|
| Status |
Public on Jun 18, 2012 |
| Title |
Msn2p_yeast_0.4mM_H2O2_4min |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Msn2Myc ChIP from S. cerevisiae
|
| Organism |
Saccharomyces cerevisiae S288C |
| Characteristics |
strain: BY4741
genotype/variation: integrated Msn2-Myc construct
time: 4 min
antibody: anti-c-Myc
|
| 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 cross-lined with 1% formaldehyde for 30 minutes at 25C and quenched with 125mM glycine for 5 minutes at 25C. Lysate was sonicated to produce chromatin fragments ~250-300bp in length. An aliquot was retained as Whole Cell Extract and an additional 1-2.5mg of protein was incubated with 5ul anti-c-Myc antibody (9E11, Abcam) overnight at 4C. Samples were amplified by the Ligation-mediated PCR method.
|
| 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 |
Input DNA from S. cerevisiae
|
| Organism |
Saccharomyces cerevisiae S288C |
| Characteristics |
strain: BY4741
genotype/variation: integrated Msn2-Myc construct
time: 4 min
antibody: none, input DNA
|
| 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 cross-lined with 1% formaldehyde for 30 minutes at 25C and quenched with 125mM glycine for 5 minutes at 25C. Lysate was sonicated to produce chromatin fragments ~250-300bp in length. An aliquot was retained as Whole Cell Extract and an additional 1-2.5mg of protein was incubated with 5ul anti-c-Myc antibody (9E11, Abcam) overnight at 4C. Samples were amplified by the Ligation-mediated PCR method.
|
| 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 ChIP and Whole Cell Extract 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 |
348473-1
|
| 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 were normalized by median centering at the probe level.
|
| |
|
| 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) |
| GSE30898 |
Msn2p occupancy dynamics in yeast BY4741 responding to 0.4mM H2O2 over time (0-60 min) |
| GSE30901 |
Dynamic changes to nucleosome occupancy and genomic expression in yeast responding to oxidative stress |
|
