CGP violacein treatment Vs. control
Description
A collection of ~6000 heterozygous yeast strains, was treated with sublethal doses of violacein or vehicle treated control for 10 generations in a way to identify violacein-induced happloinsufficiency profile. Each strain had one copy of each of the predicted S. cerevisiae open reading frame (ORF) replaced by an antibiotic resistance marker (KANMX4) flanked by 20 bp DNA sequences (barcodes), allowing quantitative analysis of differential growth through barcode sequencing. This dataset shows barcodes that were differentially expressed in the comparisons between violacein treatment and vehicle treated control. We considered as hits, strains that were most affected by violacein treatment, p-value <0.001 and log2 fold change <0.
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Steps to reproduce
Genomic DNA was extracted using a Wizard® Genomic DNA Purification Kit (Promega), according to the manufacturer’s conditions. Purified genomic DNA was sent for barcode sequencing at the Centro de Sequenciamento Genômico da Universidade de São Paulo/ESALQ. Data obtained from Illumina sequencing were subsequently analyzed and processed for barcode quantification at the Laboratório de Genômica e Expressão/UNICAMP. Briefly, the DESeq2 package (version 1.20.0) was used to normalize the barcodes counts and to estimate the differential abundance between treated samples and their respective controls. A filter was further established to remove the barcodes with a low count along the samples (<10 observations in triplicate). Differentially depleted barcodes were identified using a maximum likelihood ratio test (LRT), which consists of a generalized linear model in which the number of observations of a given barcode is described by a negative binomial distribution whose average is given by the treatment. Normalization between samples was achieved by library size factor method, using only amplicon sequence variants (ASVs) with the number of observations >0. Barcodes that were differentially expressed in the comparisons between treatment and control were considered statistically significant (hits) for p-value <0.001 and log2 fold change <0.