|
| Status |
Public on Jun 18, 2012 |
| Title |
MNase_yeast_0.4mM_H2O2_msn24_0min |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Nucleosomes from S. cerevisiae
|
| Organism |
Saccharomyces cerevisiae S288C |
| Characteristics |
strain: BY4741 msn2∆msn4∆
time: 0 min
|
| Treatment protocol |
0.4 mM H2O2
|
| Growth protocol |
yeast were grown at least 10 generations to log phase (OD600 ~0.6) in YPD at 30C
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Yeast were grown at least 10 generations to OD(600) ~0.6. Unstressed and cells treated with 0.4mM H2O2 were treated with formaldehyde (1%) for 15 minutes at 25C and quenched with 125mM glycine. Cells were digested to spheroplasts with Zymolyase and treated with micrococcal nuclease for 20 minutes at 37C. DNA was purified and amplified using the In vitro transcription method as described in Liu et al (PLoS Biol, 2005).
|
| Label |
Oyster 650 cyanine dye
|
| Label protocol |
Indirect labelling using amino-allyl-dUTP as described in Gasch AP, Methods in Enzymology 350:393-415.
|
| |
|
| Channel 2 |
| Source name |
Sheared genomic DNA from S. cerevisiae
|
| Organism |
Saccharomyces cerevisiae S288C |
| Characteristics |
strain: BY4741 msn2∆msn4∆
time: 0 min
|
| Treatment protocol |
0.4 mM H2O2
|
| Growth protocol |
yeast were grown at least 10 generations to log phase (OD600 ~0.6) in YPD at 30C
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Yeast were grown at least 10 generations to OD(600) ~0.6. Unstressed and cells treated with 0.4mM H2O2 were treated with formaldehyde (1%) for 15 minutes at 25C and quenched with 125mM glycine. Cells were digested to spheroplasts with Zymolyase and treated with micrococcal nuclease for 20 minutes at 37C. DNA was purified and amplified using the In vitro transcription method as described in Liu et al (PLoS Biol, 2005).
|
| Label |
Oyster 550 cyanine dye
|
| Label protocol |
Indirect labelling using amino-allyl-dUTP as described in Gasch AP, Methods in Enzymology 350:393-415.
|
| |
|
| |
| Hybridization protocol |
DNA from Nucleosomal and gDNA samples were mixed in equal mass with 2X Nimblegen Hybridization Buffer, Nimblegen Solution A and pre-labeled CPK6 alignment oligo and applied to arrays according to standard Nimblegen protocols.
|
| Scan protocol |
Arrays were scanned on an Axon 4000B scanner according to standard Nimblegen protocols.
|
| Description |
325484-1
|
| Data processing |
Data were extracted using NimbleScan. Background was calculated based on empty regions throughout the array and data probes were removed if they had signal <2X std. dev. from the average of the empty spots. The remaining data was quantile normalized using Bioconductor.
|
| |
|
| Submission date |
Jul 25, 2011 |
| Last update date |
Jun 18, 2012 |
| Contact name |
Dana J Huebert |
| Organization name |
University of Wisconsin-Madison
|
| Department |
Genetics
|
| Lab |
Audrey Gasch
|
| Street address |
425G Henry Mall
|
| City |
Madison |
| State/province |
WI |
| ZIP/Postal code |
53706 |
| Country |
USA |
| |
|
| Platform ID |
GPL9529 |
| Series (2) |
| GSE30897 |
Nucleosome occupancy in yeast BY4741and a strain lacking MSN2 and MSN4 responding to 20 min treatment with 0.4mM H2O2 |
| GSE30901 |
Dynamic changes to nucleosome occupancy and genomic expression in yeast responding to oxidative stress |
|
