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Raw data to accompany the manuscript 'Data for Engineering Lipid Metabolism of Chinese Hamster Ovary (CHO) Cells for Enhanced Recombinant Protein Production' published in the Journal Data in Brief
<p>This repository consists of the raw western blot, microscopy and mass spectrometry data to accompany the manuscript 'Data for Engineering Lipid Metabolism of Chinese Hamster Ovary (CHO) Cells for Enhanced Recombinant Protein Production' published in the Journal Data in Brief and associated with the article '<a href="https://www.ncbi.nlm.nih.gov/pubmed/31805379">Engineering of Chinese hamster ovary cell lipid metabolism results in an expanded ER and enhanced recombinant biotherapeutic protein production</a>' published in the journal Metabolic Engineering (see DOI: 10.1016/j.ymben.2019.11.007). </p> <p>The western blot raw file is associated with Figure 1a and 1b of the Data in Brief manuscript.</p> <p>The confocal microscopy raw image files (x3) are associated with Figure 1c of the Data in Brief manuscript.</p> <p>The mass spectrometry files are the raw data that refers to the samples presented in Figure 5 of the Data in Brief manuscript. Files are labelled as in the Data in Brief and Metabolic Engineering manuscripts. The file name structures is as follows;</p> <p>CHO-Controlpoolai</p> <p>Where 'a' represents replicate 'a' of three biological replicates and 'i' refers to mass spectrometry technical analysis 1 of 3 technical analyses of each replicate (thus for each cell pool or line there are three biological replicates that are each analysed in triplicate such that there are 9 raw mass spectrometry files for each cell pool or line).</p> <p>All the mass spectrometry files are found in the compressed (zip) file named mass_spectrometry_raw_files_archive.zip</p>
Macroscopic, histological and stereological image dataset of the Striped red mullet (Mullus surmuletus) ovaries from the English Channel (ICES area 27.7.d) stock
<p><strong>Contents: </strong></p> <p>This dataset can be completed with the : <strong>Macroscopic, histological and stereological image dataset of the Striped red mullet (<em>Mullus surmuletus</em>) ovaries from the Bay of Biscay (ICES area 27.7.g,j & 27.8.a-c) stock</strong>, which can also be found on the Zenodo repository.</p> <p>This dataset contains the macroscopic and histological images of the ovaries of 214 Striped red mullet (female, <em>Mullus surmuletus</em>, Linnaeus 1758) collected from the English Channel stock (ICES area 27.7.d) in February 2021 (n=20), March 2021 (n=13), April 2021 (n=12), May 2021 (n=15), August 2021 (n=15), September 2021 (n=15), October 2021 (n=41), November 2021 (n=10), December 2021 (n=14), January 2022 (n=30), February 2022 (n=15) and August 2022 (n=14).</p> <p> </p> <p><strong>Images:</strong></p> <ul> <li><strong>Macroscopic_pictures.zip: </strong>archive in zip format of 621 pictures (.JPG; 2Mo-8Mo; JPG; 350pp) from 211 female Striped red mullets dissected during this study. Each photo was taken with a digital camera (no flash). For each individual, up to three pictures were taken when possible (Le Meleder <em>et al.</em>, 2022) with : <ul> <li>one picture of the entire fish with its abdominal cavity open with the ovaries in view</li> <li>one picture of the whole fish with the ovaries outside of the abdominal cavity</li> <li>one picture of the ovaries</li> <li>the name of the picture is the same as the fish’s ID number.</li> </ul> </li> </ul> <ul> <li><strong>Histology_slides.zip :</strong> archive in zip format containing the ovarian histological slides digitized using an Olympus V120 slide scanner, x20 lens. The pictures (.vsi from the OlympusVSI format) are of the 484 histological slides acquired during this study.</li> <li>Data was split for smaller size downloads : <ul> <li><strong>Histology_slides_1of5 :</strong> histological sections for individuals numbered 001 to 045</li> <li><strong>Histology_slides_2of5 :</strong> histological sections for individuals numbered 046 to 138</li> <li><strong>Histology_slides_3of5 :</strong> histological sections for individuals numbered 154 to 180</li> <li><strong>Histology_slides_4of5 :</strong> histological sections for individuals numbered 196 to 270</li> <li><strong>Histology_slides_5of5 :</strong> histological sections for individuals numbered 271 to 334</li> </ul> </li> </ul> <p> </p> <p><strong>Data:</strong></p> <ul> <li><strong>Readings.zip :</strong> archive in zip format containing the stereology reading results of the ovarian histological slides. In this folder, three directories are available. <ul> <li><strong>Calibration</strong> : Reading results of 4 different agents, with the first and last readings, as well as the Qupath scripts used.</li> <li><strong>Homogeneity</strong> : Reading results for 96 histological slides used to check the cellular homogeneity inter- and intra-gonad. These 96 slides belong to 16 fish, with three histological samples taken in the anterior (1), median (2) and posterior (3) sections of the left (G) and right (D) ovaries. A QuPath folder is also present, containing the scripts used.</li> <li><strong>Total </strong>: Reading results for 214 ovarian histological slides of the median position of either the left or right ovary. One median slide was read per sampled fish. A QuPath folder is also present, containing the scripts used.</li> </ul> </li> </ul> <ul> <li><strong>Macro_MULL_read_me.txt</strong> : a text file (.txt) listing the acronyms used in the <strong>Macro_MULL.xlsx</strong> file, as well as their meaning.</li> <li><strong>Macro_MULL.xlsx</strong> : Excel file (.xlsx) containing measurements of macroscopic parameters for all 214 fish sampled during this study. The information contained in this table is as follows: <ul> <li>Fish_id: identification of the fish. This id is identical to the name given to the pictures of the full ovaries (<strong>Macroscopic_pictures_Data</strong>)</li> <li>ICES _Division: International Council for the Exploration of the Sea (ICES) division where the fish was sampled in the Food and agricultural Organization of the United nations (FAO) fishing area 27</li> <li>ICES_statistical_rectangle : Statistical rectangle where the fish was sampled within the FAO fishing area 27</li> <li>Date: date the fish was caught (dd/mm/yyyy)</li> <li>Total_fish_length: total length of the fish (cm)</li> <li>Ungutted_fish_weight: total weight of the fish (g)</li> <li>Otolith_ID: unique identification number given to each sampled fish through the Imagine (Ellebode <em>et al.</em>, 2022) software used by IFREMER</li> <li>Parasite: presence (Y) or absence (N) of parasite in or on the fish</li> <li>age: age (in years) of the fish after analysis of the fish’s otolith. The IFREMER laboratory of Boulogne-sur-Mer (FRANCE) executed this analysis</li> <li>Visual_maturity : visually estimated maturity, after observation macroscopic criteria of the fish’s gonad with the naked eye, following the WKASMSF (ICES, 2018) scale</li> <li>Liver_weight: liver weight (g)</li> <li>Droite_gonad_weight : gonad weight (g) of right ovary</li> <li>Gauche_gonad_weight : gonad weight (g) of left ovary</li> <li>Sections: number of cross sections sampled for the individual</li> </ul> </li> </ul> <ul> <li><strong>Stereo_MULL_read_me.txt</strong> : a text file (.txt) listing the acronyms used in the <strong>Stereo_MULL.csv</strong> file, as well as their meaning.</li> <li><strong>Stereo_MULL.csv</strong> : a text data file (.csv) of the stereology count results of 294 slides read during this study. Among these slides, 96 were read to test the homogeneity distribution of different cell types found throughout each ovary (16 fish with 6 histological sections : a median, an anterior and a posterior histological section, for both ovaries), slides were read by multiple agents for calibration purposes (see <strong>Calibration</strong> folder for reading results of the 4 agents). Finally, 214 median histological ovarian slides were read. The information contained in this table is as follows: <ul> <li>cell_type: structure identified for one sample point (for the abbreviations, see Heude-Berthelin <em>et al.</em> 2023)</li> <li>idpt: identification number of the sampling point</li> <li>id: unique complex identification number of the sampling point generated by combining the x and y coordinates</li> <li>x: x coordinate of the sampling point</li> <li>y: y coordinate of the sampling point</li> <li>reading: Indicates if the reading data was used to test cellular homogeneity (Homogeneity) or to the sexual maturity phase</li> <li>slideid: identification number of the digitized histological slide that was used for the stereological count. Shares the same 12 first characters with <strong>Fish_id</strong></li> </ul> </li> </ul>
Macroscopic, histological and stereological image dataset of the Striped red mullet (Mullus surmuletus) ovaries from the Bay of Biscay (ICES area 27.7.g,j & 27.8.a-c) stock
<p><strong>Contents: </strong></p> <p>This dataset can be completed with the : <strong>Macroscopic, histological and stereological image dataset of the Striped red mullet (<em>Mullus surmuletus</em>) ovaries from the English Channel (ICES area 27.7.d) stock</strong>, which can also be found on the Zenodo repository.</p> <p>This dataset contains the macroscopic and histological images of the ovaries of 103 Striped red mullet (female, <em>Mullus surmuletus</em>, Linnaeus 1758) collected from the Bay of Biscay stock (ICES areas 27.7.j,g & 27.8.a-c) in November 2020 (n=9), May 2021 (n=11), June 2021(n=7), July 2021 (n=15), September (n=15), October 2021 (n=3), November 2021 (n=27) and February 2022 (n=15).</p> <p> </p> <p><strong>Images:</strong></p> <ul> <li><strong>Macroscopic_pictures.zip: </strong>archive in zip format of 290 pictures (.JPG; 2Mo-8Mo; JPG; 350pp) from 103 female Striped red mullets dissected during this study. Each photo was taken with a digital camera (no flash). For each individual, up to three pictures were taken when possible (Le Meleder <em>et al.</em>, 2022) with : <ul> <li>one picture of the entire fish with its abdominal cavity open with the ovaries in view</li> <li>one picture of the whole fish with the ovaries outside of the abdominal cavity</li> <li>one picture of the ovaries</li> <li>the name of the picture is the same as the fish’s ID number.</li> </ul> </li> </ul> <ul> <li><strong>Histology_slides.zip:</strong> archive in zip format containing the ovarian histological slides digitized using an Olympus V120 slide scanner, x20 lens. The pictures (.vsi from the OlympusVSI format) are of the 264 histological slides acquired during this study. Data was split for smaller size downloads : <ul> <li><strong>Histology_slides_1of3 :</strong> histological sections for individuals numbered 062 to 094</li> <li><strong>Histology_slides_2of3 :</strong> histological sections for individuals numbered 100 to 250</li> <li><strong>Histology_slides_3of3 :</strong> histological sections for individuals numbered 290 to 304</li> </ul> </li> </ul> <p> </p> <p><strong>Data:</strong></p> <ul> <li><strong>Readings.zip:</strong> archive in zip format containing the stereology reading results of the ovarian histological slides. In this folder, three directories are available. <ul> <li><strong>Calibration </strong>: Reading results of 4 different agents, with the first and last readings, as well as the Qupath scripts used<strong>.</strong></li> <li><strong>Homogeneity</strong> : Reading results for 84 histological slides used to check the cellular homogeneity inter- and intra-gonad. These 84 slides belong to 14 fish, with three histological samples taken in the anterior (1), median (2) and posterior (3) sections of the left (G) and right (D) ovaries. A QuPath folder is also present, containing the scripts used.</li> <li><strong>Total</strong> : Reading results for 103 ovarian histological slides of the median position of either the left or right ovary. One median slide was read per sampled fish. A QuPath folder is also present, containing the scripts used.</li> </ul> </li> </ul> <ul> <li><strong>Macro_MULL_read_me.txt</strong> : a text file (.txt) listing the acronyms used in the <strong>Macro_MULL.xlsx</strong> file, as well as their meaning.</li> <li><strong>Macro_MULL.xlsx</strong> : Excel file (.xlsx) containing measurements of macroscopic parameters for all 103 fish sampled during this study. The information contained in this table is as follows: <ul> <li>Fish_id: identification of the fish. This id is identical to the name given to the pictures of the full ovaries (<strong>Macroscopic_pictures_Data</strong>)</li> <li>ICES _Division: International Council for the Exploration of the Sea (ICES) division where the fish was sampled in the Food and agricultural Organization of the United nations (FAO) fishing area 27</li> <li>ICES_statistical_rectangle : Statistical rectangle where the fish was sampled within the FAO fishing area 27</li> <li>Date: date the fish was caught (dd/mm/yyyy)</li> <li>Total_fish_length: total length of the fish (cm)</li> <li>Ungutted_fish_weight: total weight of the fish (g)</li> <li>Otolith_ID: unique identification number given to each sampled fish through the Imagine (Ellebode <em>et al.</em>, 2022) software used by IFREMER</li> <li>Parasite: presence (Y) or absence (N) of parasite in or on the fish</li> <li>age: age (in years) of the fish after analysis of the fish’s otolith. The IFREMER laboratory of Boulogne-sur-Mer (FRANCE) executed this analysis</li> <li>Visual_maturity : visually estimated maturity, after observation macroscopic criteria of the fish’s gonad with the naked eye, following the WKASMSF (ICES, 2018) scale</li> <li>Liver_weight: liver weight (g)</li> <li>Droite_gonad_weight : gonad weight (g) of right ovary</li> <li>Gauche_gonad_weight : gonad weight (g) of left ovary</li> <li>Sections: number of cross sections sampled for the individual</li> </ul> </li> </ul> <ul> <li><strong>Stereo_MULL_read_me.txt</strong> : a text file (.txt) listing the acronyms used in the <strong>Stereo_MULL.csv</strong> file, as well as their meaning.</li> <li><strong>Stereo_MULL.csv</strong> : a text data file (.csv) of the stereology count results of 173 slides read during this study. Among these slides, 84 were read to test the homogeneity distribution of different cell types found throughout each ovary (14 fish with 6 histological sections : a median, an anterior and a posterior histological section, for both ovaries), slides were read by multiple agents for calibration purposes (see <strong>Calibration</strong> folder for reading results of the 4 agents). Finally, 103 median histological ovarian slides were read. The information contained in this table is as follows: <ul> <li>cell_type: structure identified for one sample point (for the abbreviations, see Heude-Berthelin <em>et al.</em> 2023)</li> <li>idpt: identification number of the sampling point</li> <li>id: unique complex identification number of the sampling point generated by combining the x and y coordinates</li> <li>x: x coordinate of the sampling point</li> <li>y: y coordinate of the sampling point</li> <li>reading: Indicates if the reading data was used to test cellular homogeneity (Homogeneity) or to the sexual maturity phase</li> <li>slideid: identification number of the digitized histological slide that was used for the stereological count. Shares the same 12 first characters with <strong>Fish_id</strong></li> </ul> </li> </ul>
Raw data for Development of Germline Progenitors in Larval Queen Honeybee ovaries
<p>This repository contains raw files for images relating to a publication of honeybee ovary development. That work is Cullen, Delargy and Dearden 2024, <strong><span>Development of Germline Progenitors in Larval Queen Honeybee ovaries. </span></strong><span>The data is organised in folders relate to each figure, and is in .oir format, a raw data format produced by Olympus confocal systems. This data file format is able to be read by FIJI.</span></p>
Macroscopic, histological and stereological image dataset of Megrim (Lepidorhombus whiffiagonis) ovaries from the ICES Celtic Seas, south of Greater North sea or Bay of Biscay Ecoregions
<p><strong>Contents: </strong></p> <p>This dataset contains the macroscopic and histological images of the ovaries of 202 Megrim (female, <em>Lepidorhombus whiffiagonis</em>, Walbaum, 1792) collected from the ICES Celtic Seas, south Greater North sea or Bay of Biscay Ecoregions (Eco) in November 2019 (n=25; Eco=7h & 7j), November 2020 (n=14, Eco=7h & 7j), December 2020 (n=1, Eco=7h), May 2021 (n=15, Eco=7h & 7g), June 2021 (n=15, Eco=7h), July 2021 (n=15, Eco=7h & 7e), October 2021 (n=15, Eco=7g & 7f), October 2021 (n=6, Eco=8a & 8b & 8c), November 2021 (n=6, Eco=8a & 8b), November 2021 (n=15, Eco=7j), December 2021 (n=15, Eco=7e & 7g), January 2022 (n=15, Eco=7f), February 2022 (n=15, Eco=7g), March 2022 (n=15, Eco=7g) and May 2022 (n=15, Eco=7g).</p> <p> </p> <p><strong>Images:</strong></p> <ul> <li><strong>Macroscopic_pictures.zip: </strong>archive in zip format of 549 pictures (.JPG; 2Mo-8Mo; JPG; 350pp) from 202 female megrim dissected during this study. Each photo was taken with a digital camera (no flash). For each individual, up to three pictures were taken when possible (Le Meleder <em>et al.</em>, 2022) with : <ul> <li>one picture of the entire fish with its abdominal cavity open with the ovaries in view</li> <li>one picture of the whole fish with the ovaries outside of the abdominal cavity</li> <li>one picture of the ovaries</li> <li>the name of the picture is the same as the fish's ID number.</li> </ul> </li> <li><strong>Histology_slides.zip :</strong> archive in zip format containing the ovarian histological slides digitized using an Aperio CS (Scan Scope Console software, v.10.2.0.2352), x20 lens. The whole slide images (.svs) are of the 461 histological slides acquired during this study. </li> </ul> <p> </p> <p><strong>Data:</strong></p> <ul> <li><strong>Readings.zip :</strong> archive in zip format containing the stereology reading results of the ovarian histological slides. In this folder, three directories are available. <ul> <li><strong>Calibration</strong> : Reading results of 3 different agents, with the first and last readings, as well as the QuPath scripts used.</li> <li><strong>Homogeneity</strong> : Reading results for 102 histological slides used to check the cellular homogeneity inter- and intra-gonad. These 102 slides belong to 17 fish, with three histological samples taken in the anterior (1), median (2) and posterior (3) sections of the left (G) and right (D) ovaries. A QuPath folder is also present, containing the scripts used.</li> <li><strong>Total </strong>: Reading results for 202 ovarian histological slides of the median position of either the left or right ovary. One median slide was read per sampled fish. A QuPath folder is also present, containing the scripts used.</li> </ul> </li> <li><strong>Macro_WHI_read_me.txt</strong> : a text file (.txt) listing the acronyms used in the <strong>Macro_WHI.xlsx</strong> file, as well as their meaning.</li> <li><strong>Macro_WHI.xlsx</strong> : Excel file (.xlsx) containing measurements of macroscopic parameters for all 202 fish sampled during this study. The information contained in this table is as follows: <ul> <li>Fish_id: identification of the fish. This id is identical to the name given to the pictures of the full ovaries (<strong>Macroscopic_pictures_Data</strong>)</li> <li>ICES _Division: International Council for the Exploration of the Sea (ICES) division where the fish was sampled in the Food and agricultural Organization of the United nations (FAO) fishing area 27</li> <li>ICES_statistical_rectangle : Statistical rectangle where the fish was sampled within the FAO fishing area 27</li> <li>Date: date the fish was caught (dd/mm/yyyy)</li> <li>Total_fish_length: total length of the fish (cm)</li> <li>Ungutted_fish_weight: total weight of the fish (g)</li> <li>Otolith_ID: unique identification number given to each sampled fish through the Imagine (Ellebode <em>et al.</em>, 2022) software used by IFREMER</li> <li>Parasite: presence (Y) or absence (N) of parasite in or on the fish</li> <li>age: age (in years) of the fish after analysis of the fish's otolith. The IFREMER laboratory of Boulogne-sur-Mer (FRANCE) executed this analysis</li> <li>Visual_maturity : visually estimated maturity, after observation macroscopic criteria of the fish's gonad with the naked eye, following the WKASMSF (ICES, 2018) scale</li> <li>Liver_weight: liver weight (g)</li> <li>Droite_gonad_weight : gonad weight (g) of right ovary</li> <li>Gauche_gonad_weight : gonad weight (g) of left ovary</li> <li>Sections: number of cross sections sampled for the individual</li> </ul> </li> <li><strong>Stereo_WHI_read_me.txt</strong> : a text file (.txt) listing the acronyms used in the <strong>Stereo_WHI.csv</strong> file, as well as their meaning.</li> <li><strong>Stereo_WHI.csv</strong> : a text data file (.csv) of the stereology count results of 287 slides read during this study. Among these slides, 102 were read to test the homogeneity distribution of different cell types found throughout each ovary (17 fish with 6 histological sections : a median, an anterior and a posterior histological section, for both ovaries), slides were read by multiple agents for calibration purposes (see <strong>Calibration</strong> folder for reading results of the 3 agents). Finally, 202 median histological ovarian slides were read. The information contained in this table is as follows: <ul> <li>cell_type: structure identified for one sample point (for the abbreviations, see Heude-Berthelin <em>et al.</em> 2023)</li> <li>idpt: identification number of the sampling point</li> <li>id: unique complex identification number of the sampling point generated by combining the x and y coordinates</li> <li>x: x coordinate of the sampling point</li> <li>y: y coordinate of the sampling point</li> <li>reading: Indicates if the reading data was used to test cellular homogeneity (Homogeneity) or to the sexual maturity phase</li> <li>slideid: identification number of the digitized histological slide that was used for the stereological count. Shares the same 12 first characters with <strong>Fish_id</strong></li> </ul> </li> </ul> <p> </p> <p><strong>Contact :</strong></p> <p>This dataset was established under the MATO (MATurité Objectif des poissons par l'histologie quantitative) project, during the PhD of Carine Sauger (October 2021-2023), financed by France Fillière Pêche (FFP/2020/AM/MF/109), under the supervision of IFREMER (Institut Français de Recherche pour l'Exploitation de la Mer) and BOREA (Biologie des Organismes et Ecosystèmes Aquatiques), and with the collaboration of a research facility from the University of Caen-Normandie : CMABIO3 (Centre de Microscopie Appliquée à la Biologie). For any enquiries, please contact: carine.sauger@gmail.com or laurent.dubroca@ifremer.fr</p>
Assembled transcriptomes of ovary, testis, and brain (male and female) of Amphibolurus muricatus (jacky dragon) generated using Trinity v2.11.0
<p><strong><em>A. muricatus</em> transcriptome assemblies generated using Trinity v2.11.0 (Haas et al. 2013; Grabherr et al. 2011; Henschel et al. 2012)</strong><br> • Amphibolurus-muricatus_brain.fa.tar.gz: Combined Trinity assembly of <em>A. muricatus</em> brain (male and female).<br> • Amphibolurus-muricatus_combined.fa.tar.gz: Combined Trinity assembly of <em>A. muricatus</em> ovary, testis, and brain (male and female).<br> • Amphibolurus-muricatus_female_brain.fa.tar.gz: Trinity assembly of female <em>A. muricatus</em> brain.<br> • Amphibolurus-muricatus_male_brain.fa.tar.gz: Trinity assembly of male <em>A. muricatus</em> brain.<br> • Amphibolurus-muricatus_ovary.fa.tar.gz: Trinity assembly of <em>A. muricatus</em> ovary.<br> • Amphibolurus-muricatus_testis.fa.tar.gz: Trinity assembly of <em>A. muricatus</em> testis.</p> <p> </p> <p><strong>References</strong></p> <ul> <li>Grabherr, M.G., B.J. Haas, M. Yassour, J.Z. Levin, D.A. Thompson et al., 2011 Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 29 (7):644-652.</li> <li>Haas, B.J., A. Papanicolaou, M. Yassour, M. Grabherr, P.D. Blood et al., 2013 De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat Protoc 8 (8):1494-1512.</li> <li>Henschel, R., M. Lieber, L.-S. Wu, P.M. Nista, B.J. Haas et al., 2012 Trinity RNA-Seq assembler performance optimization, pp. 45 in Proceedings of the 1st Conference of the Extreme Science and Engineering Discovery Environment: Bridging from the eXtreme to the campus and beyond. Association for Computing Machinery, Chicag, IL, USA.</li> </ul> <p> </p>
Centripetal migration in Drosophila ovary I: wild type timelapse & milestones pt1
<p>Timelapse imaging data tracking inward migration of follicle cells during centripetal migration in Drosophila ovary. </p> <p>Part of data supporting Figs 2, S1 of “Two phases for centripetal migration of Drosophila melanogaster follicle cells: initial ingression followed by epithelial migration”</p> <p>DOI: 10.1242/dev.200492</p> <p> •Timelapse imaging data of wild type samples</p> <p> •Quantitative analysis of specific milestone morphologies</p> <p> •Analysis of distances between leader FC tips from opposite sides of egg chamber prior to Milestone VII in relevant samples</p>
Centripetal migration in Drosophila ovary IX: E-cadherin null clones pt2 & E-Cadherin germ cell RNAi pt 2
<p>Part of data supporting Figs 6, 7, S3, S6, S16 of “Two phases for centripetal migration of Drosophila melanogaster follicle cells: initial ingression followed by epithelial migration”<br> DOI: 10.1242/dev.200492</p> <p><strong>Data file descriptions:</strong></p> <ul> <li><strong>“FRT G13 mitotic clones” 14.6 GB</strong></li> </ul> <p> Fixed sample image data for clones of cells with E-Cadherin mutant or control mitotic clones</p> <ul> <li><strong>“GC RNAi flipout timelapse data pt2” 28.92GB</strong></li> </ul> <p> Timelapse image data for clones of germ cells with E-Cadherin knockdown</p> <ul> <li><strong> “Image analysis of ring canals-fixed G13 control” 6 KB</strong></li> </ul> <p> Evaluation of fixed samples for ring canal position just prior to stage 11, nurse cell dumping, using</p> <ul> <li><strong>“Immuno Shg LOF clonal analysis” 98 KB</strong></li> </ul> <p> Preliminary evaluation of sample image with clones of cells with E-Cadherin mutant or control mitotic clones</p> <ul> <li><strong>“Live GC RNAi clonal data Prelim Eval” 25.2 MB</strong></li> </ul> <p> Preliminary evaluation of germ cell E-Cadherin knockdown samples</p> <p> </p>
Centripetal migration in Drosophila ovary X: E-Cadherin germ cell RNAi pt 1
<p>Part of data supporting Fig S16 of “Two phases for centripetal migration of Drosophila melanogaster follicle cells: initial ingression followed by epithelial migration”</p> <p>DOI: 10.1242/dev.200492</p> <p>Data description:</p> <ul> <li><strong>“GC RNAi flipout timelapse data pt1” 38 GB</strong></li> </ul> <p> Timelapse image data for clones of germ cells with E-Cadherin knockdown</p> <ul> <li><strong>“Live GC RNAi clonal data Prelim Eval” 25.2 MB</strong></li> </ul> <p> Preliminary evaluation of all germ cell E-Cadherin knockdown samples</p>
Centripetal migration in Drosophila ovary VIII: E-cadherin null mitotic clones pt1
<p>Data supporting Figs. 6, 7, S6 of “Two phases for centripetal migration of Drosophila melanogaster follicle cells: initial ingression followed by epithelial migration”</p> <p>DOI: 10.1242/dev.200492</p> <ul> <li><strong>“Immuno Shg LOF clonal analysis” 98 KB</strong></li> </ul> <p> Preliminary evaluation of sample image with clones of cells with E-Cadherin mutant or control mitotic clones</p> <ul> <li><strong>“Mixed control and shg mutant mitotic clones” 44.1Gb </strong></li> </ul> <p> Fixed sample image data for clones of cells with E-Cadherin mutant or control mitotic clones</p>
Centripetal migration in Drosophila ovary VII: E-cadherin RNAi clones in follicle cells timelapse
<p>Data supporting Figs. 5, S7, S8, S9, S10, S11, S12, S13, S14, S15 of “Two phases for centripetal migration of Drosophila melanogaster follicle cells: initial ingression followed by epithelial migration”</p> <p>DOI: 10.1242/dev.200492</p> <ul> <li><strong>“FC RNAi flipout timelapse data complete” 43.53GB</strong></li> </ul> <p> Timelapse image data for clones of follicle cells with E-Cadherin knockdown</p> <ul> <li><strong>“Live FC RNAi Clonal Data prelim evaluation” 22.1 MB</strong></li> </ul> <p> Preliminary evaluation of follicle cell E-Cadherin knockdown samples</p> <ul> <li><strong>“RNAi clone M2-M3-M5 quant” 12 KB</strong></li> </ul> <p> Quantitative data from specific milestones for clones of follicle cells with E-Cadherin knockdown</p>
Predictive nano-QSAR modeling of the cytotoxicity using epithelial cells obtained from Chinese hamster ovary (CHO-K1 cell line) for hybrid TiO2-based nanomaterials
<p>Results obtained from developed model indicated that the cytotoxicity of hybrid TiO2-based nanomaterials is related to additive electronegativity (χmix) of studied nanomaterials that are indirectly related to the electron generation and ROS formation. ROS production is the most common toxicity cause as discussed in the literature in the case of nanoparticles. The high efficiency of surface modified TiO2-based semiconductors can be attributed to the involvement of TiO2 band gap (Eg) excitation and absence of noble metals at the TiO2 surface. It can be expected that noble metals (i.e. Pd/Pt) may trap holes (h+), at the same time photo-generated electrons can be then transferred from the valence band to the conduction band of TiO2 and to its surface where redox processes were initiated. Thus, observed reduction of the electron–hole pair recombination influences the reactive oxygen species (ROS) formation and the photocatalytic redox process initiation.</p> <p>Since the electronegativity was positively correlated with the cytotoxicity it can be expected that some ions are released from the TiO2 surface easier than others.</p>
Text-fig. 9. The drawing shows the ratio of epigynous and hypogenous flowers in Zliv-Řídká Blana mesofossil flora. The ovary is inferior, and the flower is epigynous in 17 taxa. The ovary is superior, and the flower is hypogenous in 20 taxa. in Plant Mesofossils From The Late Cretaceous Klikov Formation, The Czech Republic
Text-fig. 9. The drawing shows the ratio of epigynous and hypogenous flowers in Zliv-Řídká Blana mesofossil flora. The ovary is inferior, and the flower is epigynous in 17 taxa. The ovary is superior, and the flower is hypogenous in 20 taxa.
Text-fig. 5. SRXTM images of Miranthus elegans gen. et sp. nov.; Mira locality, Portugal. a, b: Transverse sections of flower (a, orthoslice xy0665 close to the apex of placenta; b, orthoslice xy0800 in middle part of placenta) showing remains of calyx with distinct bundles (arrows), ovary wall (ow) and numerous ovules (ov) on the central mushroom-shaped globose placenta (pl) with central column (cc). c: Transverse section of flower (orthoslice xy0620) through perianth and ovary (ow) at a level above the placenta showing ovules (ov) and cellular preservation of the sepal bundles (arrows shown for one sepal); note abaxial surface of sepals with thick-walled epidermal cells, thick cuticle, and fine pointed verrucae. d: Longitudinal section of flower (orthoslice xz0500) showing perigynous position of calyx and semi-inferior ovary (ow, ovary wall) with a central placenta (pl), central column (cc) and numerous ovules (ov); note spiny verrucae on abaxial surface of calyx lobes. Specimens, Mira 100-S153145 (a, b), Mira 100-S170155 (c, d, holotype). Scale bars = 600 µm (a–d). in Early Flowers Of Primuloid Ericales From The Late Cretaceous Of Portugal And Their Ecological And Phytogeographic Implications
Text-fig. 5. SRXTM images of Miranthus elegans gen. et sp. nov.; Mira locality, Portugal. a, b: Transverse sections of flower (a, orthoslice xy0665 close to the apex of placenta; b, orthoslice xy0800 in middle part of placenta) showing remains of calyx with distinct bundles (arrows), ovary wall (ow) and numerous ovules (ov) on the central mushroom-shaped globose placenta (pl) with central column (cc). c: Transverse section of flower (orthoslice xy0620) through perianth and ovary (ow) at a level above the placenta showing ovules (ov) and cellular preservation of the sepal bundles (arrows shown for one sepal); note abaxial surface of sepals with thick-walled epidermal cells, thick cuticle, and fine pointed verrucae. d: Longitudinal section of flower (orthoslice xz0500) showing perigynous position of calyx and semi-inferior ovary (ow, ovary wall) with a central placenta (pl), central column (cc) and numerous ovules (ov); note spiny verrucae on abaxial surface of calyx lobes. Specimens, Mira 100-S153145 (a, b), Mira 100-S170155 (c, d, holotype). Scale bars = 600 µm (a–d).
Text-fig. 7. SEM (a) and SRXTM (b–e) images of Miranthus kvacekii sp. nov.; Mira locality, Portugal. a: Lateral view of flower bud showing corolla lobes extending beyond calyx; note surface of pedicel, calyx and corolla with small equiaxial epidermal cells and indumentum of densely spaced, short stiff trichomes. b, c: Longitudinal sections through floral bud in two directions perpendicular to each other (a, orthoslice yz1024; b, orthoslice xz0950) showing corolla (co), calyx (ca), stamens (st) and semi-inferior ovary with thin ovary wall (ow) and central mushroom-shaped globose placenta (pl) bearing numerous ovules (ov). d, e: Transverse sections through floral bud above placenta (d, orthoslice xy0915; e, orthoslice xy1095) showing calyx (ca), corolla (co), ovary wall (ow) and ovules (ov); yellow outlines indicate the positions of anthers (d) and filaments (e); orange outlines indicate the position of three of the possible staminodes. Specimen, Mira 100-S170157 (a–e, holotype). Scale bars = 600 µm (a–c), 300 µm (d, e). in Early Flowers Of Primuloid Ericales From The Late Cretaceous Of Portugal And Their Ecological And Phytogeographic Implications
Text-fig. 7. SEM (a) and SRXTM (b–e) images of Miranthus kvacekii sp. nov.; Mira locality, Portugal. a: Lateral view of flower bud showing corolla lobes extending beyond calyx; note surface of pedicel, calyx and corolla with small equiaxial epidermal cells and indumentum of densely spaced, short stiff trichomes. b, c: Longitudinal sections through floral bud in two directions perpendicular to each other (a, orthoslice yz1024; b, orthoslice xz0950) showing corolla (co), calyx (ca), stamens (st) and semi-inferior ovary with thin ovary wall (ow) and central mushroom-shaped globose placenta (pl) bearing numerous ovules (ov). d, e: Transverse sections through floral bud above placenta (d, orthoslice xy0915; e, orthoslice xy1095) showing calyx (ca), corolla (co), ovary wall (ow) and ovules (ov); yellow outlines indicate the positions of anthers (d) and filaments (e); orange outlines indicate the position of three of the possible staminodes. Specimen, Mira 100-S170157 (a–e, holotype). Scale bars = 600 µm (a–c), 300 µm (d, e).
Text-fig. 2. SEM images of Miranthus elegans gen. et sp. nov.; Mira locality, Portugal. a, b: Flowers in oblique lateral view showing remains of calyx and slightly semi-inferior ovary with elongated apical style (a); note larger openings in the floral tissue (asterisk) interpreted as schizogenous secretory cavities and the stomata-like secretory structures on the upper portion of the ovary (arrows) that are interpreted as nectariferous (b). c: Detail of ovary surface showing secretory stomata-like structures (arrows). d: Flower in lateral view showing fragmentary calyx and broken slightly semi-inferior ovary with secretory stomata-like structures; note the point of attachment of the central placenta (pl). e: Cluster of seeds removed from the ovary in (d) showing reticulate surface. f: Outer (abaxial) surface of calyx lobe showing the slightly pointed papillae and scattered, fine trichomes (arrows). g: Triaperturate pollen grains from the ovary surface. Specimens, Mira 100-S153146 (a, b), Mira 100-S170155 (c), Mira 100-S101266 (d, e), Mira 105-S100732 (f), Mira 100-S170125 (g). Scale bars = 600 µm (a, b, d), 300 µm (f), 100 µm (c, e), 10 µm (g). in Early Flowers Of Primuloid Ericales From The Late Cretaceous Of Portugal And Their Ecological And Phytogeographic Implications
Text-fig. 2. SEM images of Miranthus elegans gen. et sp. nov.; Mira locality, Portugal. a, b: Flowers in oblique lateral view showing remains of calyx and slightly semi-inferior ovary with elongated apical style (a); note larger openings in the floral tissue (asterisk) interpreted as schizogenous secretory cavities and the stomata-like secretory structures on the upper portion of the ovary (arrows) that are interpreted as nectariferous (b). c: Detail of ovary surface showing secretory stomata-like structures (arrows). d: Flower in lateral view showing fragmentary calyx and broken slightly semi-inferior ovary with secretory stomata-like structures; note the point of attachment of the central placenta (pl). e: Cluster of seeds removed from the ovary in (d) showing reticulate surface. f: Outer (abaxial) surface of calyx lobe showing the slightly pointed papillae and scattered, fine trichomes (arrows). g: Triaperturate pollen grains from the ovary surface. Specimens, Mira 100-S153146 (a, b), Mira 100-S170155 (c), Mira 100-S101266 (d, e), Mira 105-S100732 (f), Mira 100-S170125 (g). Scale bars = 600 µm (a, b, d), 300 µm (f), 100 µm (c, e), 10 µm (g).
Text-fig. 1. SEM images of flowers of Miranthus elegans gen. et sp. nov.; Mira locality, Portugal. a, b: Flowers in lateral view showing elongated pedicel, narrowly triangular sepals and elongated protruding style (a); note the large openings in the floral tissue and pedicel (asterisks) interpreted as schizogenous secretory cavities. c: Flower in lateral view with portion of the calyx missing exposing the ovary wall and slightly raised nectariferous ring with probable stomata-like secretory structures (arrow). d: Flower in lateral view showing long pedicel and three of the five tepals; note the elongated narrowly triangular form of the sepals. e: Flower in oblique lateral view with portion of the calyx missing exposing the ovary and elongated style. f, g: Flowers in apical view showing the bases of five sepals (f) and apex of the five-parted ovary; note larger openings in the floral tissue (asterisk) interpreted as schizogenous secretory cavities. Specimens, Mira 100-S170155 (a, holotype), Mira 100-S153145 (b, c, g), Mira 100- S101267 (d), Mira 105-S100732 (e), Mira 100-S101268 (f). Scale bars = 600 µm (a–g). in Early Flowers Of Primuloid Ericales From The Late Cretaceous Of Portugal And Their Ecological And Phytogeographic Implications
Text-fig. 1. SEM images of flowers of Miranthus elegans gen. et sp. nov.; Mira locality, Portugal. a, b: Flowers in lateral view showing elongated pedicel, narrowly triangular sepals and elongated protruding style (a); note the large openings in the floral tissue and pedicel (asterisks) interpreted as schizogenous secretory cavities. c: Flower in lateral view with portion of the calyx missing exposing the ovary wall and slightly raised nectariferous ring with probable stomata-like secretory structures (arrow). d: Flower in lateral view showing long pedicel and three of the five tepals; note the elongated narrowly triangular form of the sepals. e: Flower in oblique lateral view with portion of the calyx missing exposing the ovary and elongated style. f, g: Flowers in apical view showing the bases of five sepals (f) and apex of the five-parted ovary; note larger openings in the floral tissue (asterisk) interpreted as schizogenous secretory cavities. Specimens, Mira 100-S170155 (a, holotype), Mira 100-S153145 (b, c, g), Mira 100- S101267 (d), Mira 105-S100732 (e), Mira 100-S101268 (f). Scale bars = 600 µm (a–g).
Merged anvio profiles for Wolbachia MAGs from Culex pipiens midgut and ovary samples
<p>Anvi’o merged profile databases for <em>Wolbachia</em> MAGs from <em>Culex pipiens</em> midgut and ovary metagenomes. </p>
Рис. 2. Mukhina elegans (Mukhina, 1981) (самка): А — трофико-сенсорный отΔеΛ теΛа; Б — поΛовая система; В — переΔний конец теΛа; Г — хвост; À — фрагмент кутикуΛы с боковым поΛем бп — боковое поΛе, да — ΔробиΛьный аппарат, в — вуΛьва, зм — заΔняя матка, кб — карΔиаΛьный буΛьбус, кск — кΛетки среΔней кишки, нк — нервное коΛьцо, пм — переΔняя матка, р — ректум, рт — ренетта, с — сперма, ск — среΔняя кишка, сп — семяприемник, ф — фазмиΔы, хс — хейΛостома, эп — экскреторная пора, я — яичник Fig. 2. Mukhina elegans (Mukhina, 1981) (female): A — trophic-sensory part of the body; B — the reproductive system; C — the front end of the body; G — the tail; D — fragment of the cuticle with a side field бп — side field, да — crushing apparatus, в — vulva, зм — posterior uterus, кб — cardial bulb, кск — cells of the mid-intestine, нк — nerve ring, пм — anterior uterus, р — rectum, рт — renetta с — sperm, ск — mid-intestin, сп — seminal receptacle, ф — phasmids, хс — cheilostoma, эп — excretory pore, я — ovary in A New Species Sp. Nov. (Nematoda, Cephalobidae) From Primorsky Region (Russia)
Рис. 2. Mukhina elegans (Mukhina, 1981) (самка): А — трофико-сенсорный отΔеΛ теΛа; Б — поΛовая система; В — переΔний конец теΛа; Г — хвост; À — фрагмент кутикуΛы с боковым поΛем бп — боковое поΛе, да — ΔробиΛьный аппарат, в — вуΛьва, зм — заΔняя матка, кб — карΔиаΛьный буΛьбус, кск — кΛетки среΔней кишки, нк — нервное коΛьцо, пм — переΔняя матка, р — ректум, рт — ренетта, с — сперма, ск — среΔняя кишка, сп — семяприемник, ф — фазмиΔы, хс — хейΛостома, эп — экскреторная пора, я — яичник Fig. 2. Mukhina elegans (Mukhina, 1981) (female): A — trophic-sensory part of the body; B — the reproductive system; C — the front end of the body; G — the tail; D — fragment of the cuticle with a side field бп — side field, да — crushing apparatus, в — vulva, зм — posterior uterus, кб — cardial bulb, кск — cells of the mid-intestine, нк — nerve ring, пм — anterior uterus, р — rectum, рт — renetta с — sperm, ск — mid-intestin, сп — seminal receptacle, ф — phasmids, хс — cheilostoma, эп — excretory pore, я — ovary
Рис. 1. Mukhina orientalis sp. nov. (самка): А — трофико-сенсорный отΔеΛ теΛа; Б — генитаΛьнокауΔаΛьный отΔеΛ теΛа; В — трофико-сенсорный отΔеΛ теΛа второй самки; Г — переΔний конец теΛа; À — хвост второй самки бп — боковое поΛе, да — ΔробиΛьный аппарат, в — вуΛьва, зм — заΔняя матка, кб — карΔиаΛьный буΛьбус, нк — нервное коΛьцо, пм — переΔняя матка, р — ректум, рт — ренетта, ск — среΔняя кишка, скλ — скΛероции кутикуΛы, сп — семяприемник, ф — фазмиΔы, хс — хейΛостома, эп — экскреторная пора, я — яичник Fig. 1. Mukhina orientalis sp. nov. (female): A — trophic-sensory part of the body; Б — genitalcaudal part of the body; В — trophic-sensory part of the body of the second female; Г — front end of the body; À — tail of the second female бп — side field, да — crushing apparatus, в — vulva, зм — posterior uterus, кб — cardial bulb, нк — nerve ring, пм — anterior uterus, р — rectum, ск — mid-intestine, скλ — sclerotic cuticle, сп — seminal receptacle, ф — phasmids, хс — cheilostoma, эп — excretory pore, я — ovary in A New Species Sp. Nov. (Nematoda, Cephalobidae) From Primorsky Region (Russia)
Рис. 1. Mukhina orientalis sp. nov. (самка): А — трофико-сенсорный отΔеΛ теΛа; Б — генитаΛьнокауΔаΛьный отΔеΛ теΛа; В — трофико-сенсорный отΔеΛ теΛа второй самки; Г — переΔний конец теΛа; À — хвост второй самки бп — боковое поΛе, да — ΔробиΛьный аппарат, в — вуΛьва, зм — заΔняя матка, кб — карΔиаΛьный буΛьбус, нк — нервное коΛьцо, пм — переΔняя матка, р — ректум, рт — ренетта, ск — среΔняя кишка, скλ — скΛероции кутикуΛы, сп — семяприемник, ф — фазмиΔы, хс — хейΛостома, эп — экскреторная пора, я — яичник Fig. 1. Mukhina orientalis sp. nov. (female): A — trophic-sensory part of the body; Б — genitalcaudal part of the body; В — trophic-sensory part of the body of the second female; Г — front end of the body; À — tail of the second female бп — side field, да — crushing apparatus, в — vulva, зм — posterior uterus, кб — cardial bulb, нк — nerve ring, пм — anterior uterus, р — rectum, ск — mid-intestine, скλ — sclerotic cuticle, сп — seminal receptacle, ф — phasmids, хс — cheilostoma, эп — excretory pore, я — ovary
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
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International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
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