Project description:This dataset comprises L1000 and image-based cell-morphology profiles for small-molecule perturbations. Profiles were measured for ~18,000 compounds derived from diversity-oriented synthesis activities at the Broad Institute Center for the Science of Therapeutics, ~10,000 compounds selected from the Molecular Libraries Small-Molecule Repository (MLSMR), and ~2,000 known bioactive compounds. Each of the three subsets was selected to be structurally diverse. MLSMR compounds were further selected to have diverse biological performance. Imaging profiles were measured for a total of ~30,000 compounds. We used a "cell-painting" assay to stain seven major cellular components with fluorescent dyes followed by automatic image capture and analysis to extract shape, texture, and intensity parameters. The imaging assay protocol has been published by Gustafsdottir SM et al. L1000 profiles were measured for ~20,000 compounds. All experiments were performed with U-2 OS cells. Among other activities, we have analyzed these data using cheminformatics approaches to derive structure-based associations with patterns of performance in the profiles. The generation of this dataset was supported by the Molecular Libraries Program of the National Institutes of Health (U54-HG005032). Data made available as part of this project includes L1000 data and image-based cell-morphology profiles for small-molecule perturbations. Please follow the steps here to download the data: https://www.pnas.org/content/111/30/10911

2014-05-30 | LDS-1195 | LINCS

MEMA HMEC122L Staining Set C

Project description: Not available

2016-11-10 | LDS-1463 | LINCS

MEMA HMEC122L Staining Set 4

Project description:HMEC122L cells were grown in standard 8 well MEMA for 72h and then fixed using 2% paraformaldehyde. Cells were stained with DAPI (nuclei), KRT5(basal lineage), KRT19(luminal lineage) and EdU(Active S phase). The cells were imaged on a Nikon HCA microscopy system, segmented with Cell Profiler, normalized using RUV and lowess using the spatial residuals as controls, and analyzed to identify microenvironment conditions that altered phenotypes of interest.

2016-11-10 | LDS-1431 | LINCS

MEMA MCF10A Staining Set 1

Project description:MCF10A cells were grown in standard 8 well MEMA for 72h and then fixed using 2% paraformaldehyde. Cells were stained with DAPI (nuclei), phalloidin (actin), CellMask (cytoplasm) and MitoTracker (metabolic activity). The cells were imaged on a Nikon HCA microscopy system, segmented with Cell Profiler, normalized using RUV and lowess using the spatial residuals as controls, and analyzed to identify microenvironment conditions that altered phenotypes of interest.

2016-11-10 | LDS-1443 | LINCS

MEMA HMEC122L Staining Set 1

Project description:HMEC122L cells were grown in standard 8 well MEMA for 72h and then fixed using 2% paraformaldehyde. Cells were stained with DAPI (nuclei), phalloidin (actin), CellMask (cytoplasm) and MitoTracker (metabolic activity). The cells were imaged on a Nikon HCA microscopy system, segmented with Cell Profiler, normalized using RUV and lowess using the spatial residuals as controls, and analyzed to identify microenvironment conditions that altered phenotypes of interest.

2016-11-10 | LDS-1427 | LINCS

MEMA MCF10A Staining Set 3

Project description:MCF10A cells were grown in standard 8 well MEMA for 72h and then fixed using 2% paraformaldehyde. Cells were stained with DAPI (nuclei), CellMask (cytoplasm) KRT5 (basal lineage) and KRT19 (luminal lineage). The cells were imaged on a Nikon HCA microscopy system, segmented with Cell Profiler, normalized using RUV and lowess using the spatial residuals as controls, and analyzed to identify microenvironment conditions that altered phenotypes of interest.

2016-11-10 | LDS-1447 | LINCS

diMN (Exp 3) - ALS and Control (unaffected) diMN cell lines differentiated from iPS cell lines using a short and direct differeintiation protocol - ATAC-seq

Project description:ATAC-Seq was carried out on isolated nuclei obtained from induced Pluripotnent Stem Cells (iPSC) cell lines. These lines were derived from ALS, SMA and Control (unaffected) individuals (three of each).

2017-10-13 | LDS-1501 | LINCS

LINCS MCF 10A Common Project: Fixed-time-point sensitivity measures of the MCF 10A breast cell line to 8 small molecule perturbagens. Dataset 4 of 9: Mean cell count and mean normalized growth rate inhibition values for biological replicate 1

Project description: Not available

2017-02-07 | LDS-1376 | LINCS

Growth factor-induced ERK activity and FoxO3a nuclear-cytoplasmic pulsing dynamics in a mammary epithelial cell line. Dataset 1 of 1: single-cell reporter measurements.

Project description: Not available

2017-05-02 | LDS-1394 | LINCS