cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j07d2srw
title: CIL:45991, Homo sapiens. In Cell Image Library

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.
description: Plate 26071 - 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.
DOI: 10.6075/j0v69h4p
title: CIL:45989, Homo sapiens. In Cell Image Library

description: Plate 26060 - 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: 10.6075/j09s1pnb
title: CIL:45988, Homo sapiens. In Cell Image Library

description: Plate 26058 - 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.9gvzra
title: Occurrence Download

description: A dataset containing 91 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Traumatophora"
 ]
}

 The dataset includes 91 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009726-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6075/j0nk3cmz
title: CIL:46004, Homo sapiens. In Cell Image Library

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.
description: Plate 26140 - 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.
DOI: 10.6075/j0bp0225
title: CIL:715, Necturus maculosus, nucleate erythrocyte. In Cell Image Library

description: X-ray analysis shows that the nucleated erythrocytes of the amphibian Necturus maculosus (Mud Puppy) contains more ordered chromatin than most nuclei. Here, chromatin fibers were isolated from N. maculosus erythrocyte nuclei using mild micrococcal nuclease digestion, fixed briefly with glutaraldehyde, applied to thin carbon films and negatively stained with methylamine tungstate. ~30 nm fibers are seen, some exhibiting short regions with apparent structural order.
description: Preparation: unembedded tissue; glutaraldehyde fixed tissue
Relation to intact cell: isolated subcellular component
Item type: transmission electron microscopy (TEM)
Imaging mode: illumination by electrons; detection of electrons
Parameter imaged: electron density
Source of contrast: elastic scattering
Visualization methods: other negative stain
Processing history: raw unprocessed data
DOI: 10.6075/j0bz652f
title: CIL:7106, Homo sapiens, neuron. In Cell Image Library

description: The protein MeCP2 binds to symmetrically methylated CpG dinucleotides and is thought to transmit the (generally) repressive signals encoded in DNA methylation patterns. Mutations in MeCP2 lead to Rett syndrome. Here, MeCP2-DNA complexes have been imaged by AFM (Digital Instruments Nanoscope) in air using human MeCP2 and an 828 bp DNA sequence containing several methylated CpGs. MeCP2 molecules appear as bright particles in AFM images. Volume measurements of the complexes suggest that MeCP2 monomers (circular particles) and dimers (larger elliptical particles) are present and suggest that MeCP2 binds DNA cooperatively. Other images in the grouped set show looped structures and large complexes containing multiple DNA strands and MeCP2 molecules. These configurations are likely promoted by the multiple independent DNA-binding domains of MeCP2 and relevant to the in vivo interactions between MeCP2 and chromatin.
description: Preparation: glutaraldehyde fixed tissue
Relation to intact cell: isolated subcellular component
Item type: recorded image
Imaging mode: microscopy; atomic force microscopy
Parameter imaged: specimen height
Source of contrast: specimen height
Processing history: unprocessed raw data
DOI: 10.6075/j0dv1j6g
title: CIL:717, Necturus maculosus, nucleate erythrocyte. In Cell Image Library

description: Preparation: unembedded tissue; glutaraldehyde fixed tissue
Relation to intact cell: isolated subcellular component
Item type: transmission electron microscopy (TEM)
Imaging mode: illumination by electrons; detection of electrons
Parameter imaged: electron density
Source of contrast: elastic scattering
Visualization methods: other negative stain
Processing history: raw unprocessed data
description: X-ray analysis shows that the nucleated erythrocytes of the amphibian Necturus maculosus (Mud Puppy) contains more ordered chromatin than most nuclei. Here, chromatin fibers were isolated from N. maculosus erythrocyte nuclei using mild micrococcal nuclease digestion, fixed briefly with glutaraldehyde, applied to thin carbon films and negatively stained with aurothioglucose. ~30 nm fibers are seen, some exhibiting short regions with apparent structural order.
DOI: 10.6075/j0b56j1m
title: CIL:714, Necturus maculosus, nucleate erythrocyte. In Cell Image Library

description: X-ray analysis shows that the nucleated erythrocytes of the amphibian Necturus maculosus (Mud Puppy) contains more ordered chromatin than most nuclei. Here, chromatin fibers were isolated from N. maculosus erythrocyte nuclei using mild micrococcal nuclease digestion, fixed briefly with glutaraldehyde, applied to thin carbon films and negatively stained with methylamine tungstate. ~30 nm fibers are seen, some exhibiting short regions with apparent structural order.
description: Preparation: unembedded tissue; glutaraldehyde fixed tissue
Relation to intact cell: isolated subcellular component
Item type: transmission electron microscopy (TEM)
Imaging mode: illumination by electrons; detection of electrons
Parameter imaged: electron density
Source of contrast: elastic scattering
Visualization methods: other negative stain
Processing history: raw unprocessed data
DOI: 10.6075/j0ms3s0m
title: CIL:713, Necturus maculosus, nucleate erythrocyte. In Cell Image Library

description: Preparation: unembedded tissue; glutaraldehyde fixed tissue
Relation to intact cell: isolated subcellular component
Item type: transmission electron microscopy (TEM)
Imaging mode: illumination by electrons; detection of electrons
Parameter imaged: electron density
Source of contrast: elastic scattering
Visualization methods: other negative stain
Processing history: raw unprocessed data
description: X-ray analysis shows that the nucleated erythrocytes of the amphibian Necturus maculosus (Mud Puppy) contains more ordered chromatin than most nuclei. Here, chromatin fibers were isolated from N. maculosus erythrocyte nuclei using mild micrococcal nuclease digestion, fixed briefly with glutaraldehyde, applied to thin carbon films and negatively stained with methylamine tungstate. ~30 nm fibers are seen, some exhibiting short regions with apparent structural order.
DOI: 10.6075/j0dj5dph
title: CIL:7109, Homo sapiens, neuron. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue
Relation to intact cell: isolated subcellular component
Item type: recorded image
Imaging mode: microscopy; atomic force microscopy
Parameter imaged: specimen height
Source of contrast: specimen height
Processing history: unprocessed raw data
description: The protein MeCP2 binds to symmetrically methylated CpG dinucleotides and is thought to transmit the (generally) repressive signals encoded in DNA methylation patterns. Mutations in MeCP2 lead to Rett syndrome. Here, MeCP2-DNA complexes have been imaged by AFM (Digital Instruments Nanoscope) in air using human MeCP2 and an 828 bp DNA sequence containing several methylated CpGs. MeCP2 molecules appear as bright particles in AFM images. Volume measurements of the complexes suggest that MeCP2 monomers (circular particles) and dimers (larger elliptical particles) are present and suggest that MeCP2 binds DNA cooperatively. Other images in the grouped set show looped structures and large complexes containing multiple DNA strands and MeCP2 molecules. These configurations are likely promoted by the multiple independent DNA-binding domains of MeCP2 and relevant to the in vivo interactions between MeCP2 and chromatin.
DOI: 10.15468/dl.yufmtz
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ptychomeria tenella"
 ]
}

 The dataset includes 5 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009727-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6075/j0hm57j8
title: CIL:7107, Homo sapiens, neuron. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue
Relation to intact cell: isolated subcellular component
Item type: recorded image
Imaging mode: microscopy; atomic force microscopy
Parameter imaged: specimen height
Source of contrast: specimen height
Processing history: unprocessed raw data
description: The protein MeCP2 binds to symmetrically methylated CpG dinucleotides and is thought to transmit the (generally) repressive signals encoded in DNA methylation patterns. Mutations in MeCP2 lead to Rett syndrome. Here, MeCP2-DNA complexes have been imaged by AFM (Digital Instruments Nanoscope) in air using human MeCP2 and an 828 bp DNA sequence containing several methylated CpGs. MeCP2 molecules appear as bright particles in AFM images. Volume measurements of the complexes suggest that MeCP2 monomers (circular particles) and dimers (larger elliptical particles) are present and suggest that MeCP2 binds DNA cooperatively. Other images in the grouped set show looped structures and large complexes containing multiple DNA strands and MeCP2 molecules. These configurations are likely promoted by the multiple independent DNA-binding domains of MeCP2 and relevant to the in vivo interactions between MeCP2 and chromatin.
DOI: 10.6075/j08g8jsq
title: CIL:7111, Homo sapiens, neuron. In Cell Image Library

description: The protein MeCP2 binds to symmetrically methylated CpG dinucleotides and is thought to transmit the (generally) repressive signals encoded in DNA methylation patterns. Mutations in MeCP2 lead to Rett syndrome. Here, MeCP2-DNA complexes have been imaged by AFM (Digital Instruments Nanoscope) in air using human MeCP2 and an 828 bp DNA sequence containing several methylated CpGs. MeCP2 molecules appear as bright particles in AFM images. Volume measurements of the complexes suggest that MeCP2 monomers (circular particles) and dimers (larger elliptical particles) are present and suggest that MeCP2 binds DNA cooperatively. Other images in the grouped set show looped structures and large complexes containing multiple DNA strands and MeCP2 molecules. These configurations are likely promoted by the multiple independent DNA-binding domains of MeCP2 and relevant to the in vivo interactions between MeCP2 and chromatin.
description: Preparation: glutaraldehyde fixed tissue
Relation to intact cell: isolated subcellular component
Item type: recorded image
Imaging mode: microscopy; atomic force microscopy
Parameter imaged: specimen height
Source of contrast: specimen height
Processing history: unprocessed raw data
DOI: 10.6075/j0fq9vpf
title: CIL:7116, Homo sapiens, neuron. In Cell Image Library

description: The protein MeCP2 binds to symmetrically methylated CpG dinucleotides and is thought to transmit the (generally) repressive signals encoded in DNA methylation patterns. Mutations in MeCP2 lead to Rett syndrome. Here, MeCP2-DNA complexes have been imaged by AFM (Digital Instruments Nanoscope) in air using human MeCP2 and an 828 bp DNA sequence containing several methylated CpGs. MeCP2 molecules appear as bright particles in AFM images. Volume measurements of the complexes suggest that MeCP2 monomers (circular particles) and dimers (larger elliptical particles) are present and suggest that MeCP2 binds DNA cooperatively. Other images in the grouped set show looped structures and large complexes containing multiple DNA strands and MeCP2 molecules. These configurations are likely promoted by the multiple independent DNA-binding domains of MeCP2 and relevant to the in vivo interactions between MeCP2 and chromatin.
description: Preparation: glutaraldehyde fixed tissue
Relation to intact cell: isolated subcellular component
Item type: recorded image
Imaging mode: microscopy; atomic force microscopy
Parameter imaged: specimen height
Source of contrast: specimen height
Processing history: unprocessed raw data
DOI: 10.6075/j02z14n8
title: CIL:7119, Homo sapiens, neuron. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue
Relation to intact cell: isolated subcellular component
Item type: recorded image
Imaging mode: microscopy; atomic force microscopy
Parameter imaged: specimen height
Source of contrast: specimen height
Processing history: unprocessed raw data
description: The protein MeCP2 binds to symmetrically methylated CpG dinucleotides and is thought to transmit the (generally) repressive signals encoded in DNA methylation patterns. Mutations in MeCP2 lead to Rett syndrome. Here, MeCP2-DNA complexes have been imaged by AFM (Digital Instruments Nanoscope) in air using human MeCP2 and an 828 bp DNA sequence containing several methylated CpGs. MeCP2 molecules appear as bright particles in AFM images. Volume measurements of the complexes suggest that MeCP2 monomers (circular particles) and dimers (larger elliptical particles) are present and suggest that MeCP2 binds DNA cooperatively. Other images in the grouped set show looped structures and large complexes containing multiple DNA strands and MeCP2 molecules. These configurations are likely promoted by the multiple independent DNA-binding domains of MeCP2 and relevant to the in vivo interactions between MeCP2 and chromatin.