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Data released on December 05, 2016

Supporting data for "A dataset of images and morphological profiles of 30,000 small-molecule treatments using the Cell Painting assay"

Bittker, J, A; Bodycombe, N, E; Bray, M, A; Clemons, P, A; Dančík, V; Golub, T, R; Gustafsdottir, S, M; Hasaka, T, P; Hon, C, S; Kemp, M, M; Li, K; Ljosa, V; Schreiber, S, L; Singh, S; Sokolnicki, K, L; Walpita, D; Wawer, M, J; Carpenter, A, E; Shamji, A, F (2016): Supporting data for "A dataset of images and morphological profiles of 30,000 small-molecule treatments using the Cell Painting assay" GigaScience Database. http://dx.doi.org/10.5524/100200 RIS BibTeX Text

Large-scale image sets acquired by automated microscopy of perturbed samples enable a detailed comparison of cell states induced by each treatment. Highly multiplexed measurements of cellular morphology can be extracted from each image and subsequently mined for a number of applications.
This microscopy dataset includes 919,874 five-channel fields of view representing 30,616 tested compounds. The images are available at The Cell Image Library repository. All additional data files are available from GigaDB, including; morphological features derived from each cell in each image, both at the single-cell level and population-averaged (i.e., the per-image level); the image analysis workflows that generated the morphological features are also provided. Quality-control metrics are provided as metadata, indicating fields of view that are out-of-focus (blurry) or containing highly fluorescent material or debris. Lastly, chemical annotations are supplied for the compound treatments applied.
Because computational algorithms and methods for handling single-cell morphological measurements are not yet routine, the dataset serves as a useful resource for the wider scientific community applying morphological (image-based) profiling. The dataset can be mined for many purposes, including small-molecule library enrichment and chemical mechanism-of-action studies, including target identification. Integration with genetically-perturbed datasets could enable identification of small-molecule mimetics of particular disease- or gene-related phenotypes that could be useful as probes or potential starting points for development of future therapeutics.

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Related datasets:

doi:10.5524/100200 IsPreviousVersionOf doi:10.5524/100351 (It is a more recent version of this dataset)


There is a new version of this dataset available at: DOI: 10.5524/100351

Additional information:

http://www.cellimagelibrary.org/pages/project_20269

https://github.com/gigascience/paper-bray2017

Keywords:

phenotypic profiling high-content screening image-based screening cellular morphology small-molecule library U2OS 

Imaging

/images/uploads/image_upload/Images_285.png

Funding:

  • Funding body - National Science Foundation
  • Award ID - CAREER DBI-1148823
  • Comment - Anne E Carpenter (for publishing costs)

Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
U2OS cell line9606HumanhumanHomo sapiens Sex:female
Ethnicity:caucasian
Disease status:osteocarcoma
...
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Displaying 1-1 of 1 Sample(s).

Files: (FTP site) Table Settings

Columns:

File Description
Sample ID
File Type
File Format
Size
Release Date
Download Link
File Attributes

File NameSample IDFile TypeFile FormatSizeRelease Date 
tabular dataUNKNOWN4.95 MB2016-08-02
tabular dataUNKNOWN18.12 KB2016-08-02
md5sum valuesTEXT22.05 KB2016-11-15
Scriptarchive14.61 KB2016-08-02
U2OS cell lineMixed archiveTAR379.07 MB2016-08-02
U2OS cell lineMixed archiveTAR330.92 MB2016-08-02
U2OS cell lineMixed archiveTAR337.22 MB2016-08-02
U2OS cell lineMixed archiveTAR363.61 MB2016-08-02
U2OS cell lineMixed archiveTAR371.13 MB2016-08-02
U2OS cell lineMixed archiveTAR344.36 MB2016-08-02
Displaying 1-10 of 418 File(s).

History:

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