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Sample GSM940718 Query DataSets for GSM940718
Status Public on Apr 25, 2013
Title 251983810011_2_2-T15[B(5)/B(3)]
Sample type RNA
 
Channel 1
Source name T15_B
Organism Saccharomyces cerevisiae
Characteristics treatment: NaCl
time point (minutes): 15
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 Saccharomyces cerevisiae
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 GPL10786
Series (1)
GSE38478 Evolutionary principles of modular gene regulation in Yeasts

Data table header descriptions
ID_REF
VALUE normalized log2 [Cy5/Cy3]

Data table
ID_REF VALUE
A_06_P6503 0.083017498
A_06_P2668 -0.103174061
A_06_P4476 0.346490762
A_06_P5881 -4.326312802
A_06_P4363 0
A_06_P1152 -0.744089519
A_06_P5461 0.478270628
A_06_P6582 3.123384162
A_06_P1571 -0.184020707
A_06_P3669 5.667920056
A_06_P5892 -0.691682499
A_06_P2533 -0.380478277
A_06_P6342 -1.739088486
A_06_P3368 0.115481265
A_06_P4856
A_06_P5747 -1.502103092
A_06_P2805 0.068517603
A_06_P1634 0
A_06_P5363 -0.037568841
A_06_P5834 -0.141655153

Total number of rows: 6255

Table truncated, full table size 138 Kbytes.




Supplementary file Size Download File type/resource
GSM940718_251983810011_200811251102_S01_GE2-v5_10_Apr08_2_2.txt.gz 4.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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