Investigation Title "Transcription profiling by array of yeast strain FY1679 homozygous for HO deletion by KanMX4 grown in a series of nutrient limited continuous cultures carbon, nitrogen, phosphorus and sulfur limitation to determine genes which are growth rate regulated and those which are nutrient specific regulated"
Comment[Submitted Name] COGEME-JIC_Chemostat_CNPS-Limitation
Experimental Design growth_condition_design transcription profiling by array
Experimental Design Term Source REF MGED Ontology EFO
Comment[AEExperimentType] transcription profiling by array
Comment[ArrayExpressReleaseDate] 2007-05-02
Comment[AEMIAMESCORE] 5
Comment[ArrayExpressAccession] E-MEXP-115
Comment[MAGETAB TimeStamp_Version] 2011-01-23 07:31:10 Last Changed Rev: 14857
Experimental Factor Name chemostat culture dilution rate limiting nutrient
Experimental Factor Type growth condition environmental stress
Experimental Factor Term Source REF
Person Last Name Wilson
Person First Name Michael
Person Mid Initials
Person Email mwilson@cs.man.ac.uk
Person Phone 1612750647
Person Fax
Person Address Kilburn Building
Person Affiliation Bioinformatics
Person Roles submitter
Person Roles Term Source REF MGED Ontology
Quality Control Type technical_replicate
Quality Control Term Source REF MGED Ontology
Replicate Type
Replicate Term Source REF
Normalization Type
Normalization Term Source REF
Date of Experiment
Public Release Date 2007-05-02
PubMed ID 17439666
Publication DOI 17439666
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"
Publication Title Growth control of the eukaryote cell: a systems biology study in yeast
Publication Status journal_article
Publication Status Term Source REF MGED Ontology
Experiment Description "S. cerevisiae strain FY1679 homozygous for HO deletion by KanMX4 was grown in a series of nutrient limited continuous cultures carbon, nitrogen, phosphorus and sulfur limitation to determine genes which are growth rate regulated and those which are nutrient specific regulated."
Protocol Name P-MTAB-28830 P-MTAB-28831 P-MTAB-28832 P-MTAB-28833 P-MTAB-28834 P-MTAB-28835 P-MTAB-28836 P-MTAB-28837 P-MTAB-28838 P-MTAB-28839 P-MTAB-28840 P-MTAB-28841 P-MTAB-28842 P-MTAB-28843 P-MTAB-28844 P-MTAB-28845 P-MTAB-28846 P-MTAB-28847 P-MTAB-28848 P-MTAB-28849 P-MTAB-28850 P-MTAB-28851 P-MTAB-28852
Protocol Description "Aerobic chemostat cultures (above 70% of oxygen saturation) at a dilution rate of 0.07 per hour, (equal to growth rate in steady-state) wasset-up with a working volume of 1 litre in a 1.5 litre fermenter (Applikon, The Netherlands) using a synthetic defined carbon-limited medium according to the description of Baganz et al., (1997), under controlled conditions (T, 30C, pH4.5).
The glucose concentration in the medium was 2.5g/l. Ammonium sulphate (2NH4SO4) was used as nitrogen source, at a concentration of 3.13g/l.
Mineral medium composition per litre
2.0g KH2PO4,
0.55g MgSO4.7H2O,
0.1g NaCl,
90mg CaCl2.2H2O,
70ug ZnSO4.7H2O,
50ug FeCl3.6H2O,
10ug CuSO4.5H2O,
10ug H3BO3,
10ug KI,
62mg inositol,
14mg thiamine/HCl,
4mg pyridoxine,
4mg Ca-pantothenate, and
0.3mg biotin.
The medium was supplemented with 20mg uracil, adenine and the amino acids L-histidine, L-tryptophan, and 100mg L-leucineas required. The carbon source (glucose) was separately prepared and sterilized before adding it to the medium. Vitamins were filter-sterilized and added after heat sterilization of the medium.
Steady-state conditions were deemed established once biomass levels remained constant over three retention times. Following biomass sampling, the dilution rate was increased to 0.1/hr and thecultures were allowed to achieve a steady state." "Aerobic chemostat cultures (above 70% of oxygen saturation) at a dilution rate of 0.2 per hour, (equal to growth rate in steady-state) wasset-up with a working volume of 1 litre in a 1.5 litre fermenter (Applikon, The Netherlands) using a synthetic defined sulphur-limited medium according to the description of Baganz et al., (1997), under controlled conditions (T, 30C, pH4.5).
Theglucose concentration in the medium was 21g/l. Ammonium sulphate (2NH4SO4) at 24mg/l, and ammonium chloride (NH4Cl) at 2.5g/l were used as nitrogen source.
Mineral medium composition per litre
2.0g KH2PO4,
0.45g MgCl2.2H2O,
0.1gNaCl,
90mg CaCl2.2H2O,
70ug ZnSO4.7H2O,
50ug FeCl3.6H2O,
10ug CuSO4.5H2O,
10ug H3BO3,
10ug KI,
62mg inositol,
14mg thiamine/HCl,
4mg pyridoxine,
4mg Ca-pantothenate, and
0.3mg biotin.
The medium was supplemented with 20mg uracil, adenine and the amino acids L-histidine, L-tryptophan, and 100mg L-leucine as required. The carbon source (glucose) was separately prepared and sterilized before adding it to the medium. Vitamins werefilter-sterilized and added after heat sterilization of the medium.
Steady-state conditions were deemed established once biomass levels remained constant over three retention times." "A stationary-phase culture (10ml) was used to innoculate the fermenter vessel. The glucose concentration in the medium was 21g/l. Ammonium sulphate (2NH4SO4) at 24mg/l, and ammonium chloride (NH4Cl) at 2.5g/l were used as nitrogen source.
Mineral medium composition per litre
2.0g KH2PO4,
0.45g MgCl2.2H2O,
0.1g NaCl,
90mg CaCl2.2H2O,
70ug ZnSO4.7H2O,
50ug FeCl3.6H2O,
10ug CuSO4.5H2O,
10ug H3BO3,
10ug KI,
62mginositol,
14mg thiamine/HCl,
4mg pyridoxine,
4mg Ca-pantothenate, and
0.3mg biotin.
The medium was supplemented with 20mg uracil, adenine and the amino acids L-histidine, L-tryptophan, and 100mg L-leucine as required.The carbon source (glucose) was separately prepared and sterilized before adding it to the medium. Vitamins were filter-sterilized and added after heat sterilization of the medium.
Batch culture samples were harvested at an OD600 of 1.0. Following batch growth, as the cultures approached the end of the exponential phase, the fermenters were switched to continuous culture at a dilution rate of 0.07/hr.
(Parameters: time unit = seconds, min temperature = 30, temperature unit = C, media = Sulphur Limited)" "Aerobic chemostat cultures (above 70% of oxygen saturation) at a dilution rate of 0.2 per hour, (equal to growth rate in steady-state) was set-up with a working volume of 1 litre in a 1.5 litre fermenter (Applikon, The Netherlands) using a synthetic defined nitrogen-limited medium according to the description of Baganz et al., (1997), under controlled conditions (T, 30C, pH4.5).
The glucose concentration in the medium was 21g/l. Ammonium sulphate (2NH4SO4) was used as nitrogen source, the concentration was 0.46g/l.
Mineral medium composition per litre
2.0g KH2PO4,
0.55g MgSO4.7H2O,
0.1g NaCl,
90mg CaCl2.2H2O,
70ug ZnSO4.7H2O,
50ug FeCl3.6H2O,
10ug CuSO4.5H2O,
10ug H3BO3,
10ug KI,
62mg inositol,
14mg thiamine/HCl,
4mg pyridoxine,
4mg Ca-pantothenate, and
0.3mg biotin.
Themedium was supplemented with 20mg uracil, adenine and the amino acids L-histidine, L-tryptophan, and 100mg L-leucine as required. The carbon source (glucose) was separately prepared and sterilized before adding it to the medium. Vitamins were filter-sterilized and added after heat sterilization of the medium.
Steady-state conditions were deemed established once biomass levels remained constant over three retention times." "Aerobic chemostat cultures (above 70% of oxygen saturation) at a dilution rate of 0.2 per hour, (equal to growth rate in steady-state) was set-up with a working volume of 1 litre in a 1.5 litre fermenter (Applikon, The Netherlands) using a synthetic defined carbon-limited medium according to the description of Baganz et al., (1997), under controlled conditions (T, 30C, pH4.5).
Theglucose concentration in the medium was 2.5g/l. Ammonium sulphate (2NH4SO4) was used as nitrogen source, at a concentration of 3.13g/l.
Mineral medium composition per litre
2.0g KH2PO4,
0.55g MgSO4.7H2O,
0.1g NaCl,
90mg CaCl2.2H2O,
70ug ZnSO4.7H2O,
50ug FeCl3.6H2O,
10ug CuSO4.5H2O,
10ug H3BO3,
10ug KI,
62mg inositol,
14mg thiamine/HCl,
4mg pyridoxine,
4mg Ca-pantothenate, and
0.3mg biotin.
The medium was supplemented with 20mg uracil, adenine and the amino acids L-histidine, L-tryptophan, and 100mg L-leucineas required. The carbon source (glucose) was separately prepared and sterilized before adding it to the medium. Vitamins were filter-sterilized and added after heat sterilization of the medium.
Steady-state conditions were deemed established once biomass levels remained constant over three retention times." "Using manufacturers recommended protocol with fluidics protocol EukGE-WS2v4
http://www.affymetrix.com/support/downloads/manuals/expression_s2_manual.pdf
(Parameters: Chamber type = Affymetrix- GeneChip Hyb Oven 640, Quantity of label target used = 15, Mass unit = Micro gram, Tiny time unit = seconds, Volume unit = Nano litre, temperature = 25)" "Aerobic chemostat cultures (above 70% of oxygen saturation) at a dilution rate of 0.1 per hour, (equal to growth rate in steady-state) was set-up with a working volume of 1 litre in a 1.5 litre fermenter (Applikon, The Netherlands) using a synthetic defined nitrogen-limited medium according to the description of Baganz et al., (1997), under controlled conditions (T, 30C, pH4.5).
The glucose concentration in the medium was 21g/l. Ammonium sulphate (2NH4SO4) was used as nitrogen source, the concentration was 0.46g/l.
Mineral medium composition per litre
2.0g KH2PO4,
0.55g MgSO4.7H2O,
0.1g NaCl,
90mg CaCl2.2H2O,
70ug ZnSO4.7H2O,
50ug FeCl3.6H2O,
10ug CuSO4.5H2O,
10ug H3BO3,
10ug KI,
62mg inositol,
14mg thiamine/HCl,
4mg pyridoxine,
4mg Ca-pantothenate, and
0.3mg biotin.
Themedium was supplemented with 20mg uracil, adenine and the amino acids L-histidine, L-tryptophan, and 100mg L-leucine as required. The carbon source (glucose) was separately prepared and sterilized before adding it to the medium. Vitamins were filter-sterilized and added after heat sterilization of the medium.
Steady-state conditions were deemed established once biomass levels remained constant over three retention times. Following biomass sampling, the dilution rate was increased to 0.2/hr and thecultures were allowed to achieve a steady state." "A stationary-phase culture (10ml) was used to innoculate the fermenter vessel. The glucose concentration in the medium was 21g/l. Ammonium sulphate (2NH4SO4) was used as nitrogen source, the concentration was 0.46g/l.
Mineral medium composition per litre
2.0g KH2PO4,
0.55g MgSO4.7H2O,
0.1g NaCl,
90mg CaCl2.2H2O,
70ug ZnSO4.7H2O,
50ug FeCl3.6H2O,
10ug CuSO4.5H2O,
10ug H3BO3,
10ug KI,
62mg inositol,
14mg thiamine/HCl,
4mg pyridoxine,
4mg Ca-pantothenate, and
0.3mg biotin.
The medium was supplemented with 20mg uracil, adenine and the amino acids L-histidine, L-tryptophan, and 100mg L-leucine as required. The carbon source (glucose) was separately prepared and sterilized before adding it to the medium. Vitamins were filter-sterilized and added after heat sterilization of the medium.
Batch culture samples were harvested at an OD600 of 1.0. Following batch growth, as the cultures approached the end of the exponential phase, the fermenters were switched to continuous culture at a dilution rate of 0.07/hr.
(Parameters: time unit = seconds, min temperature = 30, temperature unit = C, media = Nitrogen Limited)" "1. Biomass samples (20ml) were taken via the sample port of the Applikon fermenters. The cells were pelleted by centrifugation for 5min at 5000rpm. 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 7mm-diameter tungsten carbide ball. After allowing evaporation of the liquid nitrogen the flask was reassembled and the cells disrupted by agitation at 1500rpm for 2min in a Microdismembranator (B. Braun Biotech, Germany)
2. The frozen powder was then dissolved in 1ml of TriZol reagent (Sigma-Aldrich, UK), vortexed for 1min, and then kept at room temperature for a further 5min.
3. Chloroform extraction was performed by addition of 0.2ml chloroform, shaking vigorously for 15s, then 5min incubation at room temperature.
4. Following centrifugation at 12,000rpm for 5min, the RNA (contained in the aqueous phase) was precipitated with 0.5vol of 2-propanol at room temperature for 15min.
5. After further centrifugation (12000rpm for 10min at 4C) the RNA pellet was washed twice with 70% (v/v) ethanol, briefly air-dried, and redissolved in 0.5ml diethyl pyrocarbonate (DEPC)-treated water.
6. The single-stranded RNA was precipitated once more by addition of 0.5ml of LiCl buffer (4M LiCl, 20mM Tris-HCl, pH 7.5, 10mM EDTA), thus removing tRNA and DNA from the sample.
7. After precipitation (20C for 1h) and centrifugation (12,000rpm, 30min, 4C), the RNA was washed twice in 70% (v/v) ethanol prior to being dissolved in a minimal volume of DEPC-treated water.
(Parameters: Extracted product = total_RNA, Amplification = none)" "Aerobic chemostat cultures (above 70% of oxygen saturation) at a dilution rate of 0.07 per hour, (equal to growth rate in steady-state) wasset-up with a working volume of 1 litre in a 1.5 litre fermenter (Applikon, The Netherlands) using a synthetic defined nitrogen-limited medium according to the description of Baganz et al., (1997), under controlled conditions (T, 30C, pH4.5).
The glucose concentration in the medium was 21g/l. Ammonium sulphate (2NH4SO4) was used as nitrogen source, the concentration was 0.46g/l.
Mineral medium composition per litre
2.0g KH2PO4,
0.55g MgSO4.7H2O,
0.1g NaCl,
90mg CaCl2.2H2O,
70ug ZnSO4.7H2O,
50ug FeCl3.6H2O,
10ug CuSO4.5H2O,
10ug H3BO3,
10ug KI,
62mg inositol,
14mg thiamine/HCl,
4mg pyridoxine,
4mg Ca-pantothenate, and
0.3mg biotin.
The medium was supplemented with 20mg uracil, adenine and the amino acids L-histidine, L-tryptophan, and 100mg L-leucine as required. The carbon source (glucose) was separately prepared and sterilized before adding it to the medium. Vitamins were filter-sterilized and added after heat sterilization of the medium.
Steady-state conditions were deemed established once biomass levels remained constant over three retention times. Following biomass sampling, the dilution rate was increased to 0.1/hr and the cultures were allowed to achieve a steady state." "Following manufacturers recomended protocol. http://www.affymetrix.com/support/downloads/manuals/expression_s2_manual.pdf
(Parameters: Amount of nucleic acid labeled = 15, Mass unit = Micro gram, Label used = biotin, Amplification = RNA polymerases)" Normalised using Affymetrix MAS v5.1 and RMA v0.2 software using manufacturers default settings "Aerobic chemostat cultures (above 70% of oxygen saturation) at a dilution rate of 0.1 per hour, (equal to growth rate in steady-state) wasset-up with a working volume of 1 litre in a 1.5 litre fermenter (Applikon, The Netherlands;) using a synthetic defined phosphorus-limited medium according to the description of Baganz et al., (1997), under controlled conditions (T, 30C, pH4.5).
The glucose concentration in the medium was 21g/l. Ammonium sulphate (2NH4SO4) was used as nitrogen source, the concentration was 3.13g/l.
Mineral medium composition per litre
54mg KH2PO4,
1.1g KCl,
0.55g MgSO4.7H2O,
0.1g NaCl,
90mg CaCl2.2H2O,
70ug ZnSO4.7H2O,
50ug FeCl3.6H2O,
10ug CuSO4.5H2O,
10ug H3BO3,
10ug KI,
62mg inositol,
14mg thiamine/HCl,
4mg pyridoxine,
4mg Ca-pantothenate, and
0.3mg biotin.
The medium was supplemented with 20mg uracil, adenine and the amino acids L-histidine, L-tryptophan, and 100mg L-leucine as required. The carbon source (glucose) was separately prepared and sterilized before adding it to the medium. Vitamins were filter-sterilized and added after heat sterilization of the medium.
Steady-state conditions were deemed established once biomass levels remained constant over three retention times. Following biomass sampling, the dilution rate was increased to 0.2/hr and the cultures were allowed to achieve a steady state." "The array was scanned with the default settings
http://www.affymetrix.com/support/downloads/manuals/expression_s2_manual.pdf
(Parameters: Scanning hardware = HP GeneArray [Affymetrix/HP], Scanning software = Scanning software)" "Aerobic chemostat cultures (above 70% of oxygen saturation) at a dilution rate of 0.1 per hour, (equal to growth rate in steady-state) wasset-up with a working volume of 1 litre in a 1.5 litre fermenter (Applikon, The Netherlands) using a synthetic defined sulphur-limited medium according to the description of Baganz et al., (1997), under controlled conditions (T, 30C, pH4.5).
Theglucose concentration in the medium was 21g/l. Ammonium sulphate (2NH4SO4) at 24mg/l, and ammonium chloride (NH4Cl) at 2.5g/l were used as nitrogen source.
Mineral medium composition per litre
2.0g KH2PO4,
0.45g MgCl2.2H2O,
0.1gNaCl,
90mg CaCl2.2H2O,
70ug ZnSO4.7H2O,
50ug FeCl3.6H2O,
10ug CuSO4.5H2O,
10ug H3BO3,
10ug KI,
62mg inositol,
14mg thiamine/HCl,
4mg pyridoxine,
4mg Ca-pantothenate, and
0.3mg biotin.
The medium was supplemented with 20mg uracil, adenine and the amino acids L-histidine, L-tryptophan, and 100mg L-leucine as required. The carbon source (glucose) was separately prepared and sterilized before adding it to the medium. Vitamins werefilter-sterilized and added after heat sterilization of the medium.
Steady-state conditions were deemed established once biomass levels remained constant over three retention times. Following biomass sampling, the dilution rate was increased to 0.2/hr and the cultures were allowed to achieve a steady state." "Aerobic chemostat cultures (above 70% of oxygen saturation) at a dilution rate of 0.2 per hour, (equal to growth rate in steady-state) wasset-up with a working volume of 1 litre in a 1.5 litre fermenter (Applikon, The Netherlands;) using a synthetic defined phosphorus-limited medium according to the description of Baganz et al., (1997), under controlled conditions (T, 30C, pH4.5).
The glucose concentration in the medium was 21g/l. Ammonium sulphate (2NH4SO4) was used as nitrogen source, the concentration was 3.13g/l.
Mineral medium composition per litre
54mg KH2PO4,
1.1g KCl,
0.55g MgSO4.7H2O,
0.1g NaCl,
90mg CaCl2.2H2O,
70ug ZnSO4.7H2O,
50ug FeCl3.6H2O,
10ug CuSO4.5H2O,
10ug H3BO3,
10ug KI,
62mg inositol,
14mg thiamine/HCl,
4mg pyridoxine,
4mg Ca-pantothenate, and
0.3mg biotin.
The medium was supplemented with 20mg uracil, adenine and the amino acids L-histidine, L-tryptophan, and 100mg L-leucine as required. The carbon source (glucose) was separately prepared and sterilized before adding it to the medium. Vitamins were filter-sterilized and added after heat sterilization of the medium.
Steady-state conditions were deemed established once biomass levels remained constant over three retention times." "A stationary-phase culture (10ml) was used to innoculate the fermenter vessel. The glucose concentration in the medium was 2.5g/l. Ammonium sulphate (2NH4SO4) was used as nitrogen source, at a concentration of 3.13g/l.
Mineral medium composition per litre
2.0g KH2PO4,
0.55g MgSO4.7H2O,
0.1g NaCl,
90mg CaCl2.2H2O,
70ug ZnSO4.7H2O,
50ug FeCl3.6H2O,
10ug CuSO4.5H2O,
10ug H3BO3,
10ug KI,
62mg inositol,
14mg thiamine/HCl,
4mg pyridoxine,
4mg Ca-pantothenate, and
0.3mg biotin.
The medium was supplemented with 20mg uracil, adenine and the amino acids L-histidine, L-tryptophan, and 100mg L-leucineas required. The carbon source (glucose) was separately prepared and sterilized before adding it to the medium. Vitamins were filter-sterilized and added after heat sterilization of the medium.
Batch culture samples were harvested at an OD600 of 1.0. Following batch growth, as the cultures approached the end of the exponential phase, the fermenters were switched to continuous culture at a dilution rate of 0.07/hr.
(Parameters: time unit = seconds, min temperature = 30, temperature unit = C, media = Carbon Limited)" "Data was Normalised with RMA (v0.2) with default settings, and the combined data file is the output of this process" "http://www.affymetrix.com/support/downloads/manuals/expression_s2_manual.pdf
(Parameters: Scanning hardware = 418 [Affymetrix], Scanning software = Scanning software)" "A stationary-phase culture (10ml) was used to innoculate the fermenter vessel. The glucose concentration in the medium was 21g/l. Ammonium sulphate (2NH4SO4) was used as nitrogen source, the concentration was 3.13g/l.
Mineral medium composition per litre
54mg KH2PO4,
1.1g KCl,
0.55g MgSO4.7H2O,
0.1g NaCl,
90mg CaCl2.2H2O,
70ug ZnSO4.7H2O,
50ug FeCl3.6H2O,
10ug CuSO4.5H2O,
10ug H3BO3,
10ug KI,
62mg inositol,
14mg thiamine/HCl,
4mg pyridoxine,
4mg Ca-pantothenate, and
0.3mg biotin.
The medium was supplemented with 20mg uracil, adenine and the amino acids L-histidine, L-tryptophan, and 100mg L-leucine as required. The carbon source (glucose) was separately prepared and sterilized before adding it to the medium. Vitamins were filter-sterilized and added after heat sterilization of the medium.
Batch culture samples were harvested at an OD600 of 1.0. Following batch growth, as the cultures approached the end of the exponential phase, the fermenters were switched to continuous culture at a dilution rate of 0.07/hr.
(Parameters: time unit = seconds, min temperature = 30, temperature unit = C, media = Phosphate Limited)" "Aerobic chemostat cultures (above 70% of oxygen saturation) at a dilution rate of 0.1 per hour, (equal to growth rate in steady-state) was set-up with a working volume of 1 litre in a 1.5 litre fermenter (Applikon, The Netherlands) using a synthetic defined carbon-limited medium according to the description of Baganz et al., (1997), under controlled conditions (T, 30C, pH4.5).
Theglucose concentration in the medium was 2.5g/l. Ammonium sulphate (2NH4SO4) was used as nitrogen source, at a concentration of 3.13g/l.
Mineral medium composition per litre
2.0g KH2PO4,
0.55g MgSO4.7H2O,
0.1g NaCl,
90mg CaCl2.2H2O,
70ug ZnSO4.7H2O,
50ug FeCl3.6H2O,
10ug CuSO4.5H2O,
10ug H3BO3,
10ug KI,
62mg inositol,
14mg thiamine/HCl,
4mg pyridoxine,
4mg Ca-pantothenate, and
0.3mg biotin.
The medium was supplemented with 20mg uracil, adenine and the amino acids L-histidine, L-tryptophan, and 100mg L-leucineas required. The carbon source (glucose) was separately prepared and sterilized before adding it to the medium. Vitamins were filter-sterilized and added after heat sterilization of the medium.
Steady-state conditions were deemed established once biomass levels remained constant over three retention times. Following biomass sampling, the dilution rate was increased to 0.2/hr and the cultures were allowed to achieve a steady state." "Aerobic chemostat cultures (above 70% of oxygen saturation) at a dilution rate of 0.07 per hour, (equal to growth rate in steady-state) wasset-up with a working volume of 1 litre in a 1.5 litre fermenter (Applikon, The Netherlands) using a synthetic defined sulphur-limited medium according to the description of Baganz et al., (1997), under controlled conditions (T, 30C, pH4.5).
The glucose concentration in the medium was 21g/l. Ammonium sulphate (2NH4SO4) at 24mg/l, and ammonium chloride (NH4Cl) at 2.5g/l were used as nitrogen source.
Mineral medium composition per litre
2.0g KH2PO4,
0.45g MgCl2.2H2O,
0.1g NaCl,
90mg CaCl2.2H2O,
70ug ZnSO4.7H2O,
50ug FeCl3.6H2O,
10ug CuSO4.5H2O,
10ug H3BO3,
10ug KI,
62mg inositol,
14mg thiamine/HCl,
4mg pyridoxine,
4mg Ca-pantothenate, and
0.3mg biotin.
The medium was supplemented with 20mg uracil, adenine and the amino acids L-histidine, L-tryptophan, and 100mg L-leucine as required. The carbon source (glucose) was separately prepared and sterilized before adding it to the medium. Vitamins were filter-sterilized and added after heat sterilization of the medium.
Steady-state conditions were deemed established once biomass levels remained constant over three retention times. Following biomass sampling, the dilution rate was increased to 0.1/hr and the cultures were allowed to achieve a steady state." "Aerobic chemostat cultures (above 70% of oxygen saturation) at a dilution rate of 0.07 per hour, (equal to growth rate in steady-state) was set-up with a working volume of 1 litre in a 1.5 litre fermenter (Applikon, The Netherlands;) using a synthetic defined phosphorus-limited medium according to the description of Baganz et al., (1997), under controlled conditions (T, 30C, pH4.5).
The glucose concentration in the medium was 21g/l. Ammonium sulphate (2NH4SO4) was used as nitrogen source, the concentration was 3.13g/l.
Mineral medium composition per litre
54mg KH2PO4,
1.1g KCl,
0.55g MgSO4.7H2O,
0.1g NaCl,
90mg CaCl2.2H2O,
70ug ZnSO4.7H2O,
50ug FeCl3.6H2O,
10ug CuSO4.5H2O,
10ug H3BO3,
10ug KI,
62mg inositol,
14mg thiamine/HCl,
4mg pyridoxine,
4mg Ca-pantothenate, and
0.3mgbiotin.
The medium was supplemented with 20mg uracil, adenine and the amino acids L-histidine, L-tryptophan, and 100mg L-leucine as required. The carbon source (glucose) was separately prepared and sterilized before adding it to the medium.Vitamins were filter-sterilized and added after heat sterilization of the medium.
Steady-state conditions were deemed established once biomass levels remained constant over three retention times. Following biomass sampling, the dilution rate was increased to 0.1/hr and the cultures were allowed to achieve a steady state."
Protocol Type specified_biomaterial_action specified_biomaterial_action grow specified_biomaterial_action specified_biomaterial_action hybridization specified_biomaterial_action grow nucleic_acid_extraction specified_biomaterial_action labeling bioassay_data_transformation specified_biomaterial_action image_acquisition specified_biomaterial_action specified_biomaterial_action grow bioassay_data_transformation image_acquisition grow specified_biomaterial_action specified_biomaterial_action specified_biomaterial_action
Protocol Term Source REF MGED Ontology MGED Ontology MGED Ontology MGED Ontology MGED Ontology MGED Ontology MGED Ontology MGED Ontology MGED Ontology MGED Ontology MGED Ontology MGED Ontology MGED Ontology MGED Ontology MGED Ontology MGED Ontology MGED Ontology MGED Ontology MGED Ontology MGED Ontology MGED Ontology MGED Ontology MGED Ontology
SDRF File E-MEXP-115.sdrf.txt
Term Source Name ncbitax ArrayExpress EFO MGED Ontology
Term Source File http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html http://www.ebi.ac.uk/arrayexpress http://www.ebi.ac.uk/efo/ http://mged.sourceforge.net/ontologies/MGEDontology.php
Term Source Version