Species: | M. smegmatis |
---|---|
Strain: | MC2-155 |
PATRIC Annotation: | - |
Synonyms: | |
M. tuberculosis homologs | def |
M. abscessus homologs | MAB4187 |
Gene Start: | 919024 |
Gene End: | 919617 |
Vulnerability Index (VI): | -0.6250 |
VI Lower Bound: | -0.8060 |
VI Upper Bound: | -0.4510 |
Call | Condition | Type | Source | Notes |
---|---|---|---|---|
Essential | in vitro | TnSeq | [Akusobi et al. (2022)] | |
Non Essential | in vitro | CRISPRi | [Bosch & DeJesus et al. (2021)] |
Experiment: We designed an M. tuberculosis CRISPRi library (RLC12) to target all annotated Mtb genes with single guide RNAs (sgRNAs) of varying predicted knockdown efficiencies.
In parallel, we constructed a M. smegmatis CRISPRi library (RLC11) to target all annotated Msmeg genes, similar to the Mtb sgRNA library.
RLC12 was transformed into M. tuberculosis H37Rv; RLC11 into M. smegmatis mc2-155.
We passaged both CRISPRi libraries for nearly 30 generations in the presence or absence of the CRISPRi-inducer anhydrotetracycline (ATc). At the indicated timepoints, genomic DNA was harvested and the representation of individual sgRNAs was counted using Illumina sequencing.
Here, we show sgRNA log2 fold-change values (L2FC) (plus versus minus ATc) over consecutive generations for sgRNAs targeting the gene you selected.
sgRNAs are color-coded based on their predicted strength from blue (strength=0; weak) to red (strength=1; strong).
In order to quantify gene vulnerability, data were subsequently analyzed with a hierarchical model at the sgRNA level (two-line model) and gene level (Hill curve). The vulnerability quantification is shown below. [More information]