Automatic identification of small molecules that promote cell conversion and reprogramming - plate scans, colony quantification scripts, and DECCODE ranking

NOTE: in order to apply the DECCODE approach to your custom profiles, you need to have: 1) drug-induced pathway-based expression profiles (PEPs), 2) cell type PEPs. You can download pre-computed drug-induced PEPs from here. Gene expression profiles must be differential. In order to convert your gene expression profiles to PEPs you can use the gep2pep R/Bioconductor package. Once you have 1 and 2, you can simply match drug induced to cell type PEPs using a proper distance, such as Manhattan.

Publication: https://doi.org/10.1016/j.stemcr.2021.03.028

This release includes:

• plate scans.zip:
  • 5 images (15 plates) from secondary reprogramming experiments (single drugs).
  • 1 Excel file identifying treatments and controls in the plates above.
  • 1 image (5 plates) from primary reprogramming experiments with Tazobactam (directly annotated).
• plate scans - drug pairs.zip
  • 3 plate scan images from experiments with drug pairs.
  • 1 PDF file identifying treatments in the plates above.
  • 1 TXT file containing the used ImageJ parameters for counting.
• ColonyCountingScripts.zip
  • Matlab scripts used to automatically extract well images from plate scans (secondary reprogramming)
  • ImageJ macro used to count colonies in the extracted well images
• rankedLINCSprofiles_ testedDrugs_cellClusters.xls
  • full list of LINCS expression profiles including DECCODE scores and pluripotency.
  • list of all tested drugs
  • cell type clusters
• top-30_pairs_20_each.xlsx
  • Top 30 drugs that once paired with other drugs achieve highest scores as computed by the drug-combinations approach. The top 20 pairs are reported for each of the 30 starting drugs.