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(related to Fig 1) Genomic copy number analysis.

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posted on 14.10.2020, 17:40 authored by Emily E. Wear, Jawon Song, Gregory J. Zynda, Leigh Mickelson-Young, Chantal LeBlanc, Tae-Jin Lee, David O. Deppong, George C. Allen, Robert A. Martienssen, Matthew W. Vaughn, Linda Hanley-Bowdoin, William F. Thompson

Whole genome sequence data from sorted non S-phase 2C, 4C and 8C nuclei were used to assess copy number per DNA content across the genome. To better represent the copy number of repeat regions, the primary alignment location for each read pair–even those that map to multiple locations–were included in the analysis. (A and B) Histograms of the normalized read frequency ratios, calculated in 5-kb static windows, for 2C/4C (A) and 8C/4C (B) nuclei. The black dashed lines indicate the overall mean and the red dashed lines indicate ± 2 S. D. from the mean. (C) The 8C/4C read frequency ratios plotted as a function of genomic location, which shows that the values outside ± 2 S. D. all occur as singleton 5-kb windows. (D and E) We used consensus sequences for 45S rDNA and knob180 (D), and for 5S rDNA, TR-1, CentC and CRM1–4 families (E) to individually query all of the trimmed whole genome sequence reads using BLAST software and a non-stringent E value to allow for variants of each repeat (S1 Text). The mean percentage of total reads that align to each repeat type was calculated for three biological replicates of 2C, 4C and 8C data. Black dots represent the individual biological replicate values. The apparent slight under-replication of several elements (e.g. knob180 and CRM2) is not statistically significant.

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