Parallel CRISPR-Cas9 screens clarify impacts of p53 on screen performance
Bowden, A Ramsay et al. (2020), Parallel CRISPR-Cas9 screens clarify impacts of p53 on screen performance, Dryad, Dataset, https://doi.org/10.5061/dryad.2fqz612kr
Primarily the dataset contains the results of CRISPR screens. RPE-1 cells that are TP53-null or wild-type were infected with pooled plasmid libraries targeting selected genes and grown for up to 19 days. Samples were taken at 3, 15 & 19 days. Samples were havested and DNA extracted. PCR was used to isolate and amplify barcodes on plasmids in the CRISPR library. The barcode abundances were mapped to plasmids targeting specific genomic loci, and these abundances are included here. Abundances from other screens were downloaded from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE128210. MAGeCK (https://sourceforge.net/p/mageck) was used to obtain significance values for gene enrichment/depletion from the abundances, and the output files are included. Further analysis was performed using Python, and a Python notebook (.ipynb) is included.
Python version >= 3.6 is required to run the notebook (it uses f-strings); and the packages: scipy, matplotlib, pandas, statsmodels, seaborn & jupyter (plus dependencies).
- analysis_and_charts.ipynb – Python notebook that produces all the figures in the paper.
- all_magecks.csv – Table of significance and log2 fold change values of genes, calculated by mageck.
- *.counts.tsv – Guide/barcode abundances from different screens.
- sample_replicate_details.xlsx – Details about samples in our screen.
- transomics_ddr_v2-1.csv – Details of the library used in our screen.
- OR_gene_list.txt – Names of olfactory receptor genes.
- mageck_results/* – files output by MAGeCK