|
| Status |
Public on Jun 18, 2012 |
| Title |
yeast_0.4mM_H2O2_wildtype_40min |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
total RNA from S. cerevisiae
|
| Organism |
Saccharomyces cerevisiae S288C |
| Characteristics |
strain: BY4741
time: 40 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 |
total RNA |
| Extraction protocol |
Yeast were grown at least 10 generations to OD(600) ~0.6. Total RNA was isolated from unstressed and cells treated with 0.4mM H2O2. Cell lysis and RNA extraction were performed as in Gasch AP, Methods in Enzymology 350: 393-414. cDNA synthesis was performed using both random hexamers and oligo-dT to obtain cDNA from total RNA.
|
| Label |
Oyster 650 cyanine dye
|
| Label protocol |
Indirect labelling using amino-allyl-dUTP as described in Gasch AP, Methods in Enzymology 350: 393-414
|
| |
|
| Channel 2 |
| Source name |
total RNA from S. cerevisiae
|
| Organism |
Saccharomyces cerevisiae S288C |
| Characteristics |
strain: BY4741
time: 0 min (no treatment)
|
| Treatment protocol |
none
|
| Growth protocol |
yeast were grown at least 10 generations to log phase (OD600 ~0.6) in YPD at 30C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Yeast were grown at least 10 generations to OD(600) ~0.6. Total RNA was isolated from unstressed and cells treated with 0.4mM H2O2. Cell lysis and RNA extraction were performed as in Gasch AP, Methods in Enzymology 350: 393-414. cDNA synthesis was performed using both random hexamers and oligo-dT to obtain cDNA from total RNA.
|
| Label |
Oyster 550 cyanine dye
|
| Label protocol |
Indirect labelling using amino-allyl-dUTP as described in Gasch AP, Methods in Enzymology 350: 393-414
|
| |
|
| |
| Hybridization protocol |
cDNA from stressed and unstressed 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 |
312201-4
|
| 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 probes were assigned to genes if they were fully-enclosed within the transcript boundaries and median centered at the gene 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) |
| GSE30899 |
Gene expression dynamics in yeast BY4741 and a strain lacking MSN2 and MSN4 responding to 0.4mM H2O2 over time (0-60min) |
| GSE30901 |
Dynamic changes to nucleosome occupancy and genomic expression in yeast responding to oxidative stress |
|
