sortSeq: Replication profiles for wild type and Dbf4-9myc S.cerevisiae...

In Repliscope: Replication Timing Profiling using DNA Copy Number

Replication profiles for wild type and Dbf4-9myc S.cerevisiae samples

Description

Replication profiles for wild type and Dbf4-9myc samples (T7107 and T9394 strains). The cells were stained with DNA dye and sorted based on DNA content into S or G2/M phase fractions. Extracted DNA was sequenced and mapped to sacCer3 genome. Unique reads for replicating (S) and non-replicating (G2/M) samples were calculated in 1 kb genomic bins. The ratio was created by dividing 'score' values from replicating sample by non- replicating sample 'score' values, adjusted by total number of reads. The ratio values were further adjusted by multiplying them by 1.41 and 1.402 for wild type and Dbf4-9myc samples, respectively, to put the values onto biologically relevant relative copy number scale from 1 to 2. The relative copy number values were smoothed using cubic spline and compared using z score statistics.

Usage

data(sortSeq)

Format

data frame with 22696 rows and 10 variables:

chrom

short chromosome name

chromStart

left chromosome coordinate

chromEnd

right chromosome coordinate

name.rep

replicating sample name

name.nonRep

non-replicating sample name

ratio

ratio value in the current bin

ratioFactor

adjustment factor used for the current ratio

group

Group number of the current bin

splineSmooth

Smoothed ratio value

p.value

Significance of ratio difference between Dbf4myc and W303 samples

Source

Dbf4myc S phase sample: SRA; Dbf4myc G2 sample: SRA; W303 S sample: SRA; W303 G2 sample: SRA

References

Natsume et al. (2013) Mol Cell 50(5):661-74 (PubMed)

Examples

data(sortSeq)

Repliscope documentation built on Sept. 13, 2022, 9:05 a.m.