syncSeq: Replication profiles budding yeast arrest-release samples

In Repliscope: Replication Timing Profiling using DNA Copy Number

Replication profiles budding yeast arrest-release samples

Description

Replication profiles of wild type S. cerevisiae arrest-release samples (AUY077 strain). The cells were arrested in G1 with alpha-factor followed by release using pronase. The samples were collected before the release (aFactor) and various time intervals after the release (25min,30min,35min,40min,45min,50min and 90min) Extracted DNA was sequenced and mapped to sacCer3 genome. Unique reads for replicating (post-release) and non-replicating (aFactor) samples were calculated in 1 kb genomic bins. The ratios were created by dividing 'score' values from replicating samples by non-replicating sample 'score' values, adjusted by total number of reads. The ratio values were further adjusted based on bulk genome replication (as determined by flow cytometry), 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.

Usage

data(syncSeq)

Format

List containing two data frames

data

syncSeq replication profiles data. Columns: 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)

guide

Guide dataframe for plotting the syncSeq data order (Order to plot data in), name.rep (Name of replicating sample), name.nonRep (Name of non-replicating sample), raw (Should raw data be plotted?), smooth (Should smooth data be plotted?), color (Color to plot the profile in)

Source

GEO

References

Müller et al. (2014) NAR 42(1):e3 (PubMed)

Examples

data(syncSeq)

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