1 sample(s) found by the keyword GSM474866.

  1. GEO sample ID: GSM474866
    • Sample_geo_accession: GSM474866
    • Sample_status: Public on Nov 25 2009
    • Sample_submission_date: Nov 23 2009
    • Sample_last_update_date: Nov 26 2009
    • Sample_type: RNA
    • Sample_channel_count: 1
    • Sample_source_name_ch1: Saccharomyces cerevisiae 3238-32 (MATa leu2∆1 lys2-801 ura3-52), planktonic cells.
    • Sample_organism_ch1: Saccharomyces cerevisiae
    • Sample_characteristics_ch1: cell type: cells at the bottom of the beaker (sinkers)
    • Sample_characteristics_ch1: replicate: 2
    • Sample_biomaterial_provider_ch1: Alan T. Bakalinsky
    • Sample_treatment_protocol_ch1: Cells were grown 24 h at 30°C in YEPD to a density of 5 x 108 cells/ml. At harvest, sugar was found to be depleted as measured by an enzymatic dip stick (Diastic, Bayer). Cells were pelleted and washed twice in sterile distilled water by centrifugation and then diluted 10-fold into 100 ml of Flor medium (YNB + 4% ethanol + leucine + histidine + uracil) in triplicate 250 ml beakers. Cultures were then grown statically in Flor medium at 27°C. Within a few hours following inoculation, the bulk liquid appeared to be clear, no biofilm was evident by visual observation, and a layer of settled cells was evident at the bottom of the beakers. After 48 h, a visible biofilm covered the entire surface while the thickness of the layer of settled cells appeared unchanged. After 48 h, biofilm cells (“floaters”) were collected by aseptic aspiration. Once the biofilm cells were removed, cells at the bottom of the beaker (“sinkers”) were collected similarly. Cells from both populations were washed once in sterile distilled water by centrifugation prior to RNA isolation. Significant cell clumping was evident in both populations of cells by microscopic observation. While cell viability was estimated by plating on YEPD, the resultant cfu/ml values could not be directly correlated with cell counts in a hemacytometer because clumps of cells containing at least one viable cell presumably produced only a single colony. Further, counting individual cells accurately in the numerous clumps containing large numbers of cells was not possible. Nonetheless, when cells were counted (clumps were counted as single cells) and compared to cfu/ml for the same suspension, the cfu/ml values were about 2-fold higher than the corresponding values for cell counts using the hemacytometer for both biofilm and bottom layer cells.
    • Sample_growth_protocol_ch1: See treatment protocol
    • Sample_molecule_ch1: total RNA
    • Sample_extract_protocol_ch1: Yeast cells were processed for total RNA isolation immediately after they were collected essentially as described (Schmitt et al., 1990). The RNA was subsequently purified using a commercial kit (RNA Easy, Qiagen, Valencia, CA). A260/A280 ratios for the purified RNA preparations ranged from 1.96 to 2.07.
    • Sample_label_ch1: biotin
    • Sample_label_protocol_ch1: Synthesis of labelled aRNA was done according to the manufacturers protocol (Ambion MessageAmp[TM] aRNA kit, catalog #1750); purification and aRNA fragmentation were performed according to Affymetrix protocols (GeneChip Expression Analysis Technical Manual 701021 rev. 1, Affymetrix, Santa Clara, CA).
    • Sample_hyb_protocol: Hybridization to yeast YGS98 microarrays was performed according to the manufacturer’s instructions (GeneChip Expression Analysis Technical Manual 701021 rev. 1, Affymetrix, Santa Clara, CA).
    • Sample_scan_protocol: Scanning was performed according to the manufacturer’s instructions (GeneChip Expression Analysis Technical Manual 701021 rev. 1, Affymetrix, Santa Clara, CA).
    • Sample_description: Saccharomyces cerevisiae 3238-32 (MATa leu2∆1 lys2-801 ura3-52). This strain forms a liquid-air interfacial biofilm upon depletion of a glucose in a glucose-containing medium (e.g., YPD or YNB) (Zara et al., 2005). Planktonic cells ("sinkers") were harvested.
    • Sample_data_processing: Mas5.0
    • Sample_platform_id: GPL90
    • Sample_contact_name: Alan,T,Bakalinsky
    • Sample_contact_email: alan.bakalinsky@oregonstate.edu
    • Sample_contact_phone: 541 737-6510
    • Sample_contact_fax: 541 737-1877
    • Sample_contact_department: Food Science & Technology
    • Sample_contact_institute: Alan Bakalinsky
    • Sample_contact_address: Wiegand Hall
    • Sample_contact_city: Corvallis
    • Sample_contact_state: OR
    • Sample_contact_zip/postal_code: 97331-6602
    • Sample_contact_country: United States
    • Sample_supplementary_file: ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM474nnn/GSM474866/GSM474866.CEL.gz
    • Sample_supplementary_file: ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM474nnn/GSM474866/GSM474866.CHP.gz
    • Sample_series_id: GSE19156
    • Sample_data_row_count: 9335
    • Sample_comment: Raw data provided as supplementary file
    • sample_table_begin:
    • sample_table_end:
    • Sample_title: Sinker replicate 3
    ID_REF Corrected Value VALUE ABS_CALL
    AFFX-MurIL2_at 0.173371 4.80069 A
    AFFX-MurIL10_at 0.802816 4.6044 A
    AFFX-MurIL4_at 2.18308 0.944388 A
    AFFX-MurFAS_at 5.49468 2.07446 A
    AFFX-BioB-5_at 369.386 227.929 P
    AFFX-BioB-M_at 408.76 275.983 P
    AFFX-BioB-3_at 353.958 229.408 P
    AFFX-BioC-5_at 549.206 426.879 P
    AFFX-BioC-3_at 398.173 284.321 P
    AFFX-BioDn-5_at 443.728 328.368 P
    View Full Table

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