MFAseq: Replication profile for wild type DS2 H.volcanii

In Repliscope: Replication Timing Profiling using DNA Copy Number

Replication profile for wild type DS2 H.volcanii

Description

Replication profile for H.volcanii wild isolate DS2. Genomic DNA for deep sequencing was isolated from 100 ml culture in stationary phase (A650 > 1, DS2_stat sample) or 1 litre in exponential phase (A650 0.1, DS2_exp sample). Unique reads for the two samples were calculated in 1 kb genomic bins using ASM2568v1 genome assembly. 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 1.12 to put the values onto biologically relevant relative copy number scale from 1 to 2.

Usage

data(MFAseq)

Format

data frame with 3887 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

DS2_exp exponential phase sample: SRA; DS2_stat stationary sample: SRA

References

Hawkins et al. (2013) Nature 503(7477):544-547 (PubMed)

Examples

data(MFAseq)

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