cbergman
commented
5 years ago -
4 original strains:
- DG1768: a Ty1‐less strain, (MATα his3‐Δ200hisG ura3) derived from strain 337, kindly provided by J. Adams (Wilke and Adams, 1992), as previously described (Garfinkel et al., 2003).
- DG1938 (MATa his3‐Δ200G ura3 Ty1‐less Spo+) was derived by crossing DG1768 with DG1929 [MATa his3‐Δ 200hisG ura3 Ty1his3‐AI(96)] and segregating spores for loss of the Ty1 element. DG1929 is [MATa his3‐Δ 200hisG ura3 Ty1his3‐AI(96)] derived from strain 337, kindly provided by J. Adams (Wilke and Adams, 1992), as previously described (Garfinkel et al., 2003).
- DG4005 (rederived DG2454): MATα his3-Δ200hisG ura3 gal3 Ty1-4253 Ty-less Spo−. DG1768 + Ty1-4523 (inserted in ChrX between RAD7 and CDC8, adjacent to Gly-tRNA gene
- DG2451: DG1768 + ~20-25 Ty1-H3 insertions (estimated by Southern analysis, insertion locations not determined). Papers say 20 in Genetics 2003 and 25 in PNAS 2009
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Original strains used to create 4 progenitor:
- H0: Haploid 0 Ty1s (DG1768 α)
- D0: Diploid 0 Ty1s (DG1938 a x DG1768 α)
- D1: Diploid 1 Ty1 (DG1938 a x DG4005 α)
- D20: Diploid ~20 Ty1-H3 insertions (DG1938 a x DG2451 α?)
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200 days of transfer, 1 transfer every other day
- 100 transfers, 2000 generations
- stored every 10 transfers
- sequenced 100th transfer only
- goal was 48 replicates per genotype + progenitors = ~200 total samples
- <5 replicates missing from each genotype
hollygene
JingxuanChen7
Whole-genome sequencing of S. paradoxus mutation accumulation lines DNA extracted using Zymo YeaSTAR Genomic DNA kit Libraries prepped using homemade protocol (no kit, can find out more info if needed, probably published) Sequenced on NovaSeq S4 flow cell PE 150 at Genewiz 500GB total sequencing data
Location of fastq files on Sapelo:
/scratch/hcm14449/TE_MA_Paradoxus/Illumina_Data/IL_Data/GW_run3/00_fastq(I also have backups of this on the /project/ folder for our lab, and on an external hard drive)So one potential problem I have found is that my samples have varying depth of coverage - I guess because they were pooled. My main concern is that my ancestral strains have ~25x coverage, while the progenitor lines have anywhere from 150x-2000x(!).