|
| Status |
Public on Jul 01, 2009 |
| Title |
nucleosome position |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
nucleosome position of wild type budding yeast strain
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
purified mononucleosome from gel
|
| Growth protocol |
Cells in YP + 2% glucose were collected in log phase
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Extraction was performed as previously described (yuan et al. 2005,Liu et al. 2005). For nucleosome position, we digested chromatin with Mnase to get mono nucleosome, then we purified mononucleosome from gel. For H4K16ac, we used antibody from abcam(ab61240) as the normal ChIP-chip study.
|
| Label |
Biotin
|
| Label protocol |
DNA was labeled with biotin-N6-dATP using terminal transferase TdT (Roche, 400U/ul)
|
| |
|
| Channel 2 |
| Source name |
genomic background control
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
control
|
| Growth protocol |
Cells in YP + 2% glucose were collected in log phase
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Extraction was performed as previously described (yuan et al. 2005,Liu et al. 2005). For nucleosome position, we digested chromatin with Mnase to get mono nucleosome, then we purified mononucleosome from gel. For H4K16ac, we used antibody from abcam(ab61240) as the normal ChIP-chip study.
|
| Label |
Biotin
|
| Label protocol |
DNA was labeled with biotin-N6-dATP using terminal transferase TdT (Roche, 400U/ul)
|
| |
|
| |
| Hybridization protocol |
Hybridization was performed as affymetrix protocol. Samples were hybridized for 16 hours at 42oC in a hybridization oven (GeneChip Hybridization Oven 640, Affymetrix)
|
| Scan protocol |
The washing and scanning protocol, provided by Affymetrix, was performed automatically on a fluidics station (GeneChip fluidics station 450, Affymetrix)
|
| Description |
This sample contains two replicates
Reference: Yuan GC, Liu YJ, Dion MF, Slack MD, Wu LF, Altschuler SJ, Rando OJ. Genome-scale identification of nucleosome positions in S. cerevisiae.
Reference: Liu CL, Kaplan T, Kim M, Buratowski S, Schreiber SL, Friedman N, Rando OJ. Single-nucleosome mapping of histone modifications in S. cerevisiae.
|
| Data processing |
We used affymetrix tiling array software(TAS) V1.1 to analyze our data. The raw cel data were imported into TAS as two analysis treatment group -- our IP or nucleosome sample and genomic background control. We use two side test, bandwidth is 70 for nucleosome and 150 for H4K16ac. Probe match chosen was PM/MM(perfect match/mismatch). Finally, we analyzed the intensity to get the Bar or CHP format signal files.
|
| |
|
| Submission date |
Nov 14, 2008 |
| Last update date |
Apr 21, 2009 |
| Contact name |
Claes M Gustafsson |
| E-mail(s) |
claes.gustafsson@medkem.gu.se
|
| Organization name |
Gothenburg University
|
| Department |
Department of Medical biochemistry and cell biology
|
| Street address |
Medcinaregatan 9A
|
| City |
Gothenburg |
| ZIP/Postal code |
405 30 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL7250 |
| Series (1) |
| GSE13615 |
Distinct differences in chromatin structure at telomeric X- and Y-elements in budding yeast. |
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