ena-STUDY-ENS Lyon-16-01-2019-12:16:48:321-48
Whole-genome re-sequencing of the wild isolate PB306 (Caenorhabditis elegans nematode) and three derived Mutation Accumulation Lines
This study contains whole-genome re-sequencing runs of three samples: PB306, MA418, MA450 and MA488.PB306 is a wild islate of the nematode Caenorhabditis elegans.This accession has been used in different studies, notably to explore natural phenotypic variations and as a progenitor of mutation accumulation lines (Baer CF. et. al, PNAS 2005).Genomic DNA of PB306 was extracted in Dec. 2012 directly from stocks received from Charles Baer. This stock is the true progenitor line of a set of mutation accumulation lines and was kept frozen to avoid accumulation of spontaneous mutations and genetic drift.MA418, MA450 and MA488 are three independant mutation accumulation lines derived from PB306. The stocks sequenced in the present study have been passed through single-worm bottlenecks for 250 generations. Genomic DNA were also extracted in Apr.-May 2013 directly from stocks received from Charles Baer.Short-insert random libraries were prepared for each sample by BGI and sequenced by Illumina on a HiSeq 2000 sequencer with 100-bp paired-end reads. Each sample was sequenced at a target-depth 20X in Nov. 2013. Quality scores of these raw reads are encoded old deprecated Phred+64 ASCII socres. This must be converted on Phred+33 encoding to ensure compatibility with most softwares for downstream analysis.
This study contains whole-genome re-sequencing runs of three samples: PB306, MA418, MA450 and MA488.PB306 is a wild islate of the nematode Caenorhabditis elegans.This accession has been used in different studies, notably to explore natural phenotypic variations and as a progenitor of mutation accumulation lines (Baer CF. et. al, PNAS 2005).Genomic DNA of PB306 was extracted in Dec. 2012 directly from stocks received from Charles Baer. This stock is the true progenitor line of a set of mutation accumulation lines and was kept frozen to avoid accumulation of spontaneous mutations and genetic drift.MA418, MA450 and MA488 are three independant mutation accumulation lines derived from PB306. The stocks sequenced in the present study have been passed through single-worm bottlenecks for 250 generations. Genomic DNA were also extracted in Apr.-May 2013 directly from stocks received from Charles Baer.Short-insert random libraries were prepared for each sample by BGI and sequenced by Illumina on a HiSeq 2000 sequencer with 100-bp paired-end reads. Each sample was sequenced at a target-depth 20X in Nov. 2013. Quality scores of these raw reads are encoded old deprecated Phred+64 ASCII socres. This must be converted on Phred+33 encoding to ensure compatibility with most softwares for downstream analysis.