1 sample(s) found by the keyword GSM66922.


  1. GEO sample ID: GSM66922
    • Sample_geo_accession: GSM66922
    • Sample_status: Public on Feb 24 2006
    • Sample_submission_date: Aug 01 2005
    • Sample_last_update_date: Feb 24 2006
    • Sample_type: RNA
    • Sample_channel_count: 1
    • Sample_source_name_ch1: mRNA T128
    • Sample_organism_ch1: Saccharomyces cerevisiae
    • Sample_characteristics_ch1: Typical commercial baker’s yeast used in Japan
    • Sample_treatment_protocol_ch1: Cell pellets (11,700 OD units) were suspended in 390 ml of LF medium in a 500-ml flask and then fermented at 30C for 300 min.To investigate gene expression profiles during initial stages of dough-fermentation, cell samples for DNA microarray analysis were obtained from each culture medium at 15 min, 30 min, and 60 min.(after_15min, after_30min, after_60min)
    • Sample_growth_protocol_ch1: Mini-scale fed-batch pre-cultivation was done using a jar fermentor (1-liter, B. E. Marubishi, Japan) and peristaltic pump (EYELA, Japan) with a sequential controller (B. E. Marubishi). After 18 h cultivation, cells in stationary phase were collected by centrifugation (2,700g for 5 min). Some of the cell pellets were suspended in 900 ml of sterilized water (4C). Cells for no-fermentation control were harvested after the fed-butch cultivation and stored at -80C until RNA extraction. (before_fermentation)
    • Sample_molecule_ch1: polyA RNA
    • Sample_extract_protocol_ch1: Each time samples of total RNA were extracted using the hot phenol method. Poly (A)+ RNA was isolated from the total RNA by using an Oligotex® dt30 (super) mRNA purification kit (Takara, Japan) according to the manufacturer’s instructions. Yeast genome arrays (YGS98 GeneChip®, Affymetrix, Santa Clara, CA) were used as DNA microarrays in this study.
    • Sample_label_ch1: Biotin
    • Sample_label_protocol_ch1: Labeling was done according to the Affymetrix GeneChip® Expression Analysis Technical Manual.
    • Sample_hyb_protocol: DNA microarray hybridization was done according to the Affymetrix GeneChip® Expression Analysis Technical Manual. In brief, hybridization was at 45C in a hybridization oven (model 640, Affymetrix) at 60 rpm for 16 h. The EukGE-WS2v4 fluidics protocol of the Affymetrix Microarray Suite Version 5.0 (MASv5.0) software was used to perform staining and washing procedures.
    • Sample_scan_protocol: The arrays were subsequently read using a GeneArray Scanner (Agilent technologies, Palo Alto, CA).
    • Sample_description: fermentation 30min
    • Sample_data_processing: Affymetrix Microarray Suite Version 5.0
    • Sample_platform_id: GPL90
    • Sample_contact_name: Jun,,Shima
    • Sample_contact_email: shimaj@nfri.affrc.go.jp
    • Sample_contact_laboratory: Yeast
    • Sample_contact_department: Applied Microbiology
    • Sample_contact_institute: National Food Research Institute
    • Sample_contact_address: 1-2-12 Kannondai
    • Sample_contact_city: Tsukuba
    • Sample_contact_state: Ibaraki
    • Sample_contact_zip/postal_code: 305-8642
    • Sample_contact_country: Japan
    • Sample_supplementary_file: NONE
    • Sample_series_id: GSE3043
    • Sample_data_row_count: 9335
    • sample_table_begin:
    • sample_table_end:
    • Sample_title: fermentation 60 min
    ID_REF Corrected Value VALUE ABS_CALL
    AFFX-MurIL2_at 0.8 3.1 A
    AFFX-MurIL10_at 1.9 2.1 A
    AFFX-MurIL4_at 8 1 A
    AFFX-MurFAS_at 13.6 1.3 A
    AFFX-BioB-5_at 65.5 29.1 A
    AFFX-BioB-M_at 54.9 25.6 A
    AFFX-BioB-3_at 36.8 15.3 A
    AFFX-BioC-5_at 78.9 50.5 P
    AFFX-BioC-3_at 102.9 72.1 P
    AFFX-BioDn-5_at 79.1 46.6 P
    View Full Table






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