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Download data

Primary screen

Annotation

Download the annotated siRNA library used for the primary screen.

Raw microscope TIFF images

Use the following wget command to download the raw microscope TIFF images (12-bit 1344x1024 images, 3 channels: A (Alexa 488 dye staining Tubulin), H (Hoechst 33242 dye staining DNA) and T (TRITC dye staining Actin), 2 runs). Data size is 491 GBytes.
wget -r --no-parent http://www.ebi.ac.uk/huber-srv/cellmorph/source/

Calibrated JPEG images

Use the following wget command to download the calibrated JPEG images (_rgb.jpeg), together with the thumbnails (_tb.png), segmented images (_seg.jpeg) and the annotated images with cell classes (_classes.jpeg). Data size is 176 GBytes.
wget -r --no-parent http://www.ebi.ac.uk/huber-srv/cellmorph/view/

Cell numeric features

Use the following wget command to download the cell numerical features (_ftrs.tab), computed after segmentation. Data size is 12 GBytes.
wget -r --no-parent http://www.ebi.ac.uk/huber-srv/cellmorph/data/

Phenoprints

The file phenoprints.tab contains the phenoprints of the 1820 perturbated genes in tab-delimited format.

Phenotypic map

Download the phenotypic map source, specified in the Graphviz DOT format. Use the following commands (require Graphviz to be installed) to generate the PDF from it.
gunzip phenomap.dot.gz
neato -n phenomap.dot -Tps -o phenomap.ps
ps2pdf phenomap.ps
The files phenomap.pdf and phenomap.cys contain the phenotypic map in PDF format and Cytoscape CYS format.

Secondary screens

604 candidates were retested with an independent library and two cell lines (HeLa and U2OS) in replicate. Screens are named xR3y where x denotes the cell line (H for HeLa and U for U2OS) and y is the replicate number.

Annotation

Download the annotated siRNA library used for the secondary screens.

Raw microscope TIFF images

Use the following wget commands to download the raw microscope TIFF images.
wget -r --no-parent http://www.ebi.ac.uk/huber-srv/cellmorph/source-HR
wget -r --no-parent http://www.ebi.ac.uk/huber-srv/cellmorph/source-UR

Calibrated JPEG images

Use the following wget commands to download the calibrated JPEG images (_rgb.jpeg).
wget -r --no-parent http://www.ebi.ac.uk/huber-srv/cellmorph/view-HR
wget -r --no-parent http://www.ebi.ac.uk/huber-srv/cellmorph/view-UR

Cell features

Use the following wget commands to download the cell numerical features (_ftrs.tab).
wget -r --no-parent http://www.ebi.ac.uk/huber-srv/cellmorph/data-HR
wget -r --no-parent http://www.ebi.ac.uk/huber-srv/cellmorph/data-UR
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