|
| Status |
Public on Jul 08, 2010 |
| Title |
KL (time 2) Replicate 1 Dye Swap |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Reference Pool KL
|
| Organism |
Kluyveromyces lactis |
| Characteristics |
reference: Reference Pool KL
|
| Treatment protocol |
Add fluconazole (4ug/mL for Sc and Cg, 0.06125ug/mL for Kl) at time 0
|
| Growth protocol |
Grow samples at OD600 0.05 to 0.2. Treat half of sample with drug. Take samples at 0, 1/3, 2/3, 1, 2 and 4 doubling times (both treated and untreated).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA was extracted using hot phenol chloroform method. mRNA was isolated using Poly(A) purist kit (AM1916), Pool in equal amounts untreated samples for each replicate
|
| Label |
Cy5
|
| Label protocol |
Labeling performed using GE Healthcare Cyscribe First strand total RNA synthesis kit
|
| |
|
| Channel 2 |
| Source name |
NRRL Y-1140 time 2
|
| Organism |
Kluyveromyces lactis |
| Characteristics |
test: NRRL Y-1140
doubling time: 2
|
| Treatment protocol |
Add fluconazole (4ug/mL for Sc and Cg, 0.06125ug/mL for Kl) at time 0
|
| Growth protocol |
Grow samples at OD600 0.05 to 0.2. Treat half of sample with drug. Take samples at 0, 1/3, 2/3, 1, 2 and 4 doubling times (both treated and untreated).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA was extracted using hot phenol chloroform method. mRNA was isolated using Poly(A) purist kit (AM1916), Pool in equal amounts untreated samples for each replicate
|
| Label |
Cy3
|
| Label protocol |
Labeling performed using GE Healthcare Cyscribe First strand total RNA synthesis kit
|
| |
|
| |
| Hybridization protocol |
Oligoarray control targets and hybridization buffer were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially
|
| Scan protocol |
Arrays scanned using Genepix 4000A scanner and GenePix 6.0 software
|
| Description |
dye swap replicate
|
| Data processing |
Background subtraction and LOESS, missing values replaced by KNNimpute algorithm. Data was subsequently quantile normalized
|
| |
|
| Submission date |
Apr 16, 2009 |
| Last update date |
Jul 08, 2010 |
| Contact name |
Dwight Kuo |
| Organization name |
UCSD
|
| Department |
Bioengineering
|
| Lab |
Trey Ideker
|
| Street address |
9500 Gilman Dr.
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093 |
| Country |
USA |
| |
|
| Platform ID |
GPL8452 |
| Series (1) |
| GSE15710 |
Evolutionary divergence in the fungal response to fluconazole revealed by soft clustering (S. cerevisiae, C. glabrata, K. lactis) |
|
