|
| Status |
Public on Mar 31, 2013 |
| Title |
rad53.MMS vs. rad53.UT, rep2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
rad53, untreated
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
genetic background: BY4741
genotype/variation: rad53Δ
treatment: none
|
| Treatment protocol |
Conditions are untreated (UT) or methyl methanesulfonate (MMS-0.033%) treated.
|
| Growth protocol |
For these experiments, 100 ml cultures for each strain were grown to an OD600 density of 0.8-1.0 at 30oC, split into two 50 ml cultures, and incubated for one additional hour either in the presence (MMS-treated) or absence (untreated) of 0.03% MMS (methyl methanesulfonate; Sigma 129925).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated by hot phenol/chloroform extraction and enriched for mRNA via the Poly(A) Purist Kit (Ambion AM1916, Austin, TX, USA).
|
| Label |
Cy3
|
| Label protocol |
As described in Kuo D, Tan K, Zinman G, Ravasi T, Bar-Joseph Z, Ideker T (2010) Evolutionary divergence in the fungal response to fluconazole revealed by soft clustering. Genome Biol 11: R77 (PMID 20653936).
|
| |
|
| Channel 2 |
| Source name |
rad53, MMS
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
genetic background: BY4741
genotype/variation: rad53Δ
treatment: methyl methanesulfonate (MMS)
|
| Treatment protocol |
Conditions are untreated (UT) or methyl methanesulfonate (MMS-0.033%) treated.
|
| Growth protocol |
For these experiments, 100 ml cultures for each strain were grown to an OD600 density of 0.8-1.0 at 30oC, split into two 50 ml cultures, and incubated for one additional hour either in the presence (MMS-treated) or absence (untreated) of 0.03% MMS (methyl methanesulfonate; Sigma 129925).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated by hot phenol/chloroform extraction and enriched for mRNA via the Poly(A) Purist Kit (Ambion AM1916, Austin, TX, USA).
|
| Label |
Cy5
|
| Label protocol |
As described in Kuo D, Tan K, Zinman G, Ravasi T, Bar-Joseph Z, Ideker T (2010) Evolutionary divergence in the fungal response to fluconazole revealed by soft clustering. Genome Biol 11: R77 (PMID 20653936).
|
| |
|
| |
| Hybridization protocol |
According to the protocol recommended by Agilent.
|
| Scan protocol |
GenePix 4000A Scanner, Quantitation w/ GenePix 6.0.
|
| Description |
US22502657_251507211177_S01_H_flip_1-4.avg
|
| Data processing |
Lowess normalized, quantile normalized, LIMMA model.
|
| |
|
| Submission date |
Aug 23, 2012 |
| Last update date |
May 07, 2013 |
| Contact name |
Eric Jaehnig |
| E-mail(s) |
ejaehnig@ucsd.edu
|
| Organization name |
Ludwig Institute for Cancer Research
|
| Department |
Laboratory of Cancer Genetics
|
| Lab |
Kolodner
|
| Street address |
9500 Gilman Dr
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093 |
| Country |
USA |
| |
|
| Platform ID |
GPL9294 |
| Series (1) |
| GSE40351 |
DNA damage checkpoint kinases regulate a global network of transcription factors |
|
