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Sample GSM239212 Query DataSets for GSM239212
Status Public on Nov 01, 2007
Title Recovery from freezing (15 min) 1st
Sample type RNA
 
Channel 1
Source name Recovery from freezing (15 min), Cy5
Organism Saccharomyces cerevisiae
Characteristics strain S288C
Biomaterial provider Odani M
Treatment protocol Recovery from freezing (15 min)
Growth protocol Yeast strain S288C was grown until the exponential phase (A660, 1.0) in 600 ml YPD medium in a 3 L Erlenmeyer flask at 30 °C. An aliquot of 400 ml in a 3 L Erlenmeyer flask was frozen at −80 C without the addition of a cryoprotectant, and stored for 1 week. The frozen cell culture was then thawed at 30 °C in a water-bath for 25 min. The thawed cells were further incubated and an aliquot of 100 ml was sampled from the culture at 15 min after complete thawing.
Extracted molecule polyA RNA
Extraction protocol Hot-phenol and oligotex dt mRNA purification kit (TaKaRa)
Label Cy5-dUTP
Label protocol At least 4 µg of mRNA and a 0.4 µM oligo dT12-17 primer (GIBCO BRL; Life Technologies) were denatured at 70 ºC for 5 min, and the labeled cDNA was synthesized. The reaction mixture contained 0.5 mM each of dATP, dGTP, and dCTP; 0.2 mM dTTP (GIBCO BRL; Life Technologies); 15 mM Cy5-labeled dUTP (PE Applied Biosystems); 200 units of PowerScript Reverse Transcriptase (CLONTEC, Palo Alto, CA); and an appropriate buffer and RNase inhibiter (GIBCO BRL; Life Technologies). The reactions were performed at 42 ºC for 1h and 30 min. Another 200 units of transcriptase was added in the tubes 40 min after the beginning of reverse transcription. The template mRNA was dissolved by the addition of 0.5 N NaOH for 1 h at 65 ºC. After neutralization with 1 M Tris-HCl, Cy3- and Cy5-labeled cDNA solution was mixed and filtered on Microcon 30 (AMICON).
 
Channel 2
Source name control (before freezing treatment), Cy3
Organism Saccharomyces cerevisiae
Characteristics strain S288C
Biomaterial provider Odani M
Treatment protocol before freezing treatment
Growth protocol Yeast strain S288C was grown until the exponential phase (A660, 1.0) in 600 ml YPD medium in a 3 L Erlenmeyer flask at 30 °C. An aliquot of 200 ml was taken from the cell culture and used as the control without freezing.
Extracted molecule polyA RNA
Extraction protocol Hot-phenol and oligotex dt mRNA purification kit (TaKaRa)
Label Cy3-dUTP
Label protocol At least 4 µg of mRNA and a 0.4 µM oligo dT12-17 primer (GIBCO BRL; Life Technologies) were denatured at 70 ºC for 5 min, and the labeled cDNA was synthesized. The reaction mixture contained 0.5 mM each of dATP, dGTP, and dCTP; 0.2 mM dTTP (GIBCO BRL; Life Technologies); 15 mM Cy3-labeled dUTP (PE Applied Biosystems); 200 units of PowerScript Reverse Transcriptase (CLONTEC, Palo Alto, CA); and an appropriate buffer and RNase inhibiter (GIBCO BRL; Life Technologies). The reactions were performed at 42 ºC for 1h and 30 min. Another 200 units of transcriptase was added in the tubes 40 min after the beginning of reverse transcription. The template mRNA was dissolved by the addition of 0.5 N NaOH for 1 h at 65 ºC. After neutralization with 1 M Tris-HCl, Cy3- and Cy5-labeled cDNA solution was mixed and filtered on Microcon 30 (AMICON).
 
 
Hybridization protocol Hybridized for 16-18 h at 65 C
Scan protocol Scan Array 4000 (PerkinElmer Japan Co., Ltd) was used for scanning. Array images were analyzed with Gene Pix Pro 4.0 (Axon Instrument).
Description Data with flag value 0 were used for LOWESS normalization processing.
Data processing GeneSpring ver 7.3.1 (Agilent Technologies Inc.)
 
Submission date Oct 23, 2007
Last update date Aug 14, 2011
Contact name Emiko Kitagawa
E-mail(s) hitoshi.iwahashi@aist.go.jp
Phone +81-29-861-8508
Fax +81-29-861-8508
Organization name National Institute of Advanced Industrial Science and Technology
Street address Onogawa 16-1
City Tsukuba
State/province Ibaraki
ZIP/Postal code 305-8569
Country Japan
 
Platform ID GPL5992
Series (1)
GSE9404 Recovery from freezing

Data table header descriptions
ID_REF
Normalized ratio LOWESS normalized ratio (non-log)
VALUE LOWESS normalized log2 (treated/control) ratio
Cy5F Cy5 inner intensity (median)
Cy5B Cy5 intensity surrounding each spot (background), (median)
Cy3F Cy3 inner intensity (median)
Cy3B Cy3 intensity surrounding each spot (background), (median)
Cy5FB Cy5 intensity subtracted from background intensity
Cy3FB Cy3 intensity subtracted from background intensity
FlagGPR Flag from GenePix Pro analysis
Flag Additional flags by LOCUS_NAME1 as following; TE, TE; NG, NGT; QU, _ or -; C3, Cy3; C5, Cy5; EM, empty. Additional flags by Cy5F and Cy3F as following; BL, both data Cy3F and Cy5F is less than reliable limit; 5L, Cy5F is less than reliable limit; 3L, Cy3F is less than reliable limit; BM, both data Cy3F and Cy5F is over than scanning range; 5M, Cy5F is over than scanning range; 3M, Cy3F is over than scanning range.

Data table
ID_REF Normalized ratio VALUE Cy5F Cy5B Cy3F Cy3B Cy5FB Cy3FB FlagGPR Flag
1010101 1.1165036 0.158987903 4709 1812 7263 2088 2897 5175 0 0
1010201 1.5686496 0.649523124 7679 2154 9699 2294 5525 7405 0 0
1010301 1.3284221 0.409713629 6237 2349 8559 2412 3888 6147 0 0
1010401 1.4943548 0.579522723 5702 2268 7268 2593 3434 4675 0 0
1010501 0.99904686 -0.001375746 5442 2385 9611 3123 3057 6488 0 0
1010601 1.4297163 0.5157289 21273 2282 36782 3705 18991 33077 0 0
1010701 1.3060235 0.385180856 5965 2139 9140 2986 3826 6154 0 0
1010801 0.97057146 -0.043093657 4566 1909 8145 2739 2657 5406 0 0
1010901 0.87769055 -0.188215721 4779 1844 9357 2316 2935 7041 0 0
1011001 null null 3442 1871 5379 2166 1571 3213 -50 -50
1011101 null null 3379 2049 4304 2589 1330 1715 -50 -50
1011201 0.8599968 -0.217596803 4528 2127 8209 2732 2401 5477 0 0
1011301 1.1804131 0.239291837 5045 1933 7955 2523 3112 5432 0 0
1011401 1.3897517 0.474827147 3647 1817 4854 2612 1830 2242 0 0
1010102 1.655508 0.727273982 11036 2343 14811 2517 8693 12294 0 0
1010202 1.5349818 0.61822155 7444 2517 9389 2745 4927 6644 0 0
1010302 1.5788488 0.658873017 9091 2337 11889 2233 6754 9656 0 0
1010402 1.6438766 0.717102005 8334 2493 10174 2580 5841 7594 0 0
1010502 1.4173212 0.503166746 65535 2259 65535 3100 63276 62435 0 0
1010602 2.731165 1.449516475 53002 2317 36921 3244 50685 33677 0 0

Total number of rows: 6272

Table truncated, full table size 362 Kbytes.




Supplementary file Size Download File type/resource
GSM239212.gpr.gz 503.6 Kb (ftp)(http) GPR
Raw data included within Sample table
Raw data provided as supplementary file
Processed data included within Sample table

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