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Sample GSM743962 Query DataSets for GSM743962
Status Public on Apr 17, 2012
Title CEN.PK113-7D, 2h oscillation period 11.13333 h
Sample type RNA
 
Source name CEN.PK113-7D, 2h oscillation period
Organism Saccharomyces cerevisiae
Characteristics strain: CEN.PK113-7D
phase angle: 568.83 degrees
Treatment protocol For cells with a ~2 h dissolved oxygen period, 32 samples (the pellet from 0.5 ml with the supernatant removed) were removed every 4 min, immediately frozen in liquid nitrogen, and store at -80 C.
Growth protocol CEN.PK113-7D (MATa), grown overnight in 20 ml YPD at 275 rpm and 30C, was inoculated into the fermentor. The fermentor maintained the pH, agitation speed, aeration, and temperature at 4.0, 750 rpm, 150 ml/min, and 30 oC, respectively. Cells were grown in either the B. Braun Biotech Biolab CP (Aylesbury, Buckinghamshire, UK) at 650 ml or the New Brunswick Scientific Bioflo 110 Fermentor/Bioreactor (Edison, NJ) at 850 ml volume. Continuous flow was started after 24-30 h by pumping in fermenter media (19.25 g/l D(+)glucose monohydrate, 5 g/l (NH4)2SO4, 2 g/l KH2PO4, 0.5 g/l MgSO4, 1 g/l yeast extract, 0.2 ml/l antifoam A, 0.1 g/l CaCl2, 0.02 g/l FeSO4, 0.01 g/l ZnSO4, 0.005 g/l CuSO4, 0.001 g/l MnCl2, and 1 ml/l 75% H2SO4) at a dilution rate of 0.086/h. Media with excess cells was pumped out of the fermentor to maintain a constant fermentor volume. The media was maintained at pH 4.0 with 2.5 N NaOH. The dilution rate was adjusted to 0.06-0.086/h to maintain the period.
Extracted molecule total RNA
Extraction protocol RNA was purified from the cells and DNA was digested with DNase 1 using the RiboPureTM Yeast kit (Ambion, Austin, TX) according to the manufacturer’s instructions, except the cells were lysed in a minibead beater (BioSpec Products, Bartlesville, OK) rather than by vortexing. The isolated RNA was analyzed for concentration and purity with the NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific, Wilmington, DE) and on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).
Label Biotin
Label protocol GeneChip Expression 3'-Amplification Reagents One-Cycle cDNA Synthesis Kit (Affymetrix, Santa Clara, CA) and oligo(dT) primers containing T7 RNA polymerase promoter was used to synthesize double-stranded cDNA from RNA adjusted to 1 mg/ml for each sample. Then, biotinylated cRNA was synthesized using the GeneChip IVT labeling kit from Affymetrix. After framentation to 35-200 bases according to the Affymetrix protocol, 5 micrograms was hybridized to Affymetrix GeneChip Yeast Genome 2.0 Array (Santa Clara, CA) for 16 h at 45°C. The arrays were washed and stained with streptavidin-phycoerythrin using an Affymetrix Fluidics Station 450.
 
Hybridization protocol Standard Affymetrix protocol
Scan protocol GeneChips were scanned using an Affymetrix GeneArray scanner according to the manufacturer’s instructions.
Description B583_yeast-R20
Data processing MicroArray Suite 6.1 and GCOS were used to quantify and analyze results. The submitted files show raw and unnormalized data adjusted for hybridization efficiency using biotinylated Escherichia coli standards.
 
Submission date Jun 17, 2011
Last update date Apr 17, 2012
Contact name shwe lynn chin
E-mail(s) shwe2414@yahoo.com
Organization name Beckman Research Institute
Department Biology
Street address 1500 E Duarte Rd.
City Duarte
ZIP/Postal code 91010
Country USA
 
Platform ID GPL2529
Series (2)
GSE30051 Dynamics of two oscillation phenotypes in S. cerevisiae [2hr]
GSE30053 Dynamics of two oscillation phenotypes in S. cerevisiae reveal a network of genome-wide transcriptional and cell cycle oscillators.

Data table header descriptions
ID_REF
VALUE MAS 6.1 signal intensity
ABS_CALL

Data table
ID_REF VALUE ABS_CALL
AFFX-BioB-5_at 335.2 P
AFFX-BioB-M_at 444 P
AFFX-BioB-3_at 333.9 P
AFFX-BioC-5_at 629 P
AFFX-BioC-3_at 944.4 P
AFFX-BioDn-5_at 1724.8 P
AFFX-BioDn-3_at 3840.4 P
AFFX-CreX-5_at 8647.3 P
AFFX-CreX-3_at 10051.8 P
AFFX-DapX-5_at 556.8 P
AFFX-DapX-M_at 1129 P
AFFX-DapX-3_at 1425.3 P
AFFX-LysX-5_at 66.1 P
AFFX-LysX-M_at 100.6 P
AFFX-LysX-3_at 280.6 P
AFFX-PheX-5_at 104.7 P
AFFX-PheX-M_at 141.7 P
AFFX-PheX-3_at 164.8 P
AFFX-ThrX-5_at 145.1 P
AFFX-ThrX-M_at 266.5 P

Total number of rows: 10928

Table truncated, full table size 199 Kbytes.




Supplementary file Size Download File type/resource
GSM743962.CEL.gz 1.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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