|
| Status |
Public on Oct 02, 2014 |
| Title |
MS_42.1 EtOH 30 min rep2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
MS_42.1 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected 30 min rep2
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
treatment: grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected 30 min rep2
strain: MS_42.1
|
| Treatment protocol |
Ethanol was added to a final concentration of 5% (v/v) for 30 min
|
| Growth protocol |
Cells were grown in YPD (2% peptone, 2% dextrose, 1% yeast extract) for 4 generations to an OD600 of 0.3. A sample of unstressed cells was collected directly prior to ethanol treatment.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Hot phenol extraction as in Gasch, Methods in Enzymology, 2002
|
| Label |
Oyster cyanine 650 dye
|
| Label protocol |
Cyanine dyes (Flownamics, Madison, WI) were used; otherwise, as in Gasch, Methods in Enzymology, 2002
|
| |
|
| Channel 2 |
| Source name |
MS_42.1 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected 30 min rep2
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
treatment: grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected 30 min rep2
strain: MS_42.1
|
| Treatment protocol |
Ethanol was added to a final concentration of 5% (v/v) for 30 min
|
| Growth protocol |
Cells were grown in YPD (2% peptone, 2% dextrose, 1% yeast extract) for 4 generations to an OD600 of 0.3. A sample of unstressed cells was collected directly prior to ethanol treatment.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Hot phenol extraction as in Gasch, Methods in Enzymology, 2002
|
| Label |
Oyster 550 cyanine dye
|
| Label protocol |
Cyanine dyes (Flownamics, Madison, WI) were used; otherwise, as in Gasch, Methods in Enzymology, 2002
|
| |
|
| |
| Hybridization protocol |
Hybridized for 16 hours on a Maui hybridization machine as per Nimblegen protocol.
|
| Scan protocol |
Arrays were scanned using GenePix (4000B from Axon Instruments)
|
| Data processing |
Data were extracted and background subtracted using Nimblescan version 2.6.0.0. Probe data from the entire data set were quantile normalized together using the bioconductor affy package. Gene expression changes were calculated as the median log2 ratio for all of the probes that completely encompassed the open reading frame of interest. Probes with mismatches against either the YPS163 or M22 genome sequences were excluded from the analysis.
|
| |
|
| Submission date |
Jan 17, 2014 |
| Last update date |
Oct 02, 2014 |
| Contact name |
Jeffrey A. Lewis |
| E-mail(s) |
[email protected]
|
| Phone |
608-347-3661
|
| Organization name |
University of Arkansas
|
| Department |
Biological Sciences
|
| Lab |
Lewis Lab
|
| Street address |
850 W. Dickson St.
|
| City |
Fayetteville |
| State/province |
AR |
| ZIP/Postal code |
72701 |
| Country |
USA |
| |
|
| Platform ID |
GPL13254 |
| Series (1) |
| GSE54196 |
eQTL Mapping of the Yeast Ethanol Response |
|
