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a_proteome
s_BII-S-1
BII-1_investigation
Sheet1
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| Sample Name | Protocol REF | Extract Name | Protocol REF | Labeled Extract Name | Label | Term Source REF | Term Accession Number | MS Assay Name | Comment[PRIDE Accession] | Comment[PRIDE Processed Data Accession] | Raw Spectral Data File | Normalization Name | Protein Assignment File | Peptide Assignment File | Post Translational Modification Assignment File | Data Transformation Name | Derived Spectral Data File | Factor Value[limiting nutrient] | Term Source REF | Term Accession Number | Factor Value[rate] | Unit | Term Source REF | Term Accession Number |
| S-0.1-aliquot11 | protein extraction | S-0.1 | ITRAQ labeling | JC_S-0.1 | iTRAQ reagent 117 | 8761 | 8761 | 8761 | spectrum.mzdata | norm1 | proteins.csv | peptides.csv | ptms.csv | datatransformation1 | PRIDE_Exp_Complete_Ac_8761.xml | sulphur | 0.1 | l/hr | ||||||
| C-0.1-aliquot11 | protein extraction | C-0.1 | ITRAQ labeling | JC_C-0.1 | iTRAQ reagent 116 | 8761 | 8761 | 8761 | spectrum.mzdata | norm1 | proteins.csv | peptides.csv | ptms.csv | datatransformation1 | PRIDE_Exp_Complete_Ac_8761.xml | carbon | EFO | http://purl.obolibrary.org/obo/CHEBI_27594 | 0.1 | l/hr | ||||
| N-0.1-aliquot11 | protein extraction | N-0.1 | ITRAQ labeling | JC_N-0.1 | iTRAQ reagent 115 | 8761 | 8761 | 8761 | spectrum.mzdata | norm1 | proteins.csv | peptides.csv | ptms.csv | datatransformation1 | PRIDE_Exp_Complete_Ac_8761.xml | nitrogen | 0.1 | l/hr | ||||||
| S-0.1-aliquot11 | protein extraction | S-0.1 | ITRAQ labeling | Pool1 | iTRAQ reagent 114 | 8761 | 8761 | 8761 | spectrum.mzdata | norm1 | proteins.csv | peptides.csv | ptms.csv | datatransformation1 | PRIDE_Exp_Complete_Ac_8761.xml | l/hr | ||||||||
| C-0.1-aliquot11 | protein extraction | C-0.1 | ITRAQ labeling | Pool1 | iTRAQ reagent 114 | 8761 | 8761 | 8761 | spectrum.mzdata | norm1 | proteins.csv | peptides.csv | ptms.csv | datatransformation1 | PRIDE_Exp_Complete_Ac_8761.xml | l/hr | ||||||||
| N-0.1-aliquot11 | protein extraction | N-0.1 | ITRAQ labeling | Pool1 | iTRAQ reagent 114 | 8761 | 8761 | 8761 | spectrum.mzdata | norm1 | proteins.csv | peptides.csv | ptms.csv | datatransformation1 | PRIDE_Exp_Complete_Ac_8761.xml | l/hr | ||||||||
| C-0.2-aliquot11 | protein extraction | C-0.2 | ITRAQ labeling | JC_C-0.2 | iTRAQ reagent 117 | 8762 | 8762 | 8762 | spectrum.mzdata | norm2 | proteins.csv | peptides.csv | ptms.csv | datatransformation2 | PRIDE_Exp_Complete_Ac_8762.xml | carbon | EFO | http://purl.obolibrary.org/obo/CHEBI_27594 | 0.2 | l/hr | ||||
| N-0.2-aliquot11 | protein extraction | N-0.2 | ITRAQ labeling | JC_N-0.2 | iTRAQ reagent 116 | 8762 | 8762 | 8762 | spectrum.mzdata | norm2 | proteins.csv | peptides.csv | ptms.csv | datatransformation2 | PRIDE_Exp_Complete_Ac_8762.xml | nitrogen | 0.2 | l/hr | ||||||
| P-0.1-aliquot11 | protein extraction | P-0.1 | ITRAQ labeling | JC_P-0.1 | iTRAQ reagent 115 | 8762 | 8762 | 8762 | spectrum.mzdata | norm2 | proteins.csv | peptides.csv | ptms.csv | datatransformation2 | PRIDE_Exp_Complete_Ac_8762.xml | phosphorus | EFO | http://purl.obolibrary.org/obo/CHEBI_28659 | 0.1 | l/hr | ||||
| C-0.2-aliquot11 | protein extraction | C-0.2 | ITRAQ labeling | Pool2 | iTRAQ reagent 114 | 8762 | 8762 | 8762 | spectrum.mzdata | norm2 | proteins.csv | peptides.csv | ptms.csv | datatransformation2 | PRIDE_Exp_Complete_Ac_8762.xml | l/hr | ||||||||
| N-0.2-aliquot11 | protein extraction | N-0.2 | ITRAQ labeling | Pool2 | iTRAQ reagent 114 | 8762 | 8762 | 8762 | spectrum.mzdata | norm2 | proteins.csv | peptides.csv | ptms.csv | datatransformation2 | PRIDE_Exp_Complete_Ac_8762.xml | l/hr | ||||||||
| P-0.1-aliquot11 | protein extraction | P-0.1 | ITRAQ labeling | Pool2 | iTRAQ reagent 114 | 8762 | 8762 | 8762 | spectrum.mzdata | norm2 | proteins.csv | peptides.csv | ptms.csv | datatransformation2 | PRIDE_Exp_Complete_Ac_8762.xml | l/hr | ||||||||
| P-0.2-aliquot11 | protein extraction | P-0.2 | ITRAQ labeling | JC_P-0.2 | iTRAQ reagent 116 | 8763 | 8763 | 8763 | spectrum.mzdata | norm3 | proteins.csv | peptides.csv | ptms.csv | datatransformation3 | PRIDE_Exp_Complete_Ac_8763.xml | phosphorus | EFO | http://purl.obolibrary.org/obo/CHEBI_28659 | 0.2 | l/hr | ||||
| S-0.2-aliquot11 | protein extraction | S-0.2 | ITRAQ labeling | JC_S-0.2 | iTRAQ reagent 115 | 8763 | 8763 | 8763 | spectrum.mzdata | norm3 | proteins.csv | peptides.csv | ptms.csv | datatransformation3 | PRIDE_Exp_Complete_Ac_8763.xml | sulphur | 0.2 | l/hr | ||||||
| P-0.2-aliquot11 | protein extraction | P-0.2 | ITRAQ labeling | Pool3 | iTRAQ reagent 117 | 8763 | 8763 | 8763 | spectrum.mzdata | norm3 | proteins.csv | peptides.csv | ptms.csv | datatransformation3 | PRIDE_Exp_Complete_Ac_8763.xml | l/hr | ||||||||
| S-0.2-aliquot11 | protein extraction | S-0.2 | ITRAQ labeling | Pool3 | iTRAQ reagent 117 | 8763 | 8763 | 8763 | spectrum.mzdata | norm3 | proteins.csv | peptides.csv | ptms.csv | datatransformation3 | PRIDE_Exp_Complete_Ac_8763.xml | l/hr | ||||||||
| P-0.2-aliquot11 | protein extraction | P-0.2 | ITRAQ labeling | Pool3 | iTRAQ reagent 114 | 8763 | 8763 | 8763 | spectrum.mzdata | norm3 | proteins.csv | peptides.csv | ptms.csv | datatransformation3 | PRIDE_Exp_Complete_Ac_8763.xml | l/hr | ||||||||
| S-0.2-aliquot11 | protein extraction | S-0.2 | ITRAQ labeling | Pool3 | iTRAQ reagent 114 | 8763 | 8763 | 8763 | spectrum.mzdata | norm3 | proteins.csv | peptides.csv | ptms.csv | datatransformation3 | PRIDE_Exp_Complete_Ac_8763.xml | l/hr | ||||||||
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| Source Name | Characteristics[organism] | Term Source REF | Term Accession Number | Characteristics[strain] | Term Source REF | Term Accession Number | Characteristics[genotype] | Term Source REF | Term Accession Number | Protocol REF | Sample Name | Factor Value[limiting nutrient] | Term Source REF | Term Accession Number | Factor Value[rate] | Unit | Term Source REF | Term Accession Number |
| culture1 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | C-0.07-aliquot1 | carbon | EFO | http://purl.obolibrary.org/obo/CHEBI_27594 | 0.07 | l/hour | ||||||||
| culture1 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | C-0.07-aliquot2 | carbon | EFO | http://purl.obolibrary.org/obo/CHEBI_27594 | 0.07 | l/hour | ||||||||
| culture1 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | C-0.07-aliquot3 | carbon | EFO | http://purl.obolibrary.org/obo/CHEBI_27594 | 0.07 | l/hour | ||||||||
| culture1 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | C-0.07-aliquot4 | carbon | EFO | http://purl.obolibrary.org/obo/CHEBI_27594 | 0.07 | l/hour | ||||||||
| culture1 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | C-0.07-aliquot5 | carbon | EFO | http://purl.obolibrary.org/obo/CHEBI_27594 | 0.07 | l/hour | ||||||||
| culture1 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | C-0.07-aliquot6 | carbon | EFO | http://purl.obolibrary.org/obo/CHEBI_27594 | 0.07 | l/hour | ||||||||
| culture1 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | C-0.07-aliquot7 | carbon | EFO | http://purl.obolibrary.org/obo/CHEBI_27594 | 0.07 | l/hour | ||||||||
| culture1 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | C-0.07-aliquot8 | carbon | EFO | http://purl.obolibrary.org/obo/CHEBI_27594 | 0.07 | l/hour | ||||||||
| culture1 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | C-0.07-aliquot9 | carbon | EFO | http://purl.obolibrary.org/obo/CHEBI_27594 | 0.07 | l/hour | ||||||||
| culture1 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | C-0.07-aliquot10 | carbon | EFO | http://purl.obolibrary.org/obo/CHEBI_27594 | 0.07 | l/hour | ||||||||
| culture2 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | C-0.1-aliquot1 | carbon | EFO | http://purl.obolibrary.org/obo/CHEBI_27594 | 0.1 | l/hour | ||||||||
| culture2 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | C-0.1-aliquot2 | carbon | EFO | http://purl.obolibrary.org/obo/CHEBI_27594 | 0.1 | l/hour | ||||||||
| culture2 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | C-0.1-aliquot3 | carbon | EFO | http://purl.obolibrary.org/obo/CHEBI_27594 | 0.1 | l/hour | ||||||||
| culture2 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | C-0.1-aliquot4 | carbon | EFO | http://purl.obolibrary.org/obo/CHEBI_27594 | 0.1 | l/hour | ||||||||
| culture2 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | C-0.1-aliquot5 | carbon | EFO | http://purl.obolibrary.org/obo/CHEBI_27594 | 0.1 | l/hour | ||||||||
| culture2 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | C-0.1-aliquot6 | carbon | EFO | http://purl.obolibrary.org/obo/CHEBI_27594 | 0.1 | l/hour | ||||||||
| culture2 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | C-0.1-aliquot7 | carbon | EFO | http://purl.obolibrary.org/obo/CHEBI_27594 | 0.1 | l/hour | ||||||||
| culture2 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | C-0.1-aliquot8 | carbon | EFO | http://purl.obolibrary.org/obo/CHEBI_27594 | 0.1 | l/hour | ||||||||
| culture2 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | C-0.1-aliquot9 | carbon | EFO | http://purl.obolibrary.org/obo/CHEBI_27594 | 0.1 | l/hour | ||||||||
| culture2 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | C-0.1-aliquot10 | carbon | EFO | http://purl.obolibrary.org/obo/CHEBI_27594 | 0.1 | l/hour | ||||||||
| culture2 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | C-0.1-aliquot11 | carbon | EFO | http://purl.obolibrary.org/obo/CHEBI_27594 | 0.1 | l/hour | ||||||||
| culture3 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | C-0.2-aliquot1 | carbon | EFO | http://purl.obolibrary.org/obo/CHEBI_27594 | 0.2 | l/hour | ||||||||
| culture3 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | C-0.2-aliquot2 | carbon | EFO | http://purl.obolibrary.org/obo/CHEBI_27594 | 0.2 | l/hour | ||||||||
| culture3 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | C-0.2-aliquot3 | carbon | EFO | http://purl.obolibrary.org/obo/CHEBI_27594 | 0.2 | l/hour | ||||||||
| culture3 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | C-0.2-aliquot4 | carbon | EFO | http://purl.obolibrary.org/obo/CHEBI_27594 | 0.2 | l/hour | ||||||||
| culture3 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | C-0.2-aliquot5 | carbon | EFO | http://purl.obolibrary.org/obo/CHEBI_27594 | 0.2 | l/hour | ||||||||
| culture3 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | C-0.2-aliquot6 | carbon | EFO | http://purl.obolibrary.org/obo/CHEBI_27594 | 0.2 | l/hour | ||||||||
| culture3 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | C-0.2-aliquot7 | carbon | EFO | http://purl.obolibrary.org/obo/CHEBI_27594 | 0.2 | l/hour | ||||||||
| culture3 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | C-0.2-aliquot8 | carbon | EFO | http://purl.obolibrary.org/obo/CHEBI_27594 | 0.2 | l/hour | ||||||||
| culture3 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | C-0.2-aliquot9 | carbon | EFO | http://purl.obolibrary.org/obo/CHEBI_27594 | 0.2 | l/hour | ||||||||
| culture3 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | C-0.2-aliquot10 | carbon | EFO | http://purl.obolibrary.org/obo/CHEBI_27594 | 0.2 | l/hour | ||||||||
| culture3 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | C-0.2-aliquot11 | carbon | EFO | http://purl.obolibrary.org/obo/CHEBI_27594 | 0.2 | l/hour | ||||||||
| culture4 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | N-0.07-aliquot1 | nitrogen | 0.07 | l/hour | ||||||||||
| culture4 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | N-0.07-aliquot2 | nitrogen | 0.07 | l/hour | ||||||||||
| culture4 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | N-0.07-aliquot3 | nitrogen | 0.07 | l/hour | ||||||||||
| culture4 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | N-0.07-aliquot4 | nitrogen | 0.07 | l/hour | ||||||||||
| culture4 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | N-0.07-aliquot5 | nitrogen | 0.07 | l/hour | ||||||||||
| culture4 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | N-0.07-aliquot6 | nitrogen | 0.07 | l/hour | ||||||||||
| culture4 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | N-0.07-aliquot7 | nitrogen | 0.07 | l/hour | ||||||||||
| culture4 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | N-0.07-aliquot8 | nitrogen | 0.07 | l/hour | ||||||||||
| culture4 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | N-0.07-aliquot9 | nitrogen | 0.07 | l/hour | ||||||||||
| culture4 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | N-0.07-aliquot10 | nitrogen | 0.07 | l/hour | ||||||||||
| culture5 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | N-0.1-aliquot1 | nitrogen | 0.1 | l/hour | ||||||||||
| culture5 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | N-0.1-aliquot2 | nitrogen | 0.1 | l/hour | ||||||||||
| culture5 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | N-0.1-aliquot3 | nitrogen | 0.1 | l/hour | ||||||||||
| culture5 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | N-0.1-aliquot4 | nitrogen | 0.1 | l/hour | ||||||||||
| culture5 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | N-0.1-aliquot5 | nitrogen | 0.1 | l/hour | ||||||||||
| culture5 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | N-0.1-aliquot6 | nitrogen | 0.1 | l/hour | ||||||||||
| culture5 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | N-0.1-aliquot7 | nitrogen | 0.1 | l/hour | ||||||||||
| culture5 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | N-0.1-aliquot8 | nitrogen | 0.1 | l/hour | ||||||||||
| culture5 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | N-0.1-aliquot9 | nitrogen | 0.1 | l/hour | ||||||||||
| culture5 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | N-0.1-aliquot10 | nitrogen | 0.1 | l/hour | ||||||||||
| culture5 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | N-0.1-aliquot11 | nitrogen | 0.1 | l/hour | ||||||||||
| culture6 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | N-0.2-aliquot1 | nitrogen | 0.2 | l/hour | ||||||||||
| culture6 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | N-0.2-aliquot2 | nitrogen | 0.2 | l/hour | ||||||||||
| culture6 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | N-0.2-aliquot3 | nitrogen | 0.2 | l/hour | ||||||||||
| culture6 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | N-0.2-aliquot4 | nitrogen | 0.2 | l/hour | ||||||||||
| culture6 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | N-0.2-aliquot5 | nitrogen | 0.2 | l/hour | ||||||||||
| culture6 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | N-0.2-aliquot6 | nitrogen | 0.2 | l/hour | ||||||||||
| culture6 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | N-0.2-aliquot7 | nitrogen | 0.2 | l/hour | ||||||||||
| culture6 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | N-0.2-aliquot8 | nitrogen | 0.2 | l/hour | ||||||||||
| culture6 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | N-0.2-aliquot9 | nitrogen | 0.2 | l/hour | ||||||||||
| culture6 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | N-0.2-aliquot10 | nitrogen | 0.2 | l/hour | ||||||||||
| culture6 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | N-0.2-aliquot10 | nitrogen | 0.2 | l/hour | ||||||||||
| culture7 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | P-0.07-aliquot1 | phosphorus | EFO | http://purl.obolibrary.org/obo/CHEBI_28659 | 0.07 | l/hour | ||||||||
| culture7 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | P-0.07-aliquot2 | phosphorus | EFO | http://purl.obolibrary.org/obo/CHEBI_28659 | 0.07 | l/hour | ||||||||
| culture7 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | P-0.07-aliquot3 | phosphorus | EFO | http://purl.obolibrary.org/obo/CHEBI_28659 | 0.07 | l/hour | ||||||||
| culture7 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | P-0.07-aliquot4 | phosphorus | EFO | http://purl.obolibrary.org/obo/CHEBI_28659 | 0.07 | l/hour | ||||||||
| culture7 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | P-0.07-aliquot5 | phosphorus | EFO | http://purl.obolibrary.org/obo/CHEBI_28659 | 0.07 | l/hour | ||||||||
| culture7 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | P-0.07-aliquot6 | phosphorus | EFO | http://purl.obolibrary.org/obo/CHEBI_28659 | 0.07 | l/hour | ||||||||
| culture7 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | P-0.07-aliquot7 | phosphorus | EFO | http://purl.obolibrary.org/obo/CHEBI_28659 | 0.07 | l/hour | ||||||||
| culture7 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | P-0.07-aliquot8 | phosphorus | EFO | http://purl.obolibrary.org/obo/CHEBI_28659 | 0.07 | l/hour | ||||||||
| culture7 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | P-0.07-aliquot9 | phosphorus | EFO | http://purl.obolibrary.org/obo/CHEBI_28659 | 0.07 | l/hour | ||||||||
| culture7 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | P-0.07-aliquot10 | phosphorus | EFO | http://purl.obolibrary.org/obo/CHEBI_28659 | 0.07 | l/hour | ||||||||
| culture8 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | P-0.1-aliquot1 | phosphorus | EFO | http://purl.obolibrary.org/obo/CHEBI_28659 | 0.1 | l/hour | ||||||||
| culture8 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | P-0.1-aliquot2 | phosphorus | EFO | http://purl.obolibrary.org/obo/CHEBI_28659 | 0.1 | l/hour | ||||||||
| culture8 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | P-0.1-aliquot3 | phosphorus | EFO | http://purl.obolibrary.org/obo/CHEBI_28659 | 0.1 | l/hour | ||||||||
| culture8 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | P-0.1-aliquot4 | phosphorus | EFO | http://purl.obolibrary.org/obo/CHEBI_28659 | 0.1 | l/hour | ||||||||
| culture8 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | P-0.1-aliquot5 | phosphorus | EFO | http://purl.obolibrary.org/obo/CHEBI_28659 | 0.1 | l/hour | ||||||||
| culture8 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | P-0.1-aliquot6 | phosphorus | EFO | http://purl.obolibrary.org/obo/CHEBI_28659 | 0.1 | l/hour | ||||||||
| culture8 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | P-0.1-aliquot7 | phosphorus | EFO | http://purl.obolibrary.org/obo/CHEBI_28659 | 0.1 | l/hour | ||||||||
| culture8 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | P-0.1-aliquot8 | phosphorus | EFO | http://purl.obolibrary.org/obo/CHEBI_28659 | 0.1 | l/hour | ||||||||
| culture8 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | P-0.1-aliquot9 | phosphorus | EFO | http://purl.obolibrary.org/obo/CHEBI_28659 | 0.1 | l/hour | ||||||||
| culture8 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | P-0.1-aliquot10 | phosphorus | EFO | http://purl.obolibrary.org/obo/CHEBI_28659 | 0.1 | l/hour | ||||||||
| culture8 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | P-0.1-aliquot11 | phosphorus | EFO | http://purl.obolibrary.org/obo/CHEBI_28659 | 0.1 | l/hour | ||||||||
| culture9 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | P-0.2-aliquot1 | phosphorus | EFO | http://purl.obolibrary.org/obo/CHEBI_28659 | 0.2 | l/hour | ||||||||
| culture9 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | P-0.2-aliquot2 | phosphorus | EFO | http://purl.obolibrary.org/obo/CHEBI_28659 | 0.2 | l/hour | ||||||||
| culture9 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | P-0.2-aliquot3 | phosphorus | EFO | http://purl.obolibrary.org/obo/CHEBI_28659 | 0.2 | l/hour | ||||||||
| culture9 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | P-0.2-aliquot4 | phosphorus | EFO | http://purl.obolibrary.org/obo/CHEBI_28659 | 0.2 | l/hour | ||||||||
| culture9 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | P-0.2-aliquot5 | phosphorus | EFO | http://purl.obolibrary.org/obo/CHEBI_28659 | 0.2 | l/hour | ||||||||
| culture9 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | P-0.2-aliquot6 | phosphorus | EFO | http://purl.obolibrary.org/obo/CHEBI_28659 | 0.2 | l/hour | ||||||||
| culture9 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | P-0.2-aliquot7 | phosphorus | EFO | http://purl.obolibrary.org/obo/CHEBI_28659 | 0.2 | l/hour | ||||||||
| culture9 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | P-0.2-aliquot8 | phosphorus | EFO | http://purl.obolibrary.org/obo/CHEBI_28659 | 0.2 | l/hour | ||||||||
| culture9 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | P-0.2-aliquot9 | phosphorus | EFO | http://purl.obolibrary.org/obo/CHEBI_28659 | 0.2 | l/hour | ||||||||
| culture9 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | P-0.2-aliquot10 | phosphorus | EFO | http://purl.obolibrary.org/obo/CHEBI_28659 | 0.2 | l/hour | ||||||||
| culture9 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | P-0.2-aliquot11 | phosphorus | EFO | http://purl.obolibrary.org/obo/CHEBI_28659 | 0.2 | l/hour | ||||||||
| culture10 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | S-0.07-aliquot1 | sulfur | 0.07 | l/hour | ||||||||||
| culture10 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | S-0.07-aliquot2 | sulfur | 0.07 | l/hour | ||||||||||
| culture10 | Saccharomyces cerevisiae (Baker's yeast) | FY1679 | KanMx4 MATa/MATalpha ura3-52/ura3-52 leu2-1/+trp1-63/+his3-D200/+ hoD KanMx4/hoD | growth protocol | S-0.07-aliquot3 | sulfur | 0.07 | l/hour |
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| 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. | |||||||||
| 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-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 | |||||||||
| Study Publication DOI | ||||||||||
| 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 | |||||||||
| Study Publication Status Term Accession Number | ||||||||||
| Study Publication Status Term Source REF | ||||||||||
| 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 |
| Study Protocol Type Term Accession Number | ||||||||||
| Study Protocol Type Term Source REF | ||||||||||
| 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. | |||||||
| Study Protocol URI | ||||||||||
| Study Protocol Version | ||||||||||
| Study Protocol Parameters Name | ;;; | |||||||||
| 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 | |||||||
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| Study Person Roles Term Source REF | ||||||||||
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