1 sample(s) found by the keyword GSM206794.


  1. GEO sample ID: GSM206794
    • Sample_geo_accession: GSM206794
    • 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 deficient, 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 2.5 microg/ml (heme-deficient) 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 2.5 microg/ml (heme-deficient) 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 2.5 microg/ml (heme-deficient) 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/GSM206794/GSM206794.CEL.gz
    • Sample_supplementary_file: ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM206nnn/GSM206794/GSM206794.CHP.gz
    • Sample_supplementary_file: ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM206nnn/GSM206794/GSM206794.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 34.934746 11.61391
    10001_at 230.907093 208.912002
    10002_i_at 3157.895281 3137.762265
    10003_f_at 3919.886268 3913.817272
    10004_at 13.995917 19.458877
    10005_at 197.315091 249.232968
    10006_at 28.949662 119.200394
    10007_at 152.455491 270.57609
    10008_at 5.679795 86.688267
    10009_at 26.392183 131.426198
    View Full Table






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