ena-STUDY-ENS Lyon-16-01-2019-11:32:20:172-39
Whole-genome re-sequencing of the wild accession HK104 (Caenorhabditis briggsae nematode) and two derived Mutation Accumulation Lines
This study contains whole-genome re-sequencing runs of three samples: HK104, MA211 and MA296.HK104 is a wild accession of the nematode Caenorhabditis briggsae.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 HK104 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.MA211 and MA296 are two independant mutation accumulation lines derived from HK104. The stocks sequenced in the present study have been passed through single-worm bottlenecks for 250 generations. Genomic DNA were also extracted in Dec. 2012 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. HK104 and MA296 have two sequencing runs of 10X target depth each (for both samples, the same library was used for the first run -in March 2013- and the second run -Nov. 2013). Only one run of target-depth 20X has been performed for sample MA211 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: HK104, MA211 and MA296.HK104 is a wild accession of the nematode Caenorhabditis briggsae.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 HK104 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.MA211 and MA296 are two independant mutation accumulation lines derived from HK104. The stocks sequenced in the present study have been passed through single-worm bottlenecks for 250 generations. Genomic DNA were also extracted in Dec. 2012 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. HK104 and MA296 have two sequencing runs of 10X target depth each (for both samples, the same library was used for the first run -in March 2013- and the second run -Nov. 2013). Only one run of target-depth 20X has been performed for sample MA211 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.