NMRMetabolomeMetadata

Selected Cell

Cell:

Value:

s_BII-S-2 a_bii-s-2_metabolite profiling_ BII-1_investigation

Source Name

Characteristics[organism]

Term Source REF

Term Accession Number

Characteristics[strain]

Term Source REF

Term Accession Number

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Term Source REF

Term Accession Number

Characteristics[mating type]

Term Source REF

Term Accession Number

Protocol REF

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Unit

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Unit

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Term Accession Number

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Term Source REF

Term Accession Number

NZ_0hrs_Grow_1

Saccharomyces cerevisiae (Baker's yeast)

FY1679

KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD

mating type alpha

EFO

http://www.ebi.ac.uk/efo/EFO_0001270

growth protocol

NZ_0hrs_Grow1_Sample_1

ng /ml

hour

http://purl.obolibrary.org/obo/UO_0000032

NZ_0hrs_Grow_1

Saccharomyces cerevisiae (Baker's yeast)

FY1679

KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD

mating type alpha

EFO

http://www.ebi.ac.uk/efo/EFO_0001270

growth protocol

NZ_1hrs_Grow1_Drug_Sample_1

200

ng /ml

hour

http://purl.obolibrary.org/obo/UO_0000032

rapamycin

NZ_0hrs_Grow_1

Saccharomyces cerevisiae (Baker's yeast)

FY1679

KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD

mating type alpha

EFO

http://www.ebi.ac.uk/efo/EFO_0001270

growth protocol

NZ_2hrs_Grow1_Drug_Sample_1

200

ng /ml

hour

http://purl.obolibrary.org/obo/UO_0000032

rapamycin

NZ_0hrs_Grow_1

Saccharomyces cerevisiae (Baker's yeast)

FY1679

KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD

mating type alpha

EFO

http://www.ebi.ac.uk/efo/EFO_0001270

growth protocol

NZ_4hrs_Grow1_Drug_Sample_1

200

ng /ml

hour

http://purl.obolibrary.org/obo/UO_0000032

rapamycin

NZ_0hrs_Grow_1

Saccharomyces cerevisiae (Baker's yeast)

FY1679

KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD

mating type alpha

EFO

http://www.ebi.ac.uk/efo/EFO_0001270

growth protocol

NZ_2hrs_Grow1_Vehicle_Sample_1

ng /ml

hour

http://purl.obolibrary.org/obo/UO_0000032

drug vehicle (90% ethanol/10% tween-20)

NZ_0hrs_Grow_1

Saccharomyces cerevisiae (Baker's yeast)

FY1679

KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD

mating type alpha

EFO

http://www.ebi.ac.uk/efo/EFO_0001270

growth protocol

NZ_4hrs_Grow1_Vehicle_Sample_1

ng /ml

hour

http://purl.obolibrary.org/obo/UO_0000032

drug vehicle (90% ethanol/10% tween-20)

NZ_0hrs_Grow_1

Saccharomyces cerevisiae (Baker's yeast)

FY1679

KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD

mating type alpha

EFO

http://www.ebi.ac.uk/efo/EFO_0001270

growth protocol

NZ_1hrs_Grow1_Vehicle_Sample_1

ng /ml

hour

http://purl.obolibrary.org/obo/UO_0000032

drug vehicle (90% ethanol/10% tween-20)

NZ_0hrs_Grow_2

Saccharomyces cerevisiae (Baker's yeast)

FY1679

KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD

mating type alpha

EFO

http://www.ebi.ac.uk/efo/EFO_0001270

growth protocol

NZ_0hrs_Grow2_Sample_2

ng /ml

hour

http://purl.obolibrary.org/obo/UO_0000032

NZ_0hrs_Grow_2

Saccharomyces cerevisiae (Baker's yeast)

FY1679

KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD

mating type alpha

EFO

http://www.ebi.ac.uk/efo/EFO_0001270

growth protocol

NZ_1hrs_Grow2_Drug_Sample_2

200

ng /ml

hour

http://purl.obolibrary.org/obo/UO_0000032

rapamycin

NZ_0hrs_Grow_2

Saccharomyces cerevisiae (Baker's yeast)

FY1679

KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD

mating type alpha

EFO

http://www.ebi.ac.uk/efo/EFO_0001270

growth protocol

NZ_4hrs_Grow2_Drug_Sample_2

200

ng /ml

hour

http://purl.obolibrary.org/obo/UO_0000032

rapamycin

NZ_0hrs_Grow_2

Saccharomyces cerevisiae (Baker's yeast)

FY1679

KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD

mating type alpha

EFO

http://www.ebi.ac.uk/efo/EFO_0001270

growth protocol

NZ_2hrs_Grow2_Drug_Sample_2

200

ng /ml

hour

http://purl.obolibrary.org/obo/UO_0000032

rapamycin

NZ_0hrs_Grow_2

Saccharomyces cerevisiae (Baker's yeast)

FY1679

KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD

mating type alpha

EFO

http://www.ebi.ac.uk/efo/EFO_0001270

growth protocol

NZ_1hrs_Grow2_Vehicle_Sample_2

ng /ml

hour

http://purl.obolibrary.org/obo/UO_0000032

drug vehicle (90% ethanol/10% tween-20)

NZ_0hrs_Grow_2

Saccharomyces cerevisiae (Baker's yeast)

FY1679

KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD

mating type alpha

EFO

http://www.ebi.ac.uk/efo/EFO_0001270

growth protocol

NZ_2hrs_Grow2_Vehicle_Sample_2

ng /ml

hour

http://purl.obolibrary.org/obo/UO_0000032

drug vehicle (90% ethanol/10% tween-20)

NZ_0hrs_Grow_2

Saccharomyces cerevisiae (Baker's yeast)

FY1679

KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD

mating type alpha

EFO

http://www.ebi.ac.uk/efo/EFO_0001270

growth protocol

NZ_4hrs_Grow2_Vehicle_Sample_2

ng /ml

hour

http://purl.obolibrary.org/obo/UO_0000032

drug vehicle (90% ethanol/10% tween-20)

Sample Name

Protocol REF

Extract Name

Protocol REF

Labeled Extract Name

Label

Term Source REF

Term Accession Number

Protocol REF

Parameter Value[instrument]

Parameter Value[NMR Probe]

Parameter Value[number of acquisition]

Parameter Value[magnetic field strength]

Unit

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Free Induction Decay Data File

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Derived Spectral Data File

Metabolite Assignment File

extraction

labeling

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nmr assay

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ONTOLOGY SOURCE REFERENCE
Term Source Name	CHEBI	EFO	OBI	EHDAA	PATO	UO
Term Source File	http://data.bioontology.org/ontologies/CHEBI	http://data.bioontology.org/ontologies/EFO	http://data.bioontology.org/ontologies/OBI	http://data.bioontology.org/ontologies/EHDAA	http://data.bioontology.org/ontologies/PATO	http://data.bioontology.org/ontologies/UO
Term Source Version	78	110	21	6	160	42
Term Source Description	Chemical Entities of Biological Interest Ontology	Experimental Factor Ontology	Ontology for Biomedical Investigations	Human Developmental Anatomy Ontology, abstract version 1	Phenotypic Quality Ontology	Units of Measurement Ontology
INVESTIGATION
Investigation Identifier	BII-I-1
Investigation Title	Growth control of the eukaryote cell: a systems biology study in yeast
Investigation Description	Background Cell growth underlies many key cellular and developmental processes, yet a limited number of studies have been carried out on cell-growth regulation. Comprehensive studies at the transcriptional, proteomic and metabolic levels under defined controlled conditions are currently lacking. Results Metabolic control analysis is being exploited in a systems biology study of the eukaryotic cell. Using chemostat culture, we have measured the impact of changes in flux (growth rate) on the transcriptome, proteome, endometabolome and exometabolome of the yeast Saccharomyces cerevisiae. Each functional genomic level shows clear growth-rate-associated trends and discriminates between carbon-sufficient and carbon-limited conditions. Genes consistently and significantly upregulated with increasing growth rate are frequently essential and encode evolutionarily conserved proteins of known function that participate in many protein-protein interactions. In contrast, more unknown, and fewer essential, genes are downregulated with increasing growth rate; their protein products rarely interact with one another. A large proportion of yeast genes under positive growth-rate control share orthologs with other eukaryotes, including humans. Significantly, transcription of genes encoding components of the TOR complex (a major controller of eukaryotic cell growth) is not subject to growth-rate regulation. Moreover, integrative studies reveal the extent and importance of post-transcriptional control, patterns of control of metabolic fluxes at the level of enzyme synthesis, and the relevance of specific enzymatic reactions in the control of metabolic fluxes during cell growth. Conclusion This work constitutes a first comprehensive systems biology study on growth-rate control in the eukaryotic cell. The results have direct implications for advanced studies on cell growth, in vivo regulation of metabolic fluxes for comprehensive metabolic engineering, and for the design of genome-scale systems biology models of the eukaryotic cell.
Investigation Submission Date	2007-04-30T0:0:0+0000
Investigation Public Release Date	2009-03-10T0:0:0+0000
Comment [Created with configuration]
Comment [Last Opened With Configuration]	isaconfig-default_v2013-02-13
Comment [Owning Organisation URI]
Comment [Consortium URI]
Comment [Principal Investigator URI]
Comment [Investigation keywords]
INVESTIGATION PUBLICATIONS
Investigation PubMed ID	17439666	1231222	1234121
Investigation Publication DOI	doi:10.1186/jbiol54
Investigation Publication Author List	Castrillo JI, Zeef LA, Hoyle DC, Zhang N, Hayes A, Gardner DC, Cornell MJ, Petty J, Hakes L, Wardleworth L, Rash B, Brown M, Dunn WB, Broadhurst D, O'Donoghue K, Hester SS, Dunkley TP, Hart SR, Swainston N, Li P, Gaskell SJ, Paton NW, Lilley KS, Kell DB, Oliver SG.	Piatnochka IT.	Monticelli G, Santori S.
Investigation Publication Title	Growth control of the eukaryote cell: a systems biology study in yeast.	Effect of prednisolone on the cardiovascular system in complex treatment of newly detected pulmonary tuberculosis	Indications for the use of prostheses in the treatment of pathological fractures due to primary malignant and metastatic tumours of bone.
Investigation Publication Status	indexed in Pubmed	Published	Published
Investigation Publication Status Term Accession Number
Investigation Publication Status Term Source REF
INVESTIGATION CONTACTS
Investigation Person Last Name	Oliver	Juan	Leo
Investigation Person First Name	Stephen	Castrillo	Zeef
Investigation Person Mid Initials	G	I	A
Investigation Person Email
Investigation Person Phone
Investigation Person Fax
Investigation Person Address	Oxford Road, Manchester M13 9PT, UK	Oxford Road, Manchester M13 9PT, UK	Oxford Road, Manchester M13 9PT, UK
Investigation Person Affiliation	Faculty of Life Sciences, Michael Smith Building, University of Manchester	Faculty of Life Sciences, Michael Smith Building, University of Manchester	Faculty of Life Sciences, Michael Smith Building, University of Manchester
Investigation Person Roles	corresponding author	author	author
Investigation Person Roles Term Accession Number
Investigation Person Roles Term Source REF
Comment[Investigation Person REF]
STUDY
Study Identifier	BII-S-1
Study Title	Study of the impact of changes in flux on the transcriptome, proteome, endometabolome and exometabolome of the yeast Saccharomyces cerevisiae under different nutrient limitations
Study Description	We wished to study the impact of growth rate on the total complement of mRNA molecules, proteins, and metabolites in S. cerevisiae, independent of any nutritional or other physiological effects. To achieve this, we carried out our analyses on yeast grown in steady-state chemostat culture under four different nutrient limitations (glucose, ammonium, phosphate, and sulfate) at three different dilution (that is, growth) rates (D = u = 0.07, 0.1, and 0.2/hour, equivalent to population doubling times (Td) of 10 hours, 7 hours, and 3.5 hours, respectively; u = specific growth rate defined as grams of biomass generated per gram of biomass present per unit time).
Comment[Study Grant Number]
Comment[Study Funding Agency]
Study Submission Date	2007-04-30T0:0:0+0000
Study Public Release Date	2009-03-10T0:0:0+0000
Study File Name	s_BII-S-1.txt
STUDY DESIGN DESCRIPTORS
Study Design Type	intervention design
Study Design Type Term Accession Number	http://purl.obolibrary.org/obo/OBI_0000115
Study Design Type Term Source REF	OBI
STUDY PUBLICATIONS
Study PubMed ID	17439666
Study Publication DOI	doi:10.1186/jbiol54
Study Publication Author List	Castrillo JI, Zeef LA, Hoyle DC, Zhang N, Hayes A, Gardner DC, Cornell MJ, Petty J, Hakes L, Wardleworth L, Rash B, Brown M, Dunn WB, Broadhurst D, O'Donoghue K, Hester SS, Dunkley TP, Hart SR, Swainston N, Li P, Gaskell SJ, Paton NW, Lilley KS, Kell DB, Oliver SG.
Study Publication Title	Growth control of the eukaryote cell: a systems biology study in yeast.
Study Publication Status	published
Study Publication Status Term Accession Number
Study Publication Status Term Source REF
STUDY FACTORS
Study Factor Name	limiting nutrient	rate
Study Factor Type	chemical compound	rate
Study Factor Type Term Accession Number		http://purl.obolibrary.org/obo/PATO_0000161
Study Factor Type Term Source REF		PATO
STUDY ASSAYS
Study Assay File Name	a_metabolome.txt	a_proteome.txt	a_transcriptome.txt
Study Assay Measurement Type	metabolite profiling	protein expression profiling	transcription profiling
Study Assay Measurement Type Term Accession Number	http://purl.obolibrary.org/obo/OBI_0000366	http://purl.obolibrary.org/obo/OBI_0000615	0000424
Study Assay Measurement Type Term Source REF	OBI	OBI	OBI
Study Assay Technology Type	mass spectrometry	mass spectrometry	DNA microarray
Study Assay Technology Type Term Accession Number			http://purl.obolibrary.org/obo/OBI_0400148
Study Assay Technology Type Term Source REF	OBI	OBI	OBI
Study Assay Technology Platform	LC-MS/MS	iTRAQ	Affymetrix
STUDY PROTOCOLS
Study Protocol Name	growth protocol	mRNA extraction	protein extraction	biotin labeling	ITRAQ labeling	EukGE-WS4	metabolite extraction
Study Protocol Type	growth	mRNA extraction	protein extraction	labeling	labeling	hybridization	extraction
Study Protocol Type Term Accession Number							http://purl.obolibrary.org/obo/OBI_0302884
Study Protocol Type Term Source REF							OBI
Study Protocol Description	1. Biomass samples (45 ml) were taken via the sample port of the Applikon fermenters. The cells were pelleted by centrifugation for 5 min at 5000 rpm. The supernatant was removed and the RNA pellet resuspended in the residual medium to form a slurry. This was added in a dropwise manner directly into a 5 ml Teflon flask (B. Braun Biotech, Germany) containing liquid nitrogen and a 7 mm-diameter tungsten carbide ball. After allowing evaporation of the liquid nitrogen the flask was reassembled and the cells disrupted by agitation at 1500 rpm for 2 min in a Microdismembranator U (B. Braun Biotech, Germany) 2. The frozen powder was then dissolved in 1 ml of TriZol reagent (Sigma-Aldrich, UK), vortexed for 1 min, and then kept at room temperature for a further 5min. 3. Chloroform extraction was performed by addition of 0.2 ml chloroform, shaking vigorously or 15 s, then 5min incubation at room temperature. 4. Following centrifugation at 12,000 rpm for 5 min, the RNA (contained in the aqueous phase) was precipitated with 0.5 vol of 2-propanol at room temperature for 15 min. 5. After further centrifugation (12,000 rpm for 10 min at 4 C) the RNA pellet was washed twice with 70 % (v/v) ethanol, briefly air-dried, and redissolved in 0.5 ml diethyl pyrocarbonate (DEPC)-treated water. 6. The single-stranded RNA was precipitated once more by addition of 0.5 ml of LiCl buffer (4 M LiCl, 20 mM Tris-HCl, pH 7.5, 10 mM EDTA), thus removing tRNA and DNA from the sample. 7. After precipitation (20 C for 1h) and centrifugation (12,000 rpm, 30 min, 4 C), the RNA was washed twice in 70 % (v/v) ethanol prior to being dissolved in a minimal volume of DEPC-treated water. 8. Total RNA quality was checked using the RNA 6000 Nano Assay, and analysed on an Agilent 2100 Bioanalyser (Agilent Technologies). RNA was quantified using the Nanodrop ultra low volume spectrophotometer (Nanodrop Technologies).	1. Biomass samples (45 ml) were taken via the sample port of the Applikon fermenters. The cells were pelleted by centrifugation for 5 min at 5000 rpm. The supernatant was removed and the RNA pellet resuspended in the residual medium to form a slurry. This was added in a dropwise manner directly into a 5 ml Teflon flask (B. Braun Biotech, Germany) containing liquid nitrogen and a 7 mm-diameter tungsten carbide ball. After allowing evaporation of the liquid nitrogen the flask was reassembled and the cells disrupted by agitation at 1500 rpm for 2 min in a Microdismembranator U (B. Braun Biotech, Germany) 2. The frozen powder was then dissolved in 1 ml of TriZol reagent (Sigma-Aldrich, UK), vortexed for 1 min, and then kept at room temperature for a further 5min. 3. Chloroform extraction was performed by addition of 0.2 ml chloroform, shaking vigorouslyor 15 s, then 5min incubation at room temperature. 4. Following centrifugation at 12,000 rpm for 5 min, the RNA (contained in the aqueous phase) was precipitated with 0.5 vol of 2-propanol at room temperature for 15 min. 5. After further centrifugation (12,000 rpm for 10 min at 4 C) the RNA pellet was washed twice with 70 % (v/v) ethanol, briefly air-dried, and redissolved in 0.5 ml diethyl pyrocarbonate (DEPC)-treated water. 6. The single-stranded RNA was precipitated once more by addition of 0.5 ml of LiCl bffer (4 M LiCl, 20 mM Tris-HCl, pH 7.5, 10 mM EDTA), thus removing tRNA and DNA from the sample. 7. After precipitation (20 C for 1 h) and centrifugation (12,000 rpm, 30 min, 4 C), the RNA was washed twice in 70 % (v/v) ethanol prior to being dissolved in a minimal volume of DEPC-treated water. 8. Total RNA quality was checked using the RNA 6000 Nano Assay, and analysed on an Agilent 2100 Bioanalyser (Agilent Technologies). RNA was quantified using the Nanodrop ultra low volume spectrophotometer (Nanodrop Technologies).		This was done using Enzo BioArrayTM HighYieldTM RNA transcript labelling kit (T7) with 5 ul cDNA. The resultant cRNA was again purified using the GeneChip ??? Sample Clean Up Module. The column was eluted in the first instance using 10 ???l RNase-free water, and for a second time using 11 ul RNase-free water. cRNA was quantified using the Nanodrop spectrophotometer. A total of 15 ug of cRNA (required for hybridisation) was fragmented. Fragmentation was carried out by using 2 ul of fragmentation buffer for every 8 ul cRNA.		For each target, a hybridisation cocktail was made using the standard array recipe as described in the GeneChip ??? Expression Analysis technical manual. GeneChip ??? control oligonucleotide and 20x eukaryotic hybridisation controls were used. Hybridisation buffer was made as detailed in the GeneChip ??? manual and the BSA and herring sperm DNA was purchased from Invitrogen. The cocktail was heated to 99 C for 5 min, transferred to 45 C for 5 min and then spun for 5 min to remove any insoluble material. Affymetrix Yeast Yg_s98 S. cerevisiae arrays were pre-hybridised with 200 ul 1x hybridisation buffer and incubated at 45 C for 10 min. 200 ul of the hybridisation cocktail was loaded onto the arrays. The probe array was incubated in a rotisserie at 45 C, rotating at 60 rpm. Following hybridisation, for 16 hr, chips were loaded onto a Fluidics station for washing and staining using the EukGe WS2v4 programme controlled using Microarray Suite 5 software.
Study Protocol URI
Study Protocol Version
Study Protocol Parameters Name		test;tes2					sampling
Study Protocol Parameters Name Term Accession Number		;
Study Protocol Parameters Name Term Source REF		;
Study Protocol Components Name
Study Protocol Components Type
Study Protocol Components Type Term Accession Number
Study Protocol Components Type Term Source REF
STUDY CONTACTS
Study Person Last Name	Oliver	Juan	Leo
Study Person First Name	Stephen	Castrillo	Zeef
Study Person Mid Initials	G	I	A
Study Person Email
Study Person Phone
Study Person Fax
Study Person Address	Oxford Road, Manchester M13 9PT, UK	Oxford Road, Manchester M13 9PT, UK	Oxford Road, Manchester M13 9PT, UK
Study Person Affiliation	Faculty of Life Sciences, Michael Smith Building, University of Manchester	Faculty of Life Sciences, Michael Smith Building, University of Manchester	Faculty of Life Sciences, Michael Smith Building, University of Manchester
Study Person Roles	corresponding author	author	author
Study Person Roles Term Accession Number
Study Person Roles Term Source REF
Comment[Study Person REF]
STUDY
Study Identifier	BII-S-2
Study Title	A time course analysis of transcription response in yeast treated with rapamycin, a specific inhibitor of the TORC1 complex: impact on yeast growth
Study Description	Comprehensive high-throughput analyses at the levels of mRNAs, proteins, and metabolites, and studies on gene expression patterns are required for systems biology studies of cell growth [4,26-29]. Although such comprehensive data sets are lacking, many studies have pointed to a central role for the target-of-rapamycin (TOR) signal transduction pathway in growth control. TOR is a serine/threonine kinase that has been conserved from yeasts to mammals; it integrates signals from nutrients or growth factors to regulate cell growth and cell-cycle progression coordinately. Although such comprehensive data sets are lacking, many studies have pointed to a central role for the target-of-rapamycin (TOR) signal transduction pathway in growth control. TOR is a serine/threonine kinase that has been conserved from yeasts to mammals; it integrates signals from nutrients or growth factors to regulate cell growth and cell-cycle progression coordinately. The effect of rapamycin were studied as follows: a culture growing at mid-exponential phase was divided into two. Rapamycin (200 ng/ml) was added to one half, and the drug's solvent to the other, as the control. Samples were taken at 0, 1, 2 and 4 h after treatment. Gene expression at the mRNA level was investigated by transcriptome analysis using Affymetrix hybridization arrays.
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Study Submission Date	2007-04-30T0:0:0+0000
Study Public Release Date	2009-03-10T0:0:0+0000
Study File Name	s_BII-S-2.txt
STUDY DESIGN DESCRIPTORS
Study Design Type	time series design
Study Design Type Term Accession Number	http://purl.obolibrary.org/obo/OBI_0500020
Study Design Type Term Source REF	OBI
STUDY PUBLICATIONS
Study PubMed ID	17439666
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Study Publication Author List
Study Publication Title	Growth control of the eukaryote cell: a systems biology study in yeast.
Study Publication Status	indexed in Pubmed
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STUDY FACTORS
Study Factor Name	compound	exposure time	dose
Study Factor Type	compound	time	dose
Study Factor Type Term Accession Number		http://www.ebi.ac.uk/efo/EFO_0000721	http://www.ebi.ac.uk/efo/EFO_0000428
Study Factor Type Term Source REF		EFO	EFO
STUDY ASSAYS
Study Assay File Name	a_microarray.txt
Study Assay Measurement Type	transcription profiling
Study Assay Measurement Type Term Accession Number	0000424
Study Assay Measurement Type Term Source REF	OBI
Study Assay Technology Type	DNA microarray
Study Assay Technology Type Term Accession Number	http://purl.obolibrary.org/obo/OBI_0400148
Study Assay Technology Type Term Source REF	OBI
Study Assay Technology Platform	Affymetrix
STUDY PROTOCOLS
Study Protocol Name	EukGE-WS4	mRNA extraction	biotin labeling	extraction	labeling	NMR spectroscopy	nmr assay	data normalization	data transformation	growth protocol
Study Protocol Type	hybridization	mRNA extraction	labeling	extraction	labeling	NMR spectroscopy	nmr assay	data normalization	data transformation	growth
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Study Protocol Description	For each target, a hybridisation cocktail was made using the standard array recipe as described in the GeneChip ??? Expression Analysis technical manual. GeneChip ??? control oligonucleotide and 20x eukaryotic hybridisation controls were used. Hybridisation buffer was made as detailed in the GeneChip ??? manual and the BSA and herring sperm DNA was purchased from Invitrogen. The cocktail was heated to 99 C for 5mins, transferred to 45 C for 5 min and then spun for 5 min to remove any insoluble material. Affymetrix Yeast Yg_s98 S. cerevisiae arrays were pre-hybridised with 200 ???l 1x hybridisation buffer and incubated at 45 C for 10 min. 200 ???l of the hybridisation cocktail was loaded onto the arrays. The probe array was incubated in a rotisserie at 45 C, rotating at 60 rpm. Following hybridisation, for 16hr, chips were loaded onto a Fluidics station for washing and staining using the EukGe WS2v4 programme controlled using Microarray Suite 5 software.	1. Biomass samples (45ml) were taken via the sample port of the Applikon fermenters. The cells were pelleted by centrifugation for 5min at 5000 rpm. The supernatant was removed and the RNA pellet resuspended in the residual medium to form a slurry. This was added in a dropwise manner directly into a 5ml Teflon flask (B. Braun Biotech, Germany) containing liquid nitrogen and a 7 mm-diameter tungsten carbide ball. After allowing evaporation of the liquid nitrogen the flask was reassembled and the cells disrupted by agitation at 1500 rpm for 2 min in a Microdismembranator U (B. Braun Biotech, Germany) 2. The frozen powder was then dissolved in 1 ml of TriZol reagent (Sigma-Aldrich, UK), vortexed for 1 min, and then kept at room temperature for a further 5 min. 3. Chloroform extraction was performed by addition of 0.2 ml chloroform, shaking vigorouslyor 15 s, then 5 min incubation at room temperature. 4. Following centrifugation at 12,000 rpm for 5 min, the RNA (contained in the aqueous phase) was precipitated with 0.5 vol of 2-propanol at room temperature for 15 min. 5. After further centrifugation (12,000 rpm for 10 min at 4 C) the RNA pellet was washed twice with 70 % (v/v) ethanol, briefly air-dried, and redissolved in 0.5 ml diethyl pyrocarbonate (DEPC)-treated water. 6. The single-stranded RNA was precipitated once more by addition of 0.5 ml of LiCl bffer (4 M LiCl, 20 mM Tris-HCl, pH 7.5, 10 mM EDTA), thus removing tRNA and DNA from the sample. 7. After precipitation (20 C for 1h) and centrifugation (12,000 rpm, 30 min, 4 C), the RNA was washed twice in 70 % (v/v) ethanol prior to being dissolved in a minimal volume of DEPC-treated water. 8. Total RNA quality was checked using the RNA 6000 Nano Assay, and analysed on an Agilent 2100 Bioanalyser (Agilent Technologies). RNA was quantified using the Nanodrop ultra low volume spectrophotometer (Nanodrop Technologies).	This was done using Enzo BioArrayTM HighYieldTM RNA transcript labelling kit (T7) with 5 ul cDNA. The resultant cRNA was again purified using the GeneChip ??? Sample Clean Up Module. The column was eluted in the first instance using 10 ???l RNase-free water, and for a second time using 11 ???l RNase-free water. cRNA was quantified using the Nanodrop spectrophotometer. A total of 15 ug of cRNA (required for hybridisation) was fragmented. Fragmentation was carried out by using 2 ul of fragmentation buffer for every 8 ul cRNA.
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STUDY CONTACTS
Study Person Last Name	Oliver	Juan	Leo
Study Person First Name	Stephen	Castrillo	Zeef
Study Person Mid Initials	G	I	A
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Study Person Phone
Study Person Fax
Study Person Address	Oxford Road, Manchester M13 9PT, UK	Oxford Road, Manchester M13 9PT, UK	Oxford Road, Manchester M13 9PT, UK
Study Person Affiliation	Faculty of Life Sciences, Michael Smith Building, University of Manchester	Faculty of Life Sciences, Michael Smith Building, University of Manchester	Faculty of Life Sciences, Michael Smith Building, University of Manchester
Study Person Roles	corresponding author	author	author
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