cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0m32tcp
title: CIL:45965, Homo sapiens. In Cell Image Library

description: Plate 25962 - Phenotypic profiling attempts to summarize multiparametric, feature-based analysis of cellular phenotypes of each sample so that similarities between profiles reflect similarities between samples. This image set provides a basis for testing image-based profiling methods wrt. to their ability to distinguish the effects of small molecules.
 
Images
The images are of U2OS cells treated with each of 1600 known bioactive compounds and labeled with six labels that characterize seven organelles (the .cell-painting. assay).
 
This pilot experiment consists of 20 plates. Each plate has 384 wells and each well has 9 fields of view for a total of 69,120 fields of view. Each field was imaged in five channels (detection wavelengths), and each channel is stored as a separate, grayscale image file, so there are 345,600 image files in 16-bit TIFF format.
description: Gustafsdottir et al. (doi:10.1371/journal.pone.0080999) have developed a multiplex cytological profiling assay that "paints the cell" with as many fluorescent markers as possible without compromising our ability to extract rich, quantitative profiles in high throughput. The assay detects seven major cellular components. In a pilot screen of bioactive compounds, the assay detected a range of cellular phenotypes and it clustered compounds with similar annotated protein targets or chemical structure based on cytological profiles. The results demonstrate that the assay captures subtle patterns in the combination of morphological labels, thereby detecting the effects of chemical compounds even though their targets are not stained directly. This image-based assay provides an unbiased approach to characterize compound- and disease-associated cell states to support future probe discovery.

Using the cell-painting assay, the Broad Institute has assembled a reference dataset of profiles for U2OS osteosarcoma cells treated with ~30,000 compounds. The compound collection includes DOS-derived compounds (20,000), as well as chemically diverse MLI compounds with biologically diverse performance identified through analysis of PubChem (10,000), and known bioactive compounds to serve as landmarks (2,500). The DOS compounds consist of structurally diverse and stereochemically rich compounds with structures distinct from the current MLSMR. The compound collection also includes 267 distinct compounds nominated by MLPCN Centers from projects for which the Centers would like to identify new chemical series with similar activities.

The experiment consists of 413 microtiter plates. Each plate has 384 wells. Each well has 9 fields of view. Each field was imaged in five channels (detection wavelengths), and each channel is stored as a separate, grayscale 16-bit TIFF image file.
DOI: 10.15468/dl.p4ea7b
title: Occurrence Download

description: A dataset containing 36 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Nepal",
 "OccurrenceStatus is Present",
 "TaxonKey is Platanista gangetica"
 ]
}

 The dataset includes 36 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009696-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yyge4t
title: Occurrence Download

description: A dataset containing 35 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Romania",
 "TaxonKey is Alchemilla mollis"
 ]
}

 The dataset includes 35 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009697-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5522/04/30416359
title: DNA sequences of prophages identified in KL16 KPSC QECH strains sequenced as part of this study, in fasta format

description: Prophages identified in bacterial genomes following long-read sequencing using Phastest (v3.0)<sup> </sup>and Cenote-Taker 3 (v3.0.0b74, database version 228), from which unique putative prophage regions were screened using CheckV (v1.0.3), including only those identified as “intact” or “high quality” based on their completeness scores.The first three letters correspond to the unique last three letters of the nine KL16 KPSC strains in the analysis, followed by the contig in which the prophage sequence was identified, and its number/ID.
DOI: 10.5522/04/30416359.v1
title: DNA sequences of prophages identified in KL16 KPSC QECH strains sequenced as part of this study, in fasta format

description: Prophages identified in bacterial genomes following long-read sequencing using Phastest (v3.0)<sup> </sup>and Cenote-Taker 3 (v3.0.0b74, database version 228), from which unique putative prophage regions were screened using CheckV (v1.0.3), including only those identified as “intact” or “high quality” based on their completeness scores.The first three letters correspond to the unique last three letters of the nine KL16 KPSC strains in the analysis, followed by the contig in which the prophage sequence was identified, and its number/ID.
DOI: 10.24400/170160/sagsa_ggm_gab_10days_rl0005
title: Oceanic dealiasing GAB 10 Days
DOI: 10.15468/dl.acz9mm
title: Occurrence Download

description: A dataset listing the 144 species recorded in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Continent is Africa",
 "Country is Namibia",
 "Geometry POLYGON((14.44461 -19.43673,14.61871 -19.43104,14.62626 -19.35009,14.59871 -19.30984,14.54971 -19.31247,14.55234 -19.25691,15.25943 -19.25034,15.30665 -19.21701,15.31081 -19.26701,15.45407 -19.25971,16.71066 -19.50078,17.0255 -19.38798,17.1458 -19.19979,17.05544 -18.63202,17.15729 -18.63128,17.17467 -18.62072,17.13703 -18.53511,17.10308 -18.50485,16.89082 -18.48445,15.66872 -18.48161,15.62518 -18.51408,15.6178 -18.62552,15.09127 -18.56608,14.56949 -18.62143,14.55326 -18.65317,14.58061 -18.77163,14.60999 -18.80304,14.35192 -19.00544,14.32098 -19.08939,14.42024 -19.27491,14.4505 -19.31107,14.43217 -19.40239,14.44461 -19.43673))",
 "OccurrenceStatus is Present",
 "TaxonKey is one of (Mammalia, Aves, Squamata, Crocodylia, Testudines, Amphibia)"
 ]
}

 The dataset's 144 records were derived from 23 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009687-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6075/j018352m
title: CIL:45963, Homo sapiens. In Cell Image Library

description: Plate 25949 - Phenotypic profiling attempts to summarize multiparametric, feature-based analysis of cellular phenotypes of each sample so that similarities between profiles reflect similarities between samples. This image set provides a basis for testing image-based profiling methods wrt. to their ability to distinguish the effects of small molecules.
 
Images
The images are of U2OS cells treated with each of 1600 known bioactive compounds and labeled with six labels that characterize seven organelles (the .cell-painting. assay).
 
This pilot experiment consists of 20 plates. Each plate has 384 wells and each well has 9 fields of view for a total of 69,120 fields of view. Each field was imaged in five channels (detection wavelengths), and each channel is stored as a separate, grayscale image file, so there are 345,600 image files in 16-bit TIFF format.
description: Gustafsdottir et al. (doi:10.1371/journal.pone.0080999) have developed a multiplex cytological profiling assay that "paints the cell" with as many fluorescent markers as possible without compromising our ability to extract rich, quantitative profiles in high throughput. The assay detects seven major cellular components. In a pilot screen of bioactive compounds, the assay detected a range of cellular phenotypes and it clustered compounds with similar annotated protein targets or chemical structure based on cytological profiles. The results demonstrate that the assay captures subtle patterns in the combination of morphological labels, thereby detecting the effects of chemical compounds even though their targets are not stained directly. This image-based assay provides an unbiased approach to characterize compound- and disease-associated cell states to support future probe discovery.

Using the cell-painting assay, the Broad Institute has assembled a reference dataset of profiles for U2OS osteosarcoma cells treated with ~30,000 compounds. The compound collection includes DOS-derived compounds (20,000), as well as chemically diverse MLI compounds with biologically diverse performance identified through analysis of PubChem (10,000), and known bioactive compounds to serve as landmarks (2,500). The DOS compounds consist of structurally diverse and stereochemically rich compounds with structures distinct from the current MLSMR. The compound collection also includes 267 distinct compounds nominated by MLPCN Centers from projects for which the Centers would like to identify new chemical series with similar activities.

The experiment consists of 413 microtiter plates. Each plate has 384 wells. Each well has 9 fields of view. Each field was imaged in five channels (detection wavelengths), and each channel is stored as a separate, grayscale 16-bit TIFF image file.
DOI: 10.15468/dl.ywedhu
title: Occurrence Download

description: A dataset containing 246 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Trachia"
 ]
}

 The dataset includes 246 records from 26 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009698-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6075/j0rf5t2g
title: CIL:8468, Rattus, multipolar neuron. In Cell Image Library

description: Development of axon and dendritic arbors in cultured hippocampal neurons after 2 days in vitro. At this timepoint, many, but not all cells are polarized, evidenced by the absence of a long, slender axon. MAP2 staining (red) is becoming segregated to the dendrites, while microtubule staining (green) reveals both the axons and dendrites in the field of view. Nonneuronal cells (e.g. glia) are infrequent, but may also be present in this preparation. 

Detailed methods: Embryonic rat hippocampal neurons were prepared as previously described (see Kaech and Banker, 2006, Nat Protoc). Cells were prepared for fluorescent staining as previously described (Withers and Banker, 1998, in Culturing Nerve Cells, MIT Press). Briefly, cells were fixed (4% formaldehyde, 4% sucrose in phosphate buffered saline, pH 7.4), permeabilized with 0.25% Triton and immunostained for tubulin (monoclonal DM1A, from Sigma with Alexa 488 conjugated secondary, excitation, 494, emission, 519 [Invitrogen, Molecular Probes]) and MAP2 (polyclonal Ab266, from S. Halpain with d549 conjugated secondary, excitation, 555, emission, 568, Jackson Immunoresearch). Images were acquired with a Leica DMRA microscope with a 40X (HCX PL APO, NA 1.25) lens, Photometrics CoolSnap ES CCD camera and MetaMorph software. This merged image was generated with the MetaMorph color combine function.
description: Preparation: formaldehyde fixed tissue; detergent permeabilized
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope
Visualization methods: primary antibody plus labeled secondary antibody
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements
DOI: 10.7910/dvn/cey4pq
title: Replication Data for: "Advancing Internal Tide Correction for SWOT Cal/Val: The Role of Ocean Forecasts"

description: Python code to reproduce the analysis and figures in the manuscript "Advancing Internal Tide Correction for SWOT Cal/Val: The Role of Ocean Forecasts" submitted to Earth and Space Science.
DOI: 10.21227/n237-4e51
title: "lidar RHI 2D scan data"

description: "Lidar RHI Scan data"
DOI: 10.48788/dvua/rrogbk
title: Study of the electronic structure of Mn2-хCoxP2O7·5H2O at x=0.6, using X-ray photoelectron spectroscopy

description: The electronic structure peculiarities of diphosphate - Mn2-xCoxP2O7·5H2O, at x=0,6, have been studied out by the XPS spectroscopy.
DOI: 10.6084/m9.figshare.30425062
title: ARIEL-data

description: We develop a fast, omics-driven sample integration tool called ARIEL, which enables effortless landmark detection, spatial alignment and information transfer for multi-sample spatial transcriptomic data. ARIEL can be applied in diverse situation, including cross-individual, cross-platform, cross-resolution, cross-omics, and cross-disease scenarios.The detailed analysis procedures and results with jupyter notebook presented in this paper are available on the Read the Docs tutorial website: https://ariel-document.readthedocs.io/.<br>And the code repository of ARIEL is available at: https://github.com/shilab-ecnu/ARIEL.<br><br><br>
DOI: 10.6084/m9.figshare.30425062.v1
title: ARIEL-data

description: We develop a fast, omics-driven sample integration tool called ARIEL, which enables effortless landmark detection, spatial alignment and information transfer for multi-sample spatial transcriptomic data. ARIEL can be applied in diverse situation, including cross-individual, cross-platform, cross-resolution, cross-omics, and cross-disease scenarios.The detailed analysis procedures and results with jupyter notebook presented in this paper are available on the Read the Docs tutorial website: https://ariel-document.readthedocs.io/.<br>And the code repository of ARIEL is available at: https://github.com/shilab-ecnu/ARIEL.<br><br><br>
DOI: 10.5517/ccdc.csd.cc2pnm99
title: CCDC 2492471: Experimental Crystal Structure Determination

description: Related Article: K.A. Alekseeva, A.V. Gurbanov, M.S. Grigoriev, E.A. Sorokina, I.A. Kolesnik, M.H. Al-Douh, T. Hökelek, K.I. Hasanov|2025|Acta Crystallogr.,Sect.E:Cryst.Commun.|81|996|doi:10.1107/S2056989025008606
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.6075/j0v123t9
title: CIL:8467, Rattus, multipolar neuron. In Cell Image Library

description: Development of axon and dendritic arbors in cultured hippocampal neurons after 2 days in vitro. At this timepoint, many, but not all cells are polarized, evidenced by the absence of a long, slender axon. MAP2 staining (red) is becoming segregated to the dendrites, while microtubule staining (green) reveals both the axons and dendrites in the field of view. Nonneuronal cells (e.g. glia) are infrequent, but may also be present in this preparation. 

Detailed methods: Embryonic rat hippocampal neurons were prepared as previously described (see Kaech and Banker, 2006, Nat Protoc). Cells were prepared for fluorescent staining as previously described (Withers and Banker, 1998, in Culturing Nerve Cells, MIT Press). Briefly, cells were fixed (4% formaldehyde, 4% sucrose in phosphate buffered saline, pH 7.4), permeabilized with 0.25% Triton and immunostained for tubulin (monoclonal DM1A, from Sigma with Alexa 488 conjugated secondary, excitation, 494, emission, 519 [Invitrogen, Molecular Probes]) and MAP2 (polyclonal Ab266, from S. Halpain with d549 conjugated secondary, excitation, 555, emission, 568, Jackson Immunoresearch). Images were acquired with a Leica DMRA microscope with a 40X (HCX PL APO, NA 1.25) lens, Photometrics CoolSnap ES CCD camera and MetaMorph software. This merged image was generated with the MetaMorph color combine function.
description: Preparation: formaldehyde fixed tissue; detergent permeabilized
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope
Visualization methods: primary antibody plus labeled secondary antibody
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements
DOI: 10.5517/ccdc.csd.cc2pnnpq
title: CCDC 2492514: Experimental Crystal Structure Determination

description: Related Article: E.R. Shelukho, V.P. Zaytsev, V.N. Khrustalev, T. Hökelek, K.I. Hasanov, N.A. Guliyeva, T.A. Javadzade, M.H. Al-Douh|2025|Acta Crystallogr.,Sect.E:Cryst.Commun.|81|1000|doi:10.1107/S2056989025008618
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2pp0kz
title: CCDC 2492851: Experimental Crystal Structure Determination

description: Related Article: I. Terpeliuk, K. Znovjyak, S. Shova, O.V. Oksiuta, V.M. Amirkhanov, I.O. Fritsky, M. Seredyuk|2025|Acta Crystallogr.,Sect.E:Cryst.Commun.|81|991|doi:10.1107/S2056989025008655
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.6075/j0m044gg
title: CIL:8465, Rattus, multipolar neuron. In Cell Image Library

description: Development of axon and dendritic arbors in cultured hippocampal neurons after 2 days in vitro. At this timepoint, many, but not all cells are polarized, evidenced by the absence of a long, slender axon. MAP2 staining (red) is becoming segregated to the dendrites, while microtubule staining (green) reveals both the axons and dendrites in the field of view. Nonneuronal cells (e.g. glia) are infrequent, but may also be present in this preparation. 

Detailed methods: Embryonic rat hippocampal neurons were prepared as previously described (see Kaech and Banker, 2006, Nat Protoc). Cells were prepared for fluorescent staining as previously described (Withers and Banker, 1998, in Culturing Nerve Cells, MIT Press). Briefly, cells were fixed (4% formaldehyde, 4% sucrose in phosphate buffered saline, pH 7.4), permeabilized with 0.25% Triton and immunostained for tubulin (monoclonal DM1A, from Sigma with Alexa 488 conjugated secondary, excitation, 494, emission, 519 [Invitrogen, Molecular Probes]) and MAP2 (polyclonal Ab266, from S. Halpain with d549 conjugated secondary, excitation, 555, emission, 568, Jackson Immunoresearch). Images were acquired with a Leica DMRA microscope with a 40X (HCX PL APO, NA 1.25) lens, Photometrics CoolSnap ES CCD camera and MetaMorph software. This merged image was generated with the MetaMorph color combine function.
description: Preparation: formaldehyde fixed tissue; detergent permeabilized
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope
Visualization methods: primary antibody plus labeled secondary antibody
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements
DOI: 10.25505/fiz.icsd.cc2pppy1
title: CSD 2493514: Experimental Crystal Structure Determination

description: Related Article: T. Wolflehner, M. Weil|2025|Acta Crystallogr.,Sect.E:Cryst.Commun.|81|1008|doi:10.1107/S2056989025008722
description: An entry from the Inorganic Crystal Structure Database, the world’s repository for inorganic crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the joint CCDC and FIZ Karlsruhe Access Structures service and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.6075/j0p55mjw
title: CIL:8464, Rattus, multipolar neuron. In Cell Image Library

description: Development of axon and dendritic arbors in cultured hippocampal neurons after 2 days in vitro. At this timepoint, many, but not all cells are polarized, evidenced by the absence of a long, slender axon. MAP2 staining (red) is becoming segregated to the dendrites, while microtubule staining (green) reveals both the axons and dendrites in the field of view. Nonneuronal cells (e.g. glia) are infrequent, but may also be present in this preparation. 

Detailed methods: Embryonic rat hippocampal neurons were prepared as previously described (see Kaech and Banker, 2006, Nat Protoc). Cells were prepared for fluorescent staining as previously described (Withers and Banker, 1998, in Culturing Nerve Cells, MIT Press). Briefly, cells were fixed (4% formaldehyde, 4% sucrose in phosphate buffered saline, pH 7.4), permeabilized with 0.25% Triton and immunostained for tubulin (monoclonal DM1A, from Sigma with Alexa 488 conjugated secondary, excitation, 494, emission, 519 [Invitrogen, Molecular Probes]) and MAP2 (polyclonal Ab266, from S. Halpain with d549 conjugated secondary, excitation, 555, emission, 568, Jackson Immunoresearch). Images were acquired with a Leica DMRA microscope with a 40X (HCX PL APO, NA 1.25) lens, Photometrics CoolSnap ES CCD camera and MetaMorph software. This merged image was generated with the MetaMorph color combine function.
description: Preparation: formaldehyde fixed tissue; detergent permeabilized
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope
Visualization methods: primary antibody plus labeled secondary antibody
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements
DOI: 10.25505/fiz.icsd.cc2pppz2
title: CSD 2493515: Experimental Crystal Structure Determination

description: Related Article: T. Wolflehner, M. Weil|2025|Acta Crystallogr.,Sect.E:Cryst.Commun.|81|1008|doi:10.1107/S2056989025008722
description: An entry from the Inorganic Crystal Structure Database, the world’s repository for inorganic crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the joint CCDC and FIZ Karlsruhe Access Structures service and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.