Computational protocol: Recurrent background mutations in WHI2 impair proteostasis and degradation of misfolded cytosolic proteins in Saccharomyces cerevisiae

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Protocol publication

[…] Whole-genome sequencing and library preparation was performed at the NextGen Sequencing facility at the University of British Columbia’s Biodiversity Research Centre. Yeast cells were grown overnight to saturation in YPD at 25°C and genomic DNA was extracted using standard protocols. Barcoded libraries for each strain were created according to Illumina protocols (Illumina 2011, all rights reserved) and 100-bp paired end fragments were sequenced by pooling all six libraries and run on a single lane of an Illumina HiSeq2000. The short-read aligner BWA was used to map sequence reads to the yeast reference genome S288C version R64 (Saccharomyces Genome Database, SDG, http://www.yeastgenome.org). Single-nucleotide variants (SNVs) were identified using the SAMtools toolbox and then each SNV was annotated with a custom-made Perl script using gene data downloaded from SDG on January 21, 2014. IGV viewer was used to visually inspect read alignments in the regions of candidate SNVs, . […]

Pipeline specifications

Software tools BWA, SAMtools, IGV
Databases SGD
Application WGS analysis
Organisms Saccharomyces cerevisiae
Diseases Congenital Abnormalities, Neoplasms, Proteostasis Deficiencies