|
Status |
Public on Apr 25, 2013 |
Title |
252035310001_2_1-T5[B(5)/B(3)] |
Sample type |
RNA |
|
|
Channel 1 |
Source name |
T5_B
|
Organism |
Naumovozyma castellii |
Characteristics |
treatment: NaCl time point (minutes): 5
|
Treatment protocol |
Salt Stress: Cultures were grown to mid-log densities (between 5x10^7 and 1x10^8 cells/mL) at 30C and treated with NaCl to a final concentration of 0.3M. Samples were harvested at different time intervals (5, 15, 30, 60 minutes after treatment)
|
Growth protocol |
Cells were plated onto BMW plates from frozen glycerol stocks. After 2 days, cells were taken from plates and grown overnight in BMW medium at 30 ° C in a New Brunswick Scientific Edison model TC-7 roller drum on the highest speed until saturated (1-2 days). These saturated cultures were then used to inoculate 300 ml BMW batch cultures in 2 liter Erlenmeyer flasks at 1 x 106 cells/mL for the glucose depletion and repletion experiments described below. Flasks were transferred to New Brunswick Scientific Edison water bath model C76 shakers set to 200 rpm.
|
Extracted molecule |
total RNA |
Extraction protocol |
Qiagen Yeast RNA extraction
|
Label |
Cy5
|
Label protocol |
Total RNA samples were reverse transcribed to cDNA and labeled with either Cy3 or Cy5 using a modification of the protocol developed by Joe Derisi (UCSF) and Rosetta Inpharmatics (Kirkland, WA) that can be obtained at www.microarrays.com.
|
|
|
Channel 2 |
Source name |
T0_B
|
Organism |
Naumovozyma castellii |
Characteristics |
time point (minutes): 0
|
Treatment protocol |
Salt Stress: Cultures were grown to mid-log densities (between 5x10^7 and 1x10^8 cells/mL) at 30C and treated with NaCl to a final concentration of 0.3M. Samples were harvested at different time intervals (5, 15, 30, 60 minutes after treatment)
|
Growth protocol |
Cells were plated onto BMW plates from frozen glycerol stocks. After 2 days, cells were taken from plates and grown overnight in BMW medium at 30 ° C in a New Brunswick Scientific Edison model TC-7 roller drum on the highest speed until saturated (1-2 days). These saturated cultures were then used to inoculate 300 ml BMW batch cultures in 2 liter Erlenmeyer flasks at 1 x 106 cells/mL for the glucose depletion and repletion experiments described below. Flasks were transferred to New Brunswick Scientific Edison water bath model C76 shakers set to 200 rpm.
|
Extracted molecule |
total RNA |
Extraction protocol |
Qiagen Yeast RNA extraction
|
Label |
Cy3
|
Label protocol |
Total RNA samples were reverse transcribed to cDNA and labeled with either Cy3 or Cy5 using a modification of the protocol developed by Joe Derisi (UCSF) and Rosetta Inpharmatics (Kirkland, WA) that can be obtained at www.microarrays.com.
|
|
|
|
Hybridization protocol |
Standard Agilent protocols for Agilent 8x15K and 4x44K Oligo Microarrays
|
Scan protocol |
Arrays were scanned using an Agilent scanner and analyzed with Agilent’s feature extraction software version 10.5.1.1.
|
Description |
Biological replicate B, technical replicate 1
|
Data processing |
Agilent Feature Extraction Software (v 10.5.1.1) was used for background subtraction and LOWESS normalization. Reported expression values for each gene are median log2 ratios across all probes.
|
|
|
Submission date |
May 31, 2012 |
Last update date |
Apr 25, 2013 |
Contact name |
Ilan Wapinski |
E-mail(s) |
ilan@broadinstitute.org
|
Organization name |
Broad Institute
|
Lab |
Aviv Regev
|
Street address |
7 Cambridge Center
|
City |
Cambridge |
State/province |
MA |
ZIP/Postal code |
02140 |
Country |
USA |
|
|
Platform ID |
GPL10501 |
Series (1) |
GSE38478 |
Evolutionary principles of modular gene regulation in Yeasts |
|