1 sample(s) found by the keyword GSM240718.- GEO sample ID: GSM240718
- Sample_geo_accession: GSM240718
- 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: mock IP RNA
- Sample_organism_ch1: Saccharomyces cerevisiae
- Sample_characteristics_ch1: Strain HFY113 (MATα ura3-1 leu2-3,112 his3-11,15 trp1-1 ade2-1 can1-100)
- 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/GSM240718/GSM240718.CEL.gz
- Sample_supplementary_file: ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM240nnn/GSM240718/GSM240718.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: Upf1p-TAP IP, replicate 4
ID_REF | Corrected Value | VALUE | ABS_CALL |
AFFX-MurIL2_at | 0.0611868 | 4.23504 | A |
AFFX-MurIL10_at | 0.305222 | 0.544516 | A |
AFFX-MurIL4_at | 2.92081 | 1.5206 | A |
AFFX-MurFAS_at | 9.55875 | 5.2554 | A |
AFFX-BioB-5_at | 188.411 | 113.838 | P |
AFFX-BioB-M_at | 256.118 | 187.626 | P |
AFFX-BioB-3_at | 215.674 | 151.277 | P |
AFFX-BioC-5_at | 278.341 | 212.619 | P |
AFFX-BioC-3_at | 270.326 | 202.604 | P |
AFFX-BioDn-5_at | 311.464 | 236.742 | P |
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