1 sample(s) found by the keyword GSM217617.

  1. GEO sample ID: GSM217617
    • Sample_geo_accession: GSM217617
    • Sample_status: Public on Nov 06 2007
    • Sample_submission_date: Aug 13 2007
    • Sample_last_update_date: Nov 06 2007
    • Sample_type: RNA
    • Sample_channel_count: 1
    • Sample_source_name_ch1: Rpl7a deletion cells grown in rich media at 30C
    • Sample_organism_ch1: Saccharomyces cerevisiae
    • Sample_characteristics_ch1: Rpl7a::KAN in BY4741 background
    • Sample_growth_protocol_ch1: 50mL cultures were grown in YPD to early log phase (OD260 0.2-0.4) at 30oC., centrifuged at room temperature and flash-frozen using liquid nitrogen.
    • Sample_molecule_ch1: total RNA
    • Sample_extract_protocol_ch1: mRNA was extracted from cell pellets using the hot phenol method and precipitated overnight in ethanol
    • Sample_label_ch1: Biotin
    • Sample_label_protocol_ch1: RNA is converted into cDNA using a T7 promoter-tailed oligo-dT primer in the synthesis of the first cDNA strand; second strand cDNA synthesis is then carried out. The double-stranded cDNA is used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates. The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using the RNeasy system (Qiagen). The cRNA is quantified spectrophotometrically and purity of the cRNA is also assessed by spectrophometric measurements.
    • Sample_hyb_protocol: The purified cRNA is fragmented in order to facilitate the subsequent hybridization step. The fragmented cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. The chips are then transferred to a fluidics instrument that performs washes to remove cRNA that has not hybridized to its complementary oligonucleotide probe. The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE.
    • Sample_scan_protocol: Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured. These measures provide the basis of subsequent biostatistical analysis.
    • Sample_description: Replicate #1 of rpl7a- mRNA sample used for analysis of ribosomal protein knockout expression levels.
    • Sample_data_processing: Gene Chip Operating System's Statistical Expression algorithm is used to analyze the cell intensities and generate both expression values and presence/absence calls
    • Sample_platform_id: GPL90
    • Sample_contact_name: Suzanne,,Komili
    • Sample_contact_institute: Harvard University
    • Sample_contact_address: 44 Binney St.
    • Sample_contact_city: Boston
    • Sample_contact_state: MA
    • Sample_contact_zip/postal_code: 02115
    • Sample_contact_country: USA
    • Sample_supplementary_file: ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM217nnn/GSM217617/GSM217617.CEL.gz
    • Sample_series_id: GSE8761
    • Sample_data_row_count: 9335
    • Sample_comment: Raw data provided as supplementary file
    • sample_table_begin:
    • sample_table_end:
    • Sample_title: Rpl7a_knockout_rep2
    ID_REF Corrected Value Stat Pairs Stat Pairs Used
    AFFX-MurIL2_at 0.1 20 20
    AFFX-MurIL10_at 0.4 20 20
    AFFX-MurIL4_at 4.1 20 20
    AFFX-MurFAS_at 11 20 20
    AFFX-BioB-5_at 161.2 20 20
    AFFX-BioB-M_at 208 20 20
    AFFX-BioB-3_at 182.6 20 20
    AFFX-BioC-5_at 365.7 20 20
    AFFX-BioC-3_at 442.6 20 20
    AFFX-BioDn-5_at 495.5 20 20
    View Full Table

Developed by Dirar Homouz, Gang Chen, and Andrzej S. Kudlicki*

Software download