheet microscopy platform, Nat Methods 10, 598\u2013599 (2013).", "\"Download micro-manager latest release:\" https://micro-manager.org/Download_Micro-Manager_Latest_Release."]}
DOI: 10.5281/zenodo.6865142
title: Synapsed homologs of meiotic mouse chromosomes visualized by TIRFM

description: Mouse testes were removed from euthanized animals, followed by decapsulation and maceration in high-glucose MEM medium. Suspension was mixed thoroughly and left to settle; the supernatant was then collected and centrifuged at 7200 rpm for 1 min. The pellet was then resuspended in a 0.5 M sucrose solution and added to PFA-treated (1% in 0.015% Triton X-100) coverslides, which were incubated for at room temperature for 2 hours in a humidified environment. After incubation, slides were rinsed twice with a wetting agent solution (Kodak, 1464510) in water and allowed to air dry. SYCP3 was labeled with primary SCP-3 (D-1) antibody (Santa Cruz Biotechnology, SC-74569) and a secondary anti-mouse antibody fused with Alexa-568 (Thermo, A11004). Surface chromosome spreads were imaged in an Elyra 7 microscope (Zeiss), with a 60x 1.4 NA oil immersion objective and an a 1.4x magnification lens. Image reconstruction was performed in ZEN Black with parameters set to default. Experimental procedures were approved by the “Ministero della Salute" of Italy, authorization n.701/2018-PR.
DOI: 10.5281/zenodo.6865141
title: Synapsed homologs of meiotic mouse chromosomes visualized by TIRFM

description: Mouse testes were removed from euthanized animals, followed by decapsulation and maceration in high-glucose MEM medium. Suspension was mixed thoroughly and left to settle; the supernatant was then collected and centrifuged at 7200 rpm for 1 min. The pellet was then resuspended in a 0.5 M sucrose solution and added to PFA-treated (1% in 0.015% Triton X-100) coverslides, which were incubated for at room temperature for 2 hours in a humidified environment. After incubation, slides were rinsed twice with a wetting agent solution (Kodak, 1464510) in water and allowed to air dry. SYCP3 was labeled with primary SCP-3 (D-1) antibody (Santa Cruz Biotechnology, SC-74569) and a secondary anti-mouse antibody fused with Alexa-568 (Thermo, A11004). Surface chromosome spreads were imaged in an Elyra 7 microscope (Zeiss), with a 60x 1.4 NA oil immersion objective and an a 1.4x magnification lens. Image reconstruction was performed in ZEN Black with parameters set to default. Experimental procedures were approved by the “Ministero della Salute" of Italy, authorization n.701/2018-PR.
DOI: 10.5281/zenodo.6865168
title: STED immunofluorescence imaging of histone protein H3K27 in a 2-cell stage mice embryo

description: In either confocal or STED mode, immunofluorescence was performed as previously described in [1], using an upright Zeiss microscope with a mounted STEDYCON module and a Zeiss 100x 1.46 NA objective. Primary antibodies used were anti-H3K27ac (Active Motif, 39034) and anti-H3K27me3 (Abcam, ab6002), both at 1:200 dilution. Secondary anti-mouse and anti-rabbit antibodies used were labeled with STAR Red (Sigma-Aldrich, 52283) and STAR Orange (Sigma-Aldrich, 41367), respectively. Excitation was provided by 640 nm (@3%) and 775 nm (@96.5%) lasers for the STAR Red channel, whereas 561 nm (@7.8%) and 775 nm (@100%) lasers were used for the STAR Orange channel. Imaging of the samples was performed with 5 µs pixel dwell time, 64 µm pinhole aperture, 15-line accumulations and a pixel size of 20 nm. Experimental procedures were approved by the EMBL Rome Animal Facility in accordance with European and Italian legislations. 1. Bošković, A., Bender, A., Gall, L., Ziegler-Birling, C., Beaujean, N., & Torres-Padilla, M.-E. Analysis of active chromatin modifications in early mammalian embryos reveals uncoupling of h2a.z acetylation and h3k36 trimethylation from embryonic genome activation. Epigenetics 7, 747–757 (2012).
DOI: 10.5281/zenodo.6865167
title: STED immunofluorescence imaging of histone protein H3K27 in a 2-cell stage mice embryo

description: In either confocal or STED mode, immunofluorescence was performed as previously described in [1], using an upright Zeiss microscope with a mounted STEDYCON module and a Zeiss 100x 1.46 NA objective. Primary antibodies used were anti-H3K27ac (Active Motif, 39034) and anti-H3K27me3 (Abcam, ab6002), both at 1:200 dilution. Secondary anti-mouse and anti-rabbit antibodies used were labeled with STAR Red (Sigma-Aldrich, 52283) and STAR Orange (Sigma-Aldrich, 41367), respectively. Excitation was provided by 640 nm (@3%) and 775 nm (@96.5%) lasers for the STAR Red channel, whereas 561 nm (@7.8%) and 775 nm (@100%) lasers were used for the STAR Orange channel. Imaging of the samples was performed with 5 µs pixel dwell time, 64 µm pinhole aperture, 15-line accumulations and a pixel size of 20 nm. Experimental procedures were approved by the EMBL Rome Animal Facility in accordance with European and Italian legislations. 1. Bošković, A., Bender, A., Gall, L., Ziegler-Birling, C., Beaujean, N., & Torres-Padilla, M.-E. Analysis of active chromatin modifications in early mammalian embryos reveals uncoupling of h2a.z acetylation and h3k36 trimethylation from embryonic genome activation. Epigenetics 7, 747–757 (2012).