Published February 18, 2020
| Version 1
Journal article
Open
Automatic identification of small molecules that promote cell conversion and reprogramming - plate scans, colony quantification scripts, and DECCODE ranking
Authors/Creators
- 1. King Abdullah University of Science and Technology (KAUST)
- 2. Telethon Institute of Genetics and Medicine (TIGEM)
- 3. RIKEN Center for Integrative Medical Sciences
- 4. Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics
Description
Preprint available on bioRxiv.
Final article available at Stem Cell Reports.
Webtool available here.
Data analysis tools for conversion of gene expression profiles to pathway expression profiles are available with the R/Bioconductor package gep2pep.
This Zenodo release includes:
- plate scans.zip:
- 5 images (15 plates) from secondary reprogramming experiments.
- 1 Excel file identifying treaments and controls in the plates above.
- 1 image (5 plates) from primary reprogramming experiments (directly annotated).
- 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