Comment[ArrayExpressAccession]	E-GEOD-18242
Public Release Date	2009-12-01												
Investigation Title	Saccharomyces cerevisiae cells: control vs positive supercoiling accumulation												
Comment[Submitted Name]	Saccharomyces cerevisiae cells: control vs positive supercoiling accumulation
Experiment Description	This SuperSeries is composed of the following subset Series: GSE18240: Saccharomyces cerevisiae cells: control vs positive supercoiling accumulation after 0, 30 and 120 min GSE18241: S. cerevisiae cells: control vs positive supercoiling accumulation in absence of telomere silencing after 0 and 120 min GSE18605: Saccharomyces cerevisiae cells: effect of Top2 depletion without accumulation of positive superhelical stress Refer to individual Series												
Date of Experiment													
Term Source Name	EFO
Term Source Version													
Term Source File	http://www.ebi.ac.uk/efo/efo.owl												
Person Last Name	Pina												
Person First Name	Benjamin												
Person Mid Initials													
Person Email	bpcbmc@cid.csic.es												
Person Affiliation	IDAEA-CSIC												
Person Phone	34 93 4006157												
Person Fax	34 93 2045904												
Person Address	IDAEA-CSIC, Jordi Girona, 18, Barcelona, Spain												
Person Roles	submitter												
Person Roles Term Source REF													
Person Roles Term Accession Number													
Normalization Type													
Normalization Term Accession Number													
Normalization Term Source REF													
Replicate Type													
Replicate Term Accession Number													
Replicate Term Source REF													
Experimental Design													
Experimental Design Term Accession Number													
Experimental Design Term Source REF													
Quality Control Type													
Quality Control Term Accession Number													
Quality Control Term Source REF													
Protocol Name	P-GSE18242-1	P-GSE18242-2	P-GSE18242-7	P-GSE18242-13	P-GSE18242-11	P-GSE18242-4	P-GSE18242-9	P-GSE18242-8	P-GSE18242-3	P-GSE18242-12	P-GSE18242-10	P-GSE18242-5	P-GSE18242-6
Protocol Description	ID_REF = <br>VALUE = Normalized log2 ratio (Cy3/Cy5) representing test/reference [(F532 Median-B532 Median)/(F635 Median-B635 Median)]	ID_REF = <br>VALUE = Normalized log2 ratio (Cy5/Cy3) representing test/reference [(F635 Median-B635 Median)/(F532 Median-B532 Median)]	Microarray prehybridization was performed in 5x SSC (SSC: 150 mM NaCl, 15mM Na-citrate, pH 7.0), 0.1% SDS, 1%BSA at 42ºC for 45 min. (Fluka, Sigma-Aldrich, Buchs SG, Switzerland). Labeled cDNA was dried in a vacuum trap and used as probe after resuspension in 110 μl of hybridization solution (50% Formamide, 5xSSC, 0.1% SDS, 100 μg/ml salmon sperm from Invitrogen, Carlsbad, CA, USA). Hybridization and washing were performed in a Lucidea Slide Pro System (GE Healthcare, Uppsala, Sweden).	Yeast cells were grown in minimal media until logarithmic phase.	JCW27-TOPA-SIR3 and JCW28-TOPA-SIR3 cells were grown in LEU- SD media until logarithmic phase.	JCW27-TOPA (delta top1) and JCW28-TOPA (delta top1 top2-4) cells were grown in LEU- SD media until logarithmic phase.	Data was filtered according to spot quality. Only those spots with intensities at least twice the background signal and with at least 75% of pixels with intensities above background plus two standard deviations were selected for further calculations. Following these criteria, over 70% of spots in each array were usually found suitable for further analysis. Ratio of medians was used to calculate the VALUEs.	GenePix 4000B fluorescence scanner and analyzed by Genepix® Pro 6.0 software (Axon Instruments, MDS Analytical Technologies, Toronto, Canada).	Upon reaching logarithmic phase, cells were passed to 35C to inactivate top2. Samples were taken at 0, 30 and 120min top2 inactivation (35C).	Upon reaching logarithmic phase, cells were passed to 35C to inactivate top2. Samples were taken at 0 and 120 min top2 inactivation (35C).	Upon reaching logarithmic phase, cells were passed to 35C to inactivate top2. Samples were taken at 0 and 120min top2 inactivation (35C).	Total RNA extracted by RiboPure RNA extraction kit (Ambion) following manufacturer's instructions.	20 µg of total RNA were used for cDNA synthesis and labeling with Cy3-dUTP and Cy5-dUTP fluorescent nucleotides, following indirect labeling protocol (CyScribe postlabeling kit, GE-Healthcare). Labeling efficiency was evaluated by measuring Cy3 or Cy5 absorbance in Nanodrop Spectrophotometer.
Protocol Software													
Protocol Hardware													
Protocol Contact													
Protocol Type	bioassay_data_transformation	bioassay_data_transformation	hybridization	grow	grow	grow	feature_extraction	image_aquisition	specified_biomaterial_action	specified_biomaterial_action	specified_biomaterial_action	nucleic_acid_extraction	labeling
Protocol Term Source REF													
Protocol Term Accession Number													
Experimental Factor Name	TREATMENT	STRAIN OR LINE	GENOTYPE										
Experimental Factor Type	treatment	strain or line	genotype										
Experimental Factor Term Source REF													
Experimental Factor Term Accession Number													
Publication Title	Positional dependence of transcriptional inhibition by DNA torsional stress in yeast chromosomes.												
Publication Author List	Joshi RS, Piña B, Roca J												
PubMed ID	20057354												
Publication DOI	10.1038/emboj.2009.391												
Publication Status													
Publication Status Term Source REF													
Publication Status Term Accession Number													
Comment[SecondaryAccession]	GSE18242												
Comment[GEOLastUpdateDate]	2012-03-21
Comment[AEExperimentType]	transcription profiling by array												
Comment[GEOReleaseDate]	2009-12-01
Comment[ArrayExpressSubmissionDate]	2009-09-22
SDRF File	E-GEOD-18242.sdrf.txt