1 sample(s) found by the keyword GSM254434.


  1. GEO sample ID: GSM254434
    • Sample_geo_accession: GSM254434
    • Sample_status: Public on Jul 30 2008
    • Sample_submission_date: Jan 04 2008
    • Sample_last_update_date: May 22 2008
    • Sample_type: RNA
    • Sample_channel_count: 1
    • Sample_source_name_ch1: Chemostat sample
    • Sample_organism_ch1: Saccharomyces cerevisiae
    • Sample_characteristics_ch1: Saccharomyces cerevisiae CEN.PK 113-7D (MATa)
    • Sample_biomaterial_provider_ch1: D. Abbott
    • Sample_treatment_protocol_ch1: Quenching in ice-cold TRIS-EDTA (pH 8)
    • Sample_growth_protocol_ch1: The laboratory reference strain CEN.PK 113-7D (MATa) was grown at 30 °C in 1.5-L chemostat fermentors (Applikon, Schiedam, The Netherlands) with a working volume of 1-L using an electronic level sensor to maintain a constant volume. All cultures, including the reference, were fed with minimal medium as described by Verduyn et al. (1992) with 25 g L-1 glucose as the limiting nutrient and 0.15 ml L-1 silicone antifoam (BDH, Poole, England) to prevent excessive foaming. The dilution rate was set to 0.10 h-1 and the pH was controlled at 3.0 with the automatic addition (ADI 1031 bio controller, Applikon) of 2 M KOH. The stirrer speed was set at 800 RPM and anaerobicity was maintained by sparging the fermentor with N2 gas at 500 ml min-1. To prevent diffusion of oxygen, the fermentor was equipped with Norprene tubing and Viton O-rings and the medium vessel was also flushed with N2 gas.
    • Sample_growth_protocol_ch1: Verduyn C, Postma E, Scheffers WA & van Dijken JP (1992) Effect of benzoic acid on metabolic fluxes in yeast: a continuous-culture study on the regulation of respiration and alcoholic fermentation. Yeast 8: 501-517.
    • Sample_molecule_ch1: total RNA
    • Sample_extract_protocol_ch1: Sampling of chemostat cultures and probe preparation was performed as described previously (Piper et al., 2002), but quenching was performed in ice-cold TRIS-EDTA rather than liquid nitrogen. Cultures were quenched in ice-cold TRIS-EDTA (TE) buffer at pH 8 (5 times the volume of sample (5x volume)), then washed in ice-cold TE buffer (2x volume) followed by ice-cold demi-water (2x volume).
    • Sample_extract_protocol_ch1: Piper MDW, Daran-Lapujade P, Bro C, Regenberg B, Knudsen S, Nielsen J & Pronk JT (2002) Reproducibility of oligonucleotide microarray transcriptome analyses. An interlaboratory comparison using chemostat cultures of Saccharomyces cerevisiae. J Biol Chem 277: 37001-37008.
    • Sample_label_ch1: SAPE
    • Sample_label_protocol_ch1: Sampling of chemostat cultures, probe preparation and hybridization to Affymetrix GeneChip microarrays was performed as described previously (Piper et al., 2002), but with the following modifications. Double-stranded cDNA synthesis was carried out using 15 μg of total RNA and the components of the One Cycle cDNA Synthesis Kit (Affymetrix). The double-stranded cDNA was purified (Genechip Sample Cleanup Module, Qiagen) before in vitro transcription and labeling (GeneChip IVT Labeling Kit, Affymetrix). Finally, labeled cRNA was purified (GeneChip Sample Cleanup Module) prior to fragmentation and hybridization of 15 μg of biotinylated cRNA.
    • Sample_label_protocol_ch1: Piper MDW, Daran-Lapujade P, Bro C, Regenberg B, Knudsen S, Nielsen J & Pronk JT (2002) Reproducibility of oligonucleotide microarray transcriptome analyses. An interlaboratory comparison using chemostat cultures of Saccharomyces cerevisiae. J Biol Chem 277: 37001-37008.
    • Sample_hyb_protocol: According to manufacturer's procedures
    • Sample_scan_protocol: Data acquisition was performed using the Affymetrix scanner 3000, quantification of array images and data filtering were performed with the Affymetrix software packages Microarray Suite v5.0, MicroDB v3.0 and Data Mining Tool v3.0.
    • Sample_description: C-lim anaerobic reference (pH 3) #2
    • Sample_data_processing: Chip file GCOS (Affymetrix - version 1.2.0.037)
    • Sample_platform_id: GPL90
    • Sample_contact_name: Jean-Marc,,Daran
    • Sample_contact_email: j.g.daran@tudelft.nl
    • Sample_contact_phone: +31 15 278 2412
    • Sample_contact_fax: +31 15 278 23 55
    • Sample_contact_laboratory: Kluyver centre for genomics of industrial organisms
    • Sample_contact_department: Department of Biotechnology
    • Sample_contact_institute: Delft University of Technology
    • Sample_contact_address: Julianalaan 67
    • Sample_contact_city: Delft
    • Sample_contact_zip/postal_code: 2628BC
    • Sample_contact_country: Netherlands
    • Sample_supplementary_file: ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM254nnn/GSM254434/GSM254434.CEL.gz
    • Sample_supplementary_file: ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/samples/GSM254nnn/GSM254434/GSM254434.CHP.gz
    • Sample_series_id: GSE10066
    • Sample_data_row_count: 9335
    • Sample_comment: Raw data provided as supplementary file
    • sample_table_begin:
    • sample_table_end:
    • Sample_title: C-lim anaerobic reference (pH 3) #3
    ID_REF Corrected Value VALUE ABS_CALL
    AFFX-MurIL2_at 0.194044 0.486947 A
    AFFX-MurIL10_at 0.534398 0.199633 A
    AFFX-MurIL4_at 2.92912 0.169577 A
    AFFX-MurFAS_at 5.02576 0.509377 A
    AFFX-BioB-5_at 75.6733 34.2146 P
    AFFX-BioB-M_at 101.777 61.7057 P
    AFFX-BioB-3_at 88.9707 51.2057 P
    AFFX-BioC-5_at 139.532 100.086 P
    AFFX-BioC-3_at 172.926 133.863 P
    AFFX-BioDn-5_at 296.912 256.566 P
    View Full Table






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