10.25387/g3.10406519.v1
Elizabeth A. Morton
Elizabeth A.
Morton
Ashley Hall
Ashley
Hall
Elizabeth X. Kwan
Elizabeth X.
Kwan
Calvin Mok
Calvin
Mok
Konstantin Queitsch
Konstantin
Queitsch
Vivek Nandakumar
Vivek
Nandakumar
John Stamatoyannopoulos
John
Stamatoyannopoulos
Bonita J. Brewer
Bonita J.
Brewer
Robert Waterston
Robert
Waterston
Christine Queitsch
Christine
Queitsch
Supplemental Material for Morton et al., 2020
GSA Journals
2019
Ribosomal DNA
Repetitive DNA
Whole Genome Sequencing
Copy Number Variation
Genomics
2019-11-22 16:40:56
Dataset
https://gsajournals.figshare.com/articles/dataset/Supplemental_Material_for_Morton_et_al_2020/10406519
<p>
</p><p>Supplemental methods, figures, and tables accompanying
Morton <i>et al</i>. manuscript
"Challenges and Approaches to Genotyping Repetitive DNA"</p>
<p>File S1 contains supplemental materials and methods and a
list of tables</p>
<p>Figure S1 contains Southern blots and ethidium bromide
staining of CHEF gels</p>
<p>Figure S2 contains droplet digital PCR condition
optimization</p>
<p>Figure S3 contains details of smMIP-based copy number
estimation</p>
<p>Figure S4 contains details of rDNA locus FISH
characteristics for <i>C. elegans</i>
strains</p>
<p>Table S1 contains metrics from Nextera whole genome
sequencing of <i>C. elegans</i> strains</p>
<p>Table S2 contains percent error of rDNA copy number estimation
for <i>C. elegans</i> strains</p>
<p>Table S3 contains results of downsampling <i>C. elegans</i> WGS data</p>
<p>Table S4 contains different aligner and trimming comparisons
of <i>C. elegans</i> strains rDNA copy
number estimate</p>
<p>Table S5 contains coordinate of <i>C. elegans</i> single copy regions</p>
<p>Table S6 contains WGS counts of <i>C. elegans</i> single copy regions</p>
<p>Table S7 contains published yeast strain SRA numbers</p>
<p>Table S8 contains yeast diploid strain rDNA estimates</p>
<p>Table S9 contains yeast strain SNV genotyping</p>
<p>Table S10 contains droplet digital PCR raw data</p>
<p>Table S11 contains smMIP data</p>
<p>Table S12 contains rDNA FISH summary cell counts</p>
<p>Table S13 contains rDNA FISH data</p>
<p>Table S14 contains sequences of oligos</p>
<p>Table S15 contains band measurements from <i>C. elegans</i> CHEF gels</p>