1 sample(s) found by the keyword GSM206797.


  1. GEO sample ID: GSM206797
    • Sample_geo_accession: GSM206797
    • Sample_status: Public on Sep 10 2008
    • Sample_submission_date: Jun 30 2007
    • Sample_last_update_date: Sep 10 2008
    • Sample_type: RNA
    • Sample_channel_count: 1
    • Sample_source_name_ch1: Saccharomyces cerevisiae, MHY100, heme sufficient, replicate 2
    • Sample_organism_ch1: Saccharomyces cerevisiae
    • Sample_characteristics_ch1: Yeast strains used MHY100 (MATa, ura3-52, leu2-3, 112, his4-519, ade1-100, hem1-delta100). MHY100 was used for studies of heme regulation. MHY100 cells were grown in medium containing 250 microg/ml (heme-sufficient) 5-aminolevulinic acid. For RNA preparations, yeast cells were inoculated so that the optical density of yeast cells was in the range of 0.8-1.0 immediately before the collection of cells.
    • Sample_molecule_ch1: total RNA
    • Sample_extract_protocol_ch1: RNA was extracted from yeast cells exactly as previously described in [Ausubel FM, Brent R, Kingston RE, Moore DD, Seidman JG, Smith JA, Struhl K: Current protocols in molecular biology: John Wiley & Sons, Inc.; 2000.]. RNA samples were prepared from MHY100 cells grown in medium containing 250 microg/ml (heme-sufficient) 5-aminolevulinic acid. The quality of RNA was high as assessed by measuring absorbance at 260 and 280 nm, by gel electrophoresis, and by the quality of microarray data.
    • Sample_label_ch1: biotin
    • Sample_label_protocol_ch1: The synthesis of cDNA and biotin-labeled cRNA were carried out exactly as described in the Affymetrix GeneChip Expression Analysis Technical Manual (2000).
    • Sample_hyb_protocol: The yeast Saccharomyces cerevisiae genome 2.0 arrays were purchased from Affymetrix, Inc. Probe hybridization and data collection were carried out by the Columbia University Affymetrix GeneChip processing center. Specifically, the Affymetrix GeneChip Hybridization Oven 640 and the next generation GeneChip Fluidics Station 450 were used for hybridization and chip processing. Chip scanning was performed by using the GeneChip scanner 3000. Initial data acquisition, analysis was performed by using the Affymetrix Microarray suite. By using GCOS1.2 with the advanced PLIER (probe logarithmic intensity error) algorithm, we calculated and examined the parameters reflecting the image quality of the arrays. Arrays with a high background level in any region were discarded and replaced. The average noise or background level was limited to less than 5%. The average intensity for those genes judged to be present was at least 10-fold higher than those judged to be absent. Also, arrays that deviated considerably in the percentage of present and absent genes from the majority of the arrays were replaced. Arrays with a beta-actin 3’/5’ ratio greater than 2 were replaced.
    • Sample_scan_protocol: The yeast Saccharomyces cerevisiae genome 2.0 arrays were purchased from Affymetrix, Inc. Probe hybridization and data collection were carried out by the Columbia University Affymetrix GeneChip processing center. Specifically, the Affymetrix GeneChip Hybridization Oven 640 and the next generation GeneChip Fluidics Station 450 were used for hybridization and chip processing. Chip scanning was performed by using the GeneChip scanner 3000. Initial data acquisition, analysis was performed by using the Affymetrix Microarray suite. By using GCOS1.2 with the advanced PLIER (probe logarithmic intensity error) algorithm, we calculated and examined the parameters reflecting the image quality of the arrays. Arrays with a high background level in any region were discarded and replaced. The average noise or background level was limited to less than 5%. The average intensity for those genes judged to be present was at least 10-fold higher than those judged to be absent. Also, arrays that deviated considerably in the percentage of present and absent genes from the majority of the arrays were replaced. Arrays with a beta-actin 3’/5’ ratio greater than 2 were replaced.
    • Sample_description: MHY100 cells grown in medium containing 250 microg/ml (heme-sufficient) 5-aminolevulinic acid. Cells were grown in yeast synthetic complete media. For RNA preparations, yeast cells were inoculated so that the optical density of yeast cells was in the range of 0.8-1.0 immediately before the collection of cells.
    • Sample_data_processing: For each microarray, we converted the .DAT image files into .CEL files using the Affymetrix GCOS software. These raw .CEL files were further processed into expression values using the RMA express software by Bolstad. This software uses the robust multiarray average method by Irrizary et al. which involves a background correction and a quantile-based normalization scheme.
    • Sample_platform_id: GPL90
    • Sample_contact_name: ANSHUL,BHARAT,KUNDAJE
    • Sample_contact_email: abk2001@columbia.edu
    • Sample_contact_laboratory: COMPUTATIONAL BIOLOGY
    • Sample_contact_department: COMPUTER SCIENCE
    • Sample_contact_institute: COLUMBIA UNIVERSITY
    • Sample_contact_address: 110 MORNINGSIDE DRIVE, APT. 31A
    • Sample_contact_city: NEW YORK CITY
    • Sample_contact_state: NY
    • Sample_contact_zip/postal_code: 10027
    • Sample_contact_country: USA
    • Sample_contact_web_link: http://www.cs.columbia.edu/~abk2001
    • Sample_supplementary_file: ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM206nnn/GSM206797/GSM206797.CEL.gz
    • Sample_supplementary_file: ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM206nnn/GSM206797/GSM206797.CHP.gz
    • Sample_supplementary_file: ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM206nnn/GSM206797/GSM206797.EXP.gz
    • Sample_series_id: GSE8343
    • Sample_data_row_count: 9335
    • Sample_comment: Raw data provided as supplementary file
    • sample_table_begin:
    • sample_table_end:
    • Sample_title: YeastMHY100_[Heme+]_rep3
    ID_REF Corrected Value VALUE
    10000_at 21.685408 11.85495
    10001_at 294.786204 287.726326
    10002_i_at 2958.281607 2949.645598
    10003_f_at 4794.460466 4786.546724
    10004_at 7.876621 12.547204
    10005_at 162.195918 222.938322
    10006_at 65.093255 172.800729
    10007_at 53.223868 186.787506
    10008_at 3.400203 55.791061
    10009_at 6.894409 91.835266
    View Full Table






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