1 sample(s) found by the keyword GSM283868.


  1. GEO sample ID: GSM283868
    • Sample_geo_accession: GSM283868
    • Sample_status: Public on Feb 05 2009
    • Sample_submission_date: Apr 23 2008
    • Sample_last_update_date: Feb 05 2009
    • Sample_type: RNA
    • Sample_channel_count: 1
    • Sample_source_name_ch1: chemostat culture
    • Sample_organism_ch1: Saccharomyces cerevisiae
    • Sample_characteristics_ch1: Strain and Maintenance—
    • Sample_characteristics_ch1: This study was performed with the prototrophic laboratory strain S. cerevisiae CEN.PK113-7D (MATa) [van Dijken, J. P., Bauer, J., Brambilla, L., Duboc, P., Francois, J. M., Gancedo, C., Giuseppin, M. L. F., Heinen, J. J., Hoare, M., Lange, H. C., Madden, E. A., Niederberger, P., Nielsen, J., Parrou, J. L., Petit, T., Porro, D., Reuss, M., van Riel, N., Rizzi, M., Steensma, H. Y., Verrips, C. T., Vindelov, J., and Pronk, J. T. (2000) Enz. Microb. Technol. 26, 706–714]
    • Sample_biomaterial_provider_ch1: E Suir
    • Sample_treatment_protocol_ch1: liquid N2 quenching
    • Sample_growth_protocol_ch1: Chemostat Cultivation—
    • Sample_growth_protocol_ch1: Steady-state chemostat cultures were grown in Applikon laboratory fermentors of 1-liter working volume as described in detail elsewhere [van den Berg, M. A., de Jong-Gubbels, P., Kortland, C. J., van Dijken, J. P., Pronk, J. T., and Steensma, H. Y. (1996) J. Biol. Chem. 271, 28953–28959]. In brief, the cultures were fed with a defined mineral medium containing glucose as the growth-limiting nutrient [. Verduyn, C., Postma, E., Scheffers, W. A., and van Dijken, J. P. (1990) Microbiol.Rev. 58, 616–630]. The dilution rate (which equals the specific growth rate) in the steady-state cultures was 0.10 h_1, the temperature was 30 °C, and the culture pH was 5.0. Aerobic conditions were maintained by sparging the cultures with air (0.5 liter_min_1). The dissolved oxygen concentration, which was continuously monitored with an Ingold model 34-100-3002 probe, remained above 80% of air saturation.
    • Sample_growth_protocol_ch1: Media—
    • Sample_growth_protocol_ch1: The defined mineral medium composition was based on that described by Verduyn et al [. Verduyn, C., Postma, E., Scheffers, W. A., and van Dijken, J. P. (1990) Microbiol.Rev. 58, 616–630]. The residual glucose concentration was targeted to 17 g_liter_1 to sustain glucose repression at the same level . For sulfur-limited, the composition was 4.0 g of NH4Cl, 0.05 g of MgSO4_7H2O, 3.0 g of KH2PO4, 0.4g of MgCl2, and 42 g of glucose.
    • 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).
    • 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 and RNA Isolation—
    • 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 GCOS 1.2
    • Sample_description: ES03
    • Sample_data_processing: Chip file targetted to 150 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/GSM283nnn/GSM283868/GSM283868.CEL.gz
    • Sample_series_id: GSE11452
    • Sample_data_row_count: 9335
    • Sample_comment: Raw data provided as supplementary file
    • sample_table_begin:
    • sample_table_end:
    • Sample_title: Aerobic S-lim chemostat culture-2
    ID_REF Corrected Value VALUE ABS_CALL
    AFFX-MurIL2_at 0.1 3.1 A
    AFFX-MurIL10_at 0.3 0.3 A
    AFFX-MurIL4_at 1.6 0.5 A
    AFFX-MurFAS_at 4.2 2.8 A
    AFFX-BioB-5_at 62.6 17.5 P
    AFFX-BioB-M_at 79.4 36.2 P
    AFFX-BioB-3_at 74.7 33.7 P
    AFFX-BioC-5_at 109.9 69.3 P
    AFFX-BioC-3_at 124 83.2 P
    AFFX-BioDn-5_at 230.5 189.1 P
    View Full Table






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

Software download