1 sample(s) found by the keyword GSM240717.

  1. GEO sample ID: GSM240717
    • Sample_geo_accession: GSM240717
    • Sample_status: Public on Nov 01 2007
    • Sample_submission_date: Oct 31 2007
    • Sample_last_update_date: Oct 31 2007
    • Sample_type: RNA
    • Sample_channel_count: 1
    • Sample_source_name_ch1: Upf1p-TAP IP RNA
    • Sample_organism_ch1: Saccharomyces cerevisiae
    • Sample_characteristics_ch1: Strain MJY11 (MATα ura3-1 leu2-3,112 his3-11,15 trp1-1 ade2-1 can1-100 UPF1::TAP-K. lactis TRP1)
    • Sample_growth_protocol_ch1: Cells were grown in YEPD medium at 30ºC.
    • Sample_molecule_ch1: total RNA
    • Sample_extract_protocol_ch1: Cells were lysed by manual grinding for 30 minutes with intermittent addition of liquid nitrogen while keeping the mortar on dry ice. Ground cells were thawed on ice in 2 ml of buffer B (buffer A containing 0.5 mM DTT, 1X protease inhibitor cocktail (complete EDTA free, Roche Applied Science), 25 U/ml Protector RNase inhibitor (Roche Applied Science), 10 mM ribonucleoside-vanadyl complex (New England Biolabs)) per gram material. The crude extracts were cleared by centrifugation at 3,000 g for 5 minutes. Following a second centrifugation at 10,000 g for 30 minutes, the extracts were incubated at 4ºC for 2 hours in the presence of 200 μl of buffer A pre-washed IgG Sepharose (GE Healthcare) suspension. The remaining steps of the IgG immunopurification protocol were performed essentially as described (Puig et al., Methods, 24, 218-229, 2001). The buffers used were; 10 mM Tris-HCl pH 8.0, 140 mM KCl, 0.1% NP-40 (wash buffer) and 10 mM Tris-HCl pH 8.0, 140 mM KCl , 0.1% NP-40, 0.5 mM EDTA, 1 mM DTT (TEV cleavage buffer). RNA in the TEV (AcTEV, Invitrogen) eluates was isolated by phenol/chloroform extraction followed by isopropanol precipitation. The precipitated RNA was dissolved in RNase free water. An equivalent amount of RNA from the Upf1p-TAP and mock samples was further purified using the RNeasy Micro Kit (Qiagen).
    • Sample_label_ch1: biotin
    • Sample_label_protocol_ch1: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix).
    • Sample_hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Yeast Genome S98 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
    • Sample_scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
    • Sample_description: none
    • Sample_data_processing: The data were analyzed with Affymetrix GCOS using global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 250
    • Sample_platform_id: GPL90
    • Sample_contact_name: Marcus,J.O.,Johansson
    • Sample_contact_department: Molecular Genetics and Microbiology
    • Sample_contact_institute: University of Massachusetts Medical School
    • Sample_contact_address: 55 Lake Avenue North
    • Sample_contact_city: Worcester
    • Sample_contact_state: MA
    • Sample_contact_zip/postal_code: 01655
    • Sample_contact_country: USA
    • Sample_supplementary_file: ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM240nnn/GSM240717/GSM240717.CEL.gz
    • Sample_supplementary_file: ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM240nnn/GSM240717/GSM240717.CHP.gz
    • Sample_series_id: GSE9486
    • Sample_data_row_count: 9335
    • Sample_comment: Raw data provided as supplementary file
    • sample_table_begin:
    • sample_table_end:
    • Sample_title: mock IP, replicate 3
    ID_REF Corrected Value VALUE ABS_CALL
    AFFX-MurIL2_at 0.852458 2.90937 A
    AFFX-MurIL10_at 3.23197 1.67103 A
    AFFX-MurIL4_at 8.83659 3.06737 A
    AFFX-MurFAS_at 14.6436 5.70162 A
    AFFX-BioB-5_at 214.619 130.025 P
    AFFX-BioB-M_at 309.248 231.546 P
    AFFX-BioB-3_at 225.495 148.478 P
    AFFX-BioC-5_at 237.418 158.565 P
    AFFX-BioC-3_at 181.82 100.766 P
    AFFX-BioDn-5_at 199.969 115.761 P
    View Full Table

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