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Sample GSM21685 Query DataSets for GSM21685
Status Public on Aug 01, 2005
Title E3_T2_R1, 50% dry
Sample type RNA
 
Source name BY4743(S288C)
Organism Saccharomyces cerevisiae
Extracted molecule total RNA
 
Description Stock and seed cultures of strain BY4743 were grown in yeast extract-peptone-dextrose (YPD) medium (10 mg/ml yeast extract, 20 mg/ml bactopeptone, 20 mg/ml glucose, pH 6.5 ± 0.2), at 30°C until the A600 reached 0.8. Cells were centrifuged and the cell pellet was resuspended and dispersed in 1:20 diluted YPD medium at between 22 to 25 °C. An aliquot, which represent the control sample (T1), was removed for RNA extraction, and the remaining suspension was aliquoted into 9-cm diameter glass Petri dishes (15 ml/dish) for desiccation.
Desiccation was carried out in a custom-fabricated controlled atmosphere desiccation system, at 22 to 25 °C. For more information on the unit and software, contact the corresponding author. A series of aliquots were withdrawn from the cell suspensions 18h (T2) after the start of the drying process.
Samples were collected on a volume basis and were in the same ratio as collected at T1. Once dry (42 h), the water potential was adjusted to 20% relative humidity for a period of 72 hr. A sample was collected at this timepoint, representing the dry sample (Tdry). Dry cells were hydrated (22 to 25 °C ) using 1:20 diluted YPD medium, 15 ml per plate. Resuspended cells from the four plates were pooled in a sterile 250 ml flask. Samples were collected for various analyses at time points of 15 min (T4), 45 min (T5), 90 min (T6) and 360 min (T7) after the start of rehydration.
Total RNA was isolated essentially as described (Schmitt, M. E., Brown, T. A., and Trumpower, B. L. (1990) Nucl. Acids Res. 18, 3091-3092). RNA was quantified using a spectrophotometer, and its quality was assessed using the A260/A280 ratio.
Target cRNA was hybridized to Affymetrix Y98 chips (GPL90) and raw image data was analyzed using the GeneChip Expression Analysis Software (Affymetrix). Probe set signals were processed by a Wilcoxon’s signed rank test and consolidated using a two-step linear mixed model. This sample is known as E3_T2_R1, 50% dry.
 
Submission date Apr 14, 2004
Last update date Oct 28, 2005
Contact name Richard F. Helm
E-mail(s) helmrf@vt.edu
Phone 540-231-4088
Fax 540-231-9070
URL http://vigen.biochem.vt.edu
Organization name Virginia Polytechnic Institute and State University
Department Biochemistry, Fralin Biotechnology Center
Lab Virginia Tech Center for Genomics
Street address West Campus Drive
City Blacksburg
State/province VA
ZIP/Postal code 24061
Country USA
 
Platform ID GPL90
Series (1)
GSE1313 YDRseries3, Yeast desiccation / rehydration time course

Data table header descriptions
ID_REF
VALUE 'signal' a measure of the abundance of a transcript
ABS_CALL the call in an absolute analysis that indicates if the transcript was present (P), absent (A), marginal (M), or no call (NC)
DETECTION P-VALUE 'detection p-value', p-value that indicates the significance level of the detection call

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-MurIL2_at 3 A 0.990663
AFFX-MurIL10_at 1.2 A 0.995983
AFFX-MurIL4_at 11.2 A 0.41138
AFFX-MurFAS_at 2.5 A 0.737173
AFFX-BioB-5_at 76.9 A 0.067678
AFFX-BioB-M_at 56.8 P 0.004017
AFFX-BioB-3_at 57.4 M 0.054213
AFFX-BioC-5_at 716.3 P 0.000754
AFFX-BioC-3_at 421.7 P 0.000225
AFFX-BioDn-5_at 412.1 P 5.2e-05
AFFX-BioDn-3_at 1937.3 P 5.2e-05
AFFX-CreX-5_at 1662.7 P 4.4e-05
AFFX-CreX-3_at 2101.6 P 4.4e-05
AFFX-BioB-5_st 3.1 A 0.672921
AFFX-BioB-M_st 3.3 A 0.904333
AFFX-BioB-3_st 4.4 A 0.960339
AFFX-BioC-5_st 5.7 A 0.814869
AFFX-BioC-3_st 2.3 A 0.724854
AFFX-BioDn-5_st 8.6 A 0.916408
AFFX-BioDn-3_st 25.7 A 0.165861

Total number of rows: 9335

Table truncated, full table size 228 Kbytes.




Supplementary file Size Download File type/resource
GSM21685.CEL.gz 2.3 Mb (ftp)(http) CEL
GSM21685.DAT.gz 36.0 Mb (ftp)(http) DAT
GSM21685.EXP.gz 316 b (ftp)(http) EXP

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