1 sample(s) found by the keyword GSM172916.


  1. GEO sample ID: GSM172916
    • Sample_geo_accession: GSM172916
    • Sample_status: Public on Oct 14 2007
    • Sample_submission_date: Mar 05 2007
    • Sample_last_update_date: Aug 23 2007
    • Sample_type: RNA
    • Sample_channel_count: 1
    • Sample_source_name_ch1: Yeast, untreated-1
    • Sample_organism_ch1: Saccharomyces cerevisiae
    • Sample_characteristics_ch1: Strain 4073
    • Sample_treatment_protocol_ch1: Control cells received no gentamicin, Gent treated cells were acclimated to growth in gentamicin, 500ug/ml and grown with gentamicin throughout the experiment
    • Sample_growth_protocol_ch1: Cell were grown overnight in YPD +/- gentamicin, diluted to 5x106 cells/ml and grown to mid-log with and without gentamicin 500ug/ml
    • Sample_molecule_ch1: total RNA
    • Sample_extract_protocol_ch1: Total RNA was isolated using the Epicentre Masterpure Yeast RNA Purification kit (Madison,WI)
    • Sample_label_ch1: biotin
    • Sample_label_protocol_ch1: Protocols recommended by Affymetrix were used, cDNA was synthesized using a T7 promoter-dT24 oligonucleotide as primer with the Invitrogen Life technologies SuperScript Choice system. Following second strand cDNA synthesis and incubation with T4 DNA polymerase, the products are purfied using an Affymetrix Cleanup Module.
    • Sample_label_protocol_ch1: Biotinylated cRNA is made using the Affymetrix IVT kit. The cRNA is purified using Qiagen RNeasy columns, quantitated and then fragmented by incubation at high temperature with magnesium.
    • Sample_hyb_protocol: Fifteen ug of biotinylated cRNA is added to a total hybridization cocktail of 300ul, and 200ul is hybridized to a GeneChip after adding control oligonucleotides. Hybridization is at 45C for 17 h with constant rotation. The hybridization mixture is then removed and the GeneChips are washed, stained with phycoerythrin-labeled Streptavidin,
    • Sample_hyb_protocol: washed, incubated with biotinylated anti-strepavidin, and then restained with phycoerythrin-labeled Strepavidin to amplify the signals; these steps are carried out using the Affymetrix Fluidics Station. To reduce non-random error, balanced groups of samples are handled in parallel.
    • Sample_scan_protocol: Arrays are then scanned using the dedicated scanner, controlled by Affymetrix GCOS software. Images are examined for defects.
    • Sample_description: control
    • Sample_data_processing: The Affymetrix Microarray Suite version 5 (MAS5) algorithm analyzes the hybridization intensity data from GeneChip expression probe arrays and calculates a set of metrics that describe probe set performance. The average intensity on each array is normalized by global scaling to a target intensity of 1000.
    • Sample_platform_id: GPL90
    • Sample_contact_name: Mark,,Wagner
    • Sample_contact_email: wagnerm@iupui.edu
    • Sample_contact_department: Medicine/Nephrology
    • Sample_contact_institute: Indiana University Medical Ctr
    • Sample_contact_address: 950 West Walnut Street
    • Sample_contact_city: Indianapolis
    • Sample_contact_state: IN
    • Sample_contact_zip/postal_code: 46202
    • Sample_contact_country: USA
    • Sample_supplementary_file: ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM172nnn/GSM172916/GSM172916.CEL.gz
    • Sample_supplementary_file: ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM172nnn/GSM172916/GSM172916.CHP.gz
    • Sample_series_id: GSE7188
    • Sample_data_row_count: 9335
    • Sample_comment: Raw data provided as supplementary file
    • sample_table_begin:
    • sample_table_end:
    • Sample_title: Yeast-control-2
    ID_REF Corrected Value VALUE ABS_CALL
    AFFX-MurIL2_at 8.42685 5.28512 A
    AFFX-MurIL10_at 14.18 2.22805 A
    AFFX-MurIL4_at 29.9766 10.5698 A
    AFFX-MurFAS_at 42.114 1.70181 A
    AFFX-BioB-5_at 548.698 300.678 P
    AFFX-BioB-M_at 541.059 309.897 P
    AFFX-BioB-3_at 536.387 315.756 P
    AFFX-BioC-5_at 984.395 746.816 P
    AFFX-BioC-3_at 952.805 700.353 P
    AFFX-BioDn-5_at 1678.28 1418.26 P
    View Full Table






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