1 sample(s) found by the keyword GSM377496.


  1. GEO sample ID: GSM377496
    • Sample_geo_accession: GSM377496
    • Sample_status: Public on Nov 13 2009
    • Sample_submission_date: Mar 04 2009
    • Sample_last_update_date: Nov 09 2009
    • Sample_type: RNA
    • Sample_channel_count: 1
    • Sample_source_name_ch1: Chemostat culture
    • Sample_organism_ch1: Saccharomyces cerevisiae
    • Sample_characteristics_ch1: description: Saccharomyces cerevisiae prototrophic strain
    • Sample_characteristics_ch1: strain: IMK133
    • Sample_characteristics_ch1: genotype: mata mal2-8c suc2 ura3 pdr3: :loxP pdr1::loxP-kanMX-loxP p426GPD(URA3)
    • Sample_biomaterial_provider_ch1: L. Hazelwood
    • Sample_treatment_protocol_ch1: Quenching in liquid nitrogen
    • Sample_growth_protocol_ch1: Media. The composition of the synthetic medium [1] for shake-flask and chemostat cultivation was as follows: 5 g.l-1 (NH4)2SO4, 3 g.l-1 KH2PO4, 0.5 g.l-1 MgSO4 and trace elements. The media was sterilized by autoclaving at 120 oC. Glucose (25 g.l-1 for chemostat cultivation), vitamins and the anaerobic growth factors Tween-80 and ergosterol, were supplemented after sterilization [1]. The glucose was autoclaved separately at 110 oC, and the vitamins were filter sterilized.
    • Sample_growth_protocol_ch1: Chemostat cultivation. Anaerobic glucose-limited steady-state chemostat cultures at a dilution rate of 0.10 h-1 of S. cerevisiae CEN.PK113-7D were performed as previously described [2]. Iso-α-acid enriched hop extracts were filter sterilized and added at a concentration of 0.2 g.l-1. Medium reservoirs containing iso-α-acid enriched hop extracts were stored at 4ºC and protected from light.
    • Sample_growth_protocol_ch1: Reference List
    • Sample_growth_protocol_ch1: 1. Verduyn C, Postma E, Scheffers WA, van Dijken JP: Energetics of Saccharomyces cerevisiae in anaerobic glucose-limited chemostat cultures. J Gen Microbiol 1990, 136: 405-412.
    • Sample_growth_protocol_ch1: 2. Tai SL, Boer VM, Daran-Lapujade P, Walsh MC, de Winde JH, Daran JM et al.: Two-dimensional transcriptome analysis in chemostat cultures. Combinatorial effects of oxygen availability and macronutrient limitation in Saccharomyces cerevisiae. J Biol Chem 2005, 280: 437-447.
    • Sample_growth_protocol_ch1:
    • Sample_molecule_ch1: total RNA
    • Sample_extract_protocol_ch1: Microarray analysis. Sampling of cells from chemostats, total RNA extraction, cDNA synthesis and hybridization on the arrays were performed as previously described [3].
    • Sample_extract_protocol_ch1: Reference List
    • Sample_extract_protocol_ch1: 3. De Nicola R, Hazelwood LA, De Hulster EA, Walsh MC, Knijnenburg TA, Reinders MJ et al.: Physiological and transcriptional responses of Saccharomyces cerevisiae to zinc limitation in chemostat cultures. Appl Environ Microbiol 2007, 73: 7680-7692.
    • Sample_label_ch1: biotin, streptavidin phycoerythrin (SAPE)
    • Sample_label_protocol_ch1: Microarray analysis. Sampling of cells from chemostats, total RNA extraction, cDNA synthesis and hybridization on the arrays were performed as previously described [3].
    • Sample_label_protocol_ch1: Reference List
    • Sample_label_protocol_ch1: 3. De Nicola R, Hazelwood LA, De Hulster EA, Walsh MC, Knijnenburg TA, Reinders MJ et al.: Physiological and transcriptional responses of Saccharomyces cerevisiae to zinc limitation in chemostat cultures. Appl Environ Microbiol 2007, 73: 7680-7692.
    • Sample_hyb_protocol: Microarray analysis. Sampling of cells from chemostats, total RNA extraction, cDNA synthesis and hybridization on the arrays were performed as previously described [3].
    • Sample_hyb_protocol: Reference List
    • Sample_hyb_protocol: 3. De Nicola R, Hazelwood LA, De Hulster EA, Walsh MC, Knijnenburg TA, Reinders MJ et al.: Physiological and transcriptional responses of Saccharomyces cerevisiae to zinc limitation in chemostat cultures. Appl Environ Microbiol 2007, 73: 7680-7692.
    • Sample_scan_protocol: Microarray analysis. Sampling of cells from chemostats, total RNA extraction, cDNA synthesis and hybridization on the arrays were performed as previously described [3].
    • Sample_scan_protocol: Reference List
    • Sample_scan_protocol: 3. De Nicola R, Hazelwood LA, De Hulster EA, Walsh MC, Knijnenburg TA, Reinders MJ et al.: Physiological and transcriptional responses of Saccharomyces cerevisiae to zinc limitation in chemostat cultures. Appl Environ Microbiol 2007, 73: 7680-7692.
    • Sample_description: LH35
    • Sample_data_processing: GCOS software
    • Sample_data_processing: CHP file targetted at 150
    • Sample_platform_id: GPL90
    • Sample_contact_name: Jean-Marc,,Daran
    • Sample_contact_email: j.g.daran@tudelft.nl
    • Sample_contact_phone: +31 15 278 2412
    • Sample_contact_fax: +31 15 278 23 55
    • Sample_contact_laboratory: Kluyver centre for genomics of industrial organisms
    • Sample_contact_department: Department of Biotechnology
    • Sample_contact_institute: Delft University of Technology
    • Sample_contact_address: Julianalaan 67
    • Sample_contact_city: Delft
    • Sample_contact_zip/postal_code: 2628BC
    • Sample_contact_country: Netherlands
    • Sample_supplementary_file: ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM377nnn/GSM377496/GSM377496.CEL.gz
    • Sample_series_id: GSE15094
    • Sample_data_row_count: 9335
    • Sample_comment: Raw data provided as supplementary file
    • sample_table_begin:
    • sample_table_end:
    • Sample_title: Anaerobic carbon-limited chemostat culture with 0.2 g/l hop acids of pdr1,pdr3 mutant -2
    ID_REF Corrected Value VALUE ABS_CALL
    AFFX-MurIL2_at 1.1 1.8 A
    AFFX-MurIL10_at 4.2 0.6 A
    AFFX-MurIL4_at 9.2 1.1 A
    AFFX-MurFAS_at 15.7 4.1 A
    AFFX-BioB-5_at 84.3 40.3 P
    AFFX-BioB-M_at 108.7 67.8 P
    AFFX-BioB-3_at 97.7 60.1 P
    AFFX-BioC-5_at 184.6 145.9 P
    AFFX-BioC-3_at 181.5 141.0 P
    AFFX-BioDn-5_at 339.3 292.5 P
    View Full Table






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