Phenotypic screening of a CRISPRi strain library Smith et al., 2017 for acetic acid tolerance
We screened a CRISPR interference library consisting of >9000 Saccharomyces cerevisiae strains where >98% of all essential and respiratory growth-essential genes were targeted with multiple gRNAs. This repository is created to offer any user the opportunity to reproduce the entire analysis starting from the raw data.
The codes described in this project shows how to (a) prepare, (b) analyze, and (c) visualize the high-throughput phenomics data generated in this study.
In this project we used two high-thoughput phenomics platform
- Scan-o-matic Zackrisson et al., 2016
- Bioscreen microcultivation followed by PRECOG analysis Fernandez-Ricaud et al, 2016
All raw data files generated in this study are available in the folder RAW_DATA. It has the following sub folders
- SOM_AA_TITRA : Scan-o-matic Acetic acid titration raw data (Plate 7 & 8)
- SOM_ATC_TITRA : Scan-o-matic ATc (anhydrous tetracyclin) titration raw data (Plate 7 & 8)
- SOM_SCR_R001 : Scan-o-matic CRISPRi library screening raw data, Round 1
- SOM_SCR_R002 : Scan-o-matic CRISPRi library screening raw data, Round 2
- BS_VAL_SCR : Bioscreen Validation experiment with selected strains from CRISPRi library raw data.
+ STRAIN_MAP_VAL_EXP: Strains layout in bioscreen plate (well no > strain name).
+ BS_PRECOG_OUTPUT : PRECOG output (Processed and calibrated growth curve, First derivative, raw phenotypes)
The repository also provides some compiled data for the ease of analysis in the COMPILED_DATA folder. Those files will be used while running the script in the CRISPRi_Screening_AceticAcid.Rmd file.
All files in the above folders, the data, and the scripts used to process the data are explained STEP BY STEP in the CRISPRi_Screening_AceticAcid.Rmd file. User can also use the output CRISPRi_Screening_AceticAcid.html file to view the flow and the content of the analysis.
Pull requests are welcome. For major changes, please open an issue first to discuss what you would like to change.