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Sample GSM770893 Query DataSets for GSM770893
Status Public on Sep 29, 2011
Title far1Δ, glucose, biological rep2
Sample type RNA
 
Source name far1Δ, glucose
Organism Saccharomyces cerevisiae
Characteristics genotype: W303-1A (MATa ade2-1 his3-11 leu2-3,112 trp1-1 ura3-1 can1-100 far1Δ)
carbon source: glucose
Growth protocol Yeast strains were collected from glycerol stocks stored at -80°C with a hot sterile rod, without letting the stock to thaw. These cells were grown o/n and used to inoculate fresh synthetic complete medium at a density of about 2*10^5 cell/ml. Cells were then collected during exponential growth (beteween) 3*10^6 e 7*10^6 and used for RNA extraction as described in extract protocol.
Extracted molecule total RNA
Extraction protocol Typically 1*10^9 cells/sample were collected by filtration, washed two times with cold water and immediately freezed at –80°C. For RNA extraction, samples were kept on ice till they were completely thawed. Cells were resuspended in LETS 2X buffer (0.2M LiCl, 0.02M EDTA, 0.4% SDS, 0.02M Tris-HCl, pH=7.4) and phenol/chloroform/isoamylalcohol (PCI) (25:24:1, v/v). After the addition of acid-washed glass beads (Sigma), cells were broken by three vortex/ice cycles of 45 sec each on ice. Suspension was centrifuged (30’, 13000 rpm) and the upper phase was extracted twice with about one volume of PCI. The acqueous layer was collected and precipitated with LiCl (0.5M final concentration) and ethanol at -80°C. Total RNA was purified using the RNeasy RNA purification kit (Quiagen) and stored in RNase-free water.
Label biotin
Label protocol cRNA was generated by using the Affymetrix One-Cycle Target Labeling and Control Reagent kit (Affymetrix Inc., Santa Clara, CA) following the protocol of the manufacturer.
 
Hybridization protocol cRNA was generated by using the Affymetrix One-Cycle Target Labeling and Control Reagent kit (Affymetrix Inc., Santa Clara, California, USA), following the manufacturer’s protocol. The biotinylated cRNA was hybridized to the YG_S98 Affymetrix DNA chips, containing 9335 probe sets which represent approximately 7000 genes and open reading frames from S. cerevisiae Genome database. Chips were washed and scanned on the Affymetrix Complete GeneChip Instrument System, generating digitized image data (DAT) files.
Scan protocol Chips were washed and scanned on the Affymetrix Complete GeneChip Instrument System, generating digitized image data files.
Data processing GeneChip operating system (GCOS).
 
Submission date Aug 02, 2011
Last update date Oct 06, 2014
Contact name Chiara Balestrieri
E-mail(s) balestrieri.c@gmail.com
Organization name IRCCS San Raffaele Scientific Institute
Department Center for Omics Sciences
Street address Via Olgettina 58
City Milan
ZIP/Postal code 20132
Country Italy
 
Platform ID GPL90
Series (1)
GSE31143 Coordinated increase in cellular RNA and protein content induced by overexpression of Far1, a cyclin dependent kinase inhibitor, involves large transcriptional reprogramming and requires the Sfp1 protein.

Data table header descriptions
ID_REF
VALUE MAS 5.0 signal
ABS_CALL
DETECTION P-VALUE

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-MurIL2_at 0.8 A 0.868639
AFFX-MurIL10_at 0.1 A 0.966323
AFFX-MurIL4_at 0.1 A 0.996408
AFFX-MurFAS_at 0.2 A 0.981719
AFFX-BioB-5_at 118.8 P 0.00007
AFFX-BioB-M_at 205.3 P 0.000044
AFFX-BioB-3_at 162.5 P 0.000044
AFFX-BioC-5_at 216.7 P 0.000044
AFFX-BioC-3_at 231.9 P 0.000044
AFFX-BioDn-5_at 736.2 P 0.000044
AFFX-BioDn-3_at 1545.6 P 0.000044
AFFX-CreX-5_at 2207.3 P 0.000044
AFFX-CreX-3_at 2599.3 P 0.000044
AFFX-BioB-5_st 1.8 A 0.5
AFFX-BioB-M_st 0.5 A 0.772364
AFFX-BioB-3_st 5 A 0.216504
AFFX-BioC-5_st 4.5 A 0.440646
AFFX-BioC-3_st 3.1 A 0.062929
AFFX-BioDn-5_st 13.8 A 0.102165
AFFX-BioDn-3_st 11.6 P 0.002275

Total number of rows: 9335

Table truncated, full table size 219 Kbytes.




Supplementary file Size Download File type/resource
GSM770893_far1d_G_2.CEL.gz 1.0 Mb (ftp)(http) CEL
Processed data included within Sample table

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