1 sample(s) found by the keyword GSM215117.


  1. GEO sample ID: GSM215117
    • Sample_geo_accession: GSM215117
    • Sample_status: Public on Jul 31 2009
    • Sample_submission_date: Aug 03 2007
    • Sample_last_update_date: Jul 24 2008
    • Sample_type: RNA
    • Sample_channel_count: 1
    • Sample_source_name_ch1: Baker’s yeast, freeze, 3day
    • Sample_organism_ch1: Saccharomyces cerevisiae
    • Sample_characteristics_ch1: Commercial products of compressed yeast for bread making
    • Sample_treatment_protocol_ch1: The compressed yeast was suspended in liquid fermentation (LS) without sucrose and maltose LF-S medium (10 ml) at the concentration of OD600=30, and the suspension was frozen at -20oC for 3 day. The frozen samples were thawed at 30oC for 10 min in a water bath.
    • Sample_molecule_ch1: polyA RNA
    • Sample_extract_protocol_ch1: RNA was extracted from the yeast cells using the hot phenol method. Poly(A)+ RNA was enriched from total RNA by using an Oligotex dT30 (Super) mRNA purification kit (Takara Bio, Ohtsu, Japan).
    • Sample_label_ch1: Biotin
    • Sample_label_protocol_ch1: cDNA synthesis, cRNA synthesis, and labeling were performed according to the Affymetrix user’s manual (Affymetrix, Santa Clara, USA).
    • Sample_hyb_protocol: Affymetrix Yeast Genome S98 arrays were used as a DNA microarray. The probe was hybridized to a DNA microarray at 45oC for 18 h according to the Affymetrix user’s manual (Affymetrix, Santa Clara, USA).
    • Sample_scan_protocol: The washing and staining of arrays were performed using a GeneChip Fluidics Station 400. The scanning of arrays was carried out using a GeneChip scanner (Affymetrix).
    • Sample_description: We loaded freeze injuries into baker's yeast cells under different freezing period and analyzed gene expressions during recovery process from freeze injured stated.
    • Sample_data_processing: The fluorescence intensities of array images were quantified using the Affymetrix software package (GeneChip Operating Software 1.2). Statistical analysis after data acquisition and normalization of expression data were carried out using GeneSpring ver.7 (Agilent technologies, Palo Alto, USA). After data transformation (set measurements less than 0.01 to 0.01) to GeneSpring, per chip normalization to the 50th percentile was performed. Per gene normalization to control samples (freezing time was 0day) was applied to the per chip normalized values.
    • Sample_platform_id: GPL90
    • Sample_contact_name: Satomi,Mizukami,Murata
    • Sample_contact_email: samymm@affrc.go.jp
    • Sample_contact_phone: +81-298-838-8066
    • Sample_contact_fax: +81-298-838-8066
    • Sample_contact_laboratory: Yeast
    • Sample_contact_institute: National Food Research Institute
    • Sample_contact_address: Kannondai 2-1-12
    • Sample_contact_city: Tsukuba
    • Sample_contact_zip/postal_code: 305-8642
    • Sample_contact_country: Japan
    • Sample_supplementary_file: ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM215nnn/GSM215117/GSM215117.CEL.gz
    • Sample_supplementary_file: ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM215nnn/GSM215117/GSM215117.CHP.gz
    • Sample_series_id: GSE8673
    • Sample_data_row_count: 9335
    • Sample_comment: Raw data provided as supplementary file
    • sample_table_begin:
    • sample_table_end:
    • Sample_title: Baker's yeast_freeze_3day_rep2
    ID_REF Corrected Value VALUE ABS_CALL
    AFFX-MurIL2_at 1.51507 7.59117 A
    AFFX-MurIL10_at 2.98001 9.81239 A
    AFFX-MurIL4_at 5.89494 2.91375 A
    AFFX-MurFAS_at 24.2003 17.134 A
    AFFX-BioB-5_at 207.098 131.934 P
    AFFX-BioB-M_at 217.468 150.206 P
    AFFX-BioB-3_at 205.935 144.19 P
    AFFX-BioC-5_at 356.62 289.214 P
    AFFX-BioC-3_at 382.252 307.65 P
    AFFX-BioDn-5_at 449.635 372.656 P
    View Full Table






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