Dbf4myc: Sequence read coverage ratios for S.cerevisiae Dbf4-9myc...

In Repliscope: Replication Timing Profiling using DNA Copy Number

Sequence read coverage ratios for S.cerevisiae Dbf4-9myc sample.

Description

Sequence read coverage ratios for Dbf4-9myc sample (T9394 strain). 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 1.402 to put the values onto biologically relevant relative copy number scale from 1 to 2.

Usage

data(Dbf4myc)

Format

data frame with 11356 rows and 7 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

Source

S phase sample: SRA; G2 sample: SRA

References

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

Examples

data(Dbf4myc)

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