2 sample(s) found by the keyword GSM21654.

  1. GEO sample ID: GSM21654
    • Sample_geo_accession: GSM21654
    • Sample_status: Public on Aug 01 2005
    • Sample_submission_date: Apr 14 2004
    • Sample_last_update_date: Oct 28 2005
    • Sample_type: RNA
    • Sample_channel_count: 1
    • Sample_source_name_ch1: BY4743(S288C)
    • Sample_organism_ch1: Saccharomyces cerevisiae
    • Sample_molecule_ch1: total RNA
    • Sample_description: Stock and seed cultures of strain BY4743 were grown in yeast extract-peptone-dextrose (YPD) medium (10 mg/ml yeast extract, 20 mg/ml bactopeptone, 20 mg/ml glucose, pH 6.5 ± 0.2), at 30°C until the A600 reached 0.8. Cells were centrifuged and the cell pellet was resuspended and dispersed in 1:20 diluted YPD medium at between 22 to 25 °C. An aliquot, which represent the control sample (T1), was removed for RNA extraction, and the remaining suspension was aliquoted into 9-cm diameter glass Petri dishes (15 ml/dish) for desiccation.
    • Sample_description: Desiccation was carried out in a custom-fabricated controlled atmosphere desiccation system, at 22 to 25 °C. For more information on the unit and software, contact the corresponding author. A series of aliquots were withdrawn from the cell suspensions 18h (T2) after the start of the drying process.
    • Sample_description: Samples were collected on a volume basis and were in the same ratio as collected at T1. Once dry (42 h), the water potential was adjusted to 20% relative humidity for a period of 72 hr. A sample was collected at this timepoint, representing the dry sample (Tdry). Dry cells were hydrated (22 to 25 °C ) using 1:20 diluted YPD medium, 15 ml per plate. Resuspended cells from the four plates were pooled in a sterile 250 ml flask. Samples were collected for various analyses at time points of 15 min (T4), 45 min (T5), 90 min (T6) and 360 min (T7) after the start of rehydration.
    • Sample_description: Total RNA was isolated essentially as described (Schmitt, M. E., Brown, T. A., and Trumpower, B. L. (1990) Nucl. Acids Res. 18, 3091-3092). RNA was quantified using a spectrophotometer, and its quality was assessed using the A260/A280 ratio.
    • Sample_description: Target cRNA was hybridized to Affymetrix Y98 chips (GPL90) and raw image data was analyzed using the GeneChip Expression Analysis Software (Affymetrix). Probe set signals were processed by a Wilcoxon’s signed rank test and consolidated using a two-step linear mixed model. This sample is known as E1_T5_R3, 45 min. post rehydration.
    • Sample_platform_id: GPL90
    • Sample_contact_name: Richard,F.,Helm
    • Sample_contact_email: helmrf@vt.edu
    • Sample_contact_phone: 540-231-4088
    • Sample_contact_fax: 540-231-9070
    • Sample_contact_laboratory: Virginia Tech Center for Genomics
    • Sample_contact_department: Biochemistry, Fralin Biotechnology Center
    • Sample_contact_institute: Virginia Polytechnic Institute and State University
    • Sample_contact_address: West Campus Drive
    • Sample_contact_city: Blacksburg
    • Sample_contact_state: VA
    • Sample_contact_zip/postal_code: 24061
    • Sample_contact_country: USA
    • Sample_contact_web_link: http://vigen.biochem.vt.edu
    • Sample_supplementary_file: ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM21nnn/GSM21654/GSM21654.CEL.gz
    • Sample_supplementary_file: ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM21nnn/GSM21654/GSM21654.DAT.gz
    • Sample_supplementary_file: ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM21nnn/GSM21654/GSM21654.EXP.gz
    • Sample_series_id: GSE1311
    • Sample_data_row_count: 9335
    • Sample_comment: Raw data provided as supplementary file
    • sample_table_begin:
    • sample_table_end:
    • Sample_title: E1_T6_R1, 90 min. post rehydration
    ID_REF Corrected Value VALUE ABS_CALL
    AFFX-MurIL2_at 4.6 5 A
    AFFX-MurIL10_at 4 2.9 A
    AFFX-MurIL4_at 4.9 10.1 A
    AFFX-MurFAS_at 5.5 4.3 A
    AFFX-BioB-5_at 244.3 118.4 A
    AFFX-BioB-M_at 239.5 122.9 P
    AFFX-BioB-3_at 230.8 126.9 P
    AFFX-BioC-5_at 1729.8 1615.9 P
    AFFX-BioC-3_at 1175.1 1081.3 P
    AFFX-BioDn-5_at 933.4 834.1 P
    View Full Table

  2. GEO sample ID: GSM216549
    • Sample_geo_accession: GSM216549
    • Sample_status: Public on Sep 07 2007
    • Sample_submission_date: Aug 09 2007
    • Sample_last_update_date: Sep 07 2007
    • Sample_type: RNA
    • Sample_channel_count: 1
    • Sample_source_name_ch1: S.cerevisiae before LiCl treatment
    • Sample_organism_ch1: Saccharomyces cerevisiae
    • Sample_characteristics_ch1: S.cerevisiae before LiCl treatment
    • Sample_treatment_protocol_ch1: After incubation of the resultant transformants in SC-Ura or Sc-Leu-Ura medium at 25°C to the exponential growth phase, 200 mM LiCl was added. At the intervals (0-60 min), the cells were harvested and lysed.
    • Sample_growth_protocol_ch1: The media used for S. cerevisiae were SC consisting of 2% glucose, 0.67% Bacto Yeast Nitrogen Base with ammonium sulfate (Difco Laboratories, Detroit, MI) and drop-out mix lacking leucine (SC-Leu), or lacking leucine and uracil (SC-Leu-Ura).
    • Sample_molecule_ch1: total RNA
    • Sample_extract_protocol_ch1: Total RNA from S. cerevisiae was isolated by the method of Köhrer and Domdey. Poly A mRNA was enriched from total RNA by Oligotex dT30 mRNA purification kit (Takara Bio).
    • Sample_label_ch1: biotin
    • Sample_label_protocol_ch1: Accoding to the Affymetrix user's mannual
    • Sample_hyb_protocol: The biotinyated cRNA (15 µg) prob was hybridized to DNA microarray at 45°C for 18 h
    • Sample_scan_protocol: The scanning of arrays was carried out using the GeneArray scanner (Agilent technologies) Palto Alto, CA).
    • Sample_description: KIN28 overexpression 0min
    • Sample_data_processing: The fluorescence intensities of array images were quantified using the Affymetrix software package (Microarray Suite version 4.0.1). The statistical analysis after data acquisition and normalization of expression data were carried out using the GeneSpring
    • Sample_platform_id: GPL90
    • Sample_contact_name: Yoshinori,,Murata
    • Sample_contact_email: muratayo@affrc.go.jp
    • Sample_contact_phone: +81-29-838-6623
    • Sample_contact_fax: +81-29-838-6623
    • Sample_contact_department: Post-harvest Science and Technology Division
    • Sample_contact_institute: Japan International Research Center for Agricultural Science
    • Sample_contact_address: 1-1 Ohwashi
    • Sample_contact_city: Tsukuba
    • Sample_contact_state: Ibaraki
    • Sample_contact_zip/postal_code: 305-8686
    • Sample_contact_country: Japan
    • Sample_supplementary_file: ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM216nnn/GSM216549/GSM216549.CEL.gz
    • Sample_supplementary_file: ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM216nnn/GSM216549/GSM216549.CHP.gz
    • Sample_supplementary_file: ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM216nnn/GSM216549/GSM216549_Normalized_KIN28_0min.txt.gz
    • Sample_series_id: GSE8729
    • Sample_data_row_count: 9335
    • Sample_comment: Raw data provided as supplementary file
    • sample_table_begin:
    • sample_table_end:
    • Sample_title: KIN28 60min
    ID_REF Corrected Value VALUE ABS_CALL
    AFFX-MurIL2_at 0.631932 2.845 A
    AFFX-MurIL10_at 1.01651 1.38058 A
    AFFX-MurIL4_at 2.13002 1.76878 A
    AFFX-MurFAS_at 3.58227 1.45315 A
    AFFX-BioB-5_at 182.514 139.495 P
    AFFX-BioB-M_at 198.127 162.712 P
    AFFX-BioB-3_at 183.946 152.087 P
    AFFX-BioC-5_at 269.837 236.74 P
    AFFX-BioC-3_at 286.645 246.676 P
    AFFX-BioDn-5_at 463.171 427.101 P
    View Full Table

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