|
| Status |
Public on Jan 12, 2015 |
| Title |
R-1h-BPS |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
mec1_G1
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: WFA73
genotype: mec1
|
| Growth protocol |
Log phase cells were synchronized by alpha factor in G1 and released into S phase in the presence of 200 mM HU for 1h. Cells were then filtered to remove HU and allowed to recover in fresh media with or without 0.8 micromolar BPS for 1h.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DSB-labeled chromosomal DNA was extracted from agarose plugs by beta-agarase digestion and sonicated in a Bioruptor to reduce DNA fragment size to an average of 500 bp.
|
| Label |
Cy5
|
| Label protocol |
Agarose-embedded chromosomal DNA samples were differentially labeled for DSBs by End-Repair reaction (Epicentre) with Cy5- or Cy3-conjugated dUTP. All procedures were performed as previously described (Feng et al., G3(Bethesda) 2011 Oct;1(5):327-35. doi: 10.1534/g3.111.000554).
|
| |
|
| Channel 2 |
| Source name |
mec1_R-1h-BPS
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: WFA73
genotype: mec1
|
| Growth protocol |
Log phase cells were synchronized by alpha factor in G1 and released into S phase in the presence of 200 mM HU for 1h. Cells were then filtered to remove HU and allowed to recover in fresh media with or without 0.8 micromolar BPS for 1h.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DSB-labeled chromosomal DNA was extracted from agarose plugs by beta-agarase digestion and sonicated in a Bioruptor to reduce DNA fragment size to an average of 500 bp.
|
| Label |
Cy3
|
| Label protocol |
Agarose-embedded chromosomal DNA samples were differentially labeled for DSBs by End-Repair reaction (Epicentre) with Cy5- or Cy3-conjugated dUTP. All procedures were performed as previously described (Feng et al., G3(Bethesda) 2011 Oct;1(5):327-35. doi: 10.1534/g3.111.000554).
|
| |
|
| |
| Hybridization protocol |
In each experiment a G1 control sample and an S phase sample (R-1h-BPS or R-1h+BPS) were paired and the DNA cohybridized to Agilent G4493A Yeast Whole Genome ChIP-on-Chip 4x44k microarrays.
|
| Scan protocol |
Scanned on an Agilent G2565B scanner.
Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).
|
| Data processing |
Agilent Feature Extraction Software (v 9.5.1) was used for background subtraction and LOWESS normalization. Chromosome coordinates (kb) for each probe were extracted.
|
| |
|
| Submission date |
Dec 22, 2014 |
| Last update date |
Jan 12, 2015 |
| Contact name |
Wenyi Feng |
| E-mail(s) |
[email protected]
|
| Phone |
3154648701
|
| Organization name |
SUNY Upstate Medical University
|
| Department |
Biochemistry and Molecular Biology
|
| Lab |
Wenyi Feng
|
| Street address |
750 East Adams Street
|
| City |
Syracuse |
| State/province |
NY |
| ZIP/Postal code |
13210 |
| Country |
USA |
| |
|
| Platform ID |
GPL10930 |
| Series (2) |
| GSE63517 |
Break-Seq and RNA-seq analysis of gene expression during and after exposure to hydroxyurea in WT and mec1 cells in Saccharomyces cerevisiae |
| GSE64446 |
Saccharomyces cerevisiae: DSB mapping by Break-chip in a two-color experiment (G1 control vs. S phase samples) |
|
