|
| Status |
Public on Oct 01, 2012 |
| Title |
WT Sporulation timepoint 6h |
| Sample type |
genomic |
| |
|
| Source name |
sporulating cells
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
genotype/variation: WT
timepoint: 6h
strain: SK1 background
|
| Treatment protocol |
200 O.D. pellets were collected at each timepoint, crosslinked with methanol-free formaldehyde at 1% for 15min at room temperature. Crosslinking reaction was quenched by adding Glycine to 125mM for 10 min. Cells were washed twice with PBS buffer and flash frozen in liquid nitrogen.
|
| Growth protocol |
Standard budding yeast sporulation protocols
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Crosslinked cell pellets were lysed by first sonication using a Diagenode Bioruptor for two cycles of 15min with a 15min rest on ice. For samples from 8h of sporulation or later, cells were then vortexed for 1h at 4°C. This was followed by bead beating for 7 cycles of 1 min with 2 min rests on ice. Mononucleosomal DNA was prepared from these extracts as described in Lee et al. 2007 "A high-resolution atlas of nucleosome occupancy in yeast"
|
| Label |
Biotin
|
| Label protocol |
Mono-nucleosomal DNA was DNase I digested to 50-90bp fragments, then end labelled with biotin.
|
| |
|
| Hybridization protocol |
5ug of mononucleosomal DNA was hybridized per array.
|
| Scan protocol |
Affymetrix scanner 3000 7G
|
| Data processing |
Cross-quantile normalization and median centering was done with Tiling Analysis Software (TAS)
|
| |
|
| Submission date |
Sep 13, 2012 |
| Last update date |
Oct 01, 2012 |
| Contact name |
Mengshu Xu |
| E-mail(s) |
mengshu.xu@mail.utoronto.ca
|
| Phone |
416 978 7599
|
| Organization name |
University of Toronto
|
| Department |
Molecular Genetics
|
| Lab |
Meneghini
|
| Street address |
1 King's College Circle
|
| City |
Toronto |
| State/province |
ON |
| ZIP/Postal code |
m5S 1A8 |
| Country |
Canada |
| |
|
| Platform ID |
GPL13990 |
| Series (1) |
| GSE40874 |
Nucleosome occupancy microarray for WT and jhd2-delete strains though sporulation |
|
