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Sample GSM769478 Query DataSets for GSM769478
Status Public on Dec 31, 2011
Title phoP-F134-F335-35 h
Sample type RNA
 
Source name phoP-F134-F335-35 h
Organism Streptomyces coelicolor
Characteristics strain: INB201
genotype/variation: delta phoP mutant
time point: 35 h
Growth protocol Fermentations were performed using the S. coelicolor INB201 (phoP mutant, Santos-Beneit et al., 2009) strain. As described previously (Nieselt et al., 2010), 5x10^8 CFU/l of germinated spores were used to inoculate 1.8 L of growth medium in 3-liter Applikon fermenters. The growth medium led to phosphate depletion after about 41 h of cultivation, with all other components remaining in excess until the end of the fermentation trials. Dissolved oxygen levels were maintained at a minimum of 50 % by the automatic adjustment of agitation (minimal stirrer speed 300 rpm) at a constant aeration rate of 0.9 l/l-min sterile air. The medium is referred to as F134.
Extracted molecule total RNA
Extraction protocol Total RNA isolation was performed via phenol extraction and RNeasy Midi Kit (Qiagen, 2001) according to manufacturer's instruction.
Label biotin
Label protocol Biotinylated cDNA were prepared after fragmentation according to the standard Affymetrix protocol from 3 µg total RNA (Prokaryotic Sample and Array Processing, Technical Manual 701030 Rev. 5, 2004, Affymetrix).
 
Hybridization protocol 3 µg of cDNA were hybridized for 16 hr at 50°C on Array Platform GPL9471. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Scan protocol GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.
Description Medium F134
Data processing RMA (Bolstad, 2002) as implemented in the affy package of Bioconductor.
 
Submission date Jul 31, 2011
Last update date Dec 31, 2011
Contact name Kay Nieselt
E-mail(s) kay.nieselt@uni-tuebingen.de
Phone (+49) 70712978981
Organization name Institute for Bioinformatics and Medical Informatics
Department Department for Computer Science
Lab Integrative Transcriptomics
Street address Sand 14
City Tübingen
State/province DE
ZIP/Postal code 72076
Country Germany
 
Platform ID GPL9417
Series (1)
GSE31068 Metabolic switches and adaptations deduced from the proteomes of Streptomyces coelicolor wild type and phoP mutant grown in batch culture

Data table header descriptions
ID_REF
VALUE log2 median polished RMA expression summaries

Data table
ID_REF VALUE
AFFX-Athal_GAPDH_at 5.05521797380968
AFFX-Athal_actin_at 4.95312025613772
AFFX-Athal_ubq_at 5.04384656993452
AFFX-BioB-3_at 5.21933176204073
AFFX-BioB-5_at 5.27565332777778
AFFX-BioB-M_at 5.14156099048811
AFFX-BioC-3_at 5.04047500435552
AFFX-BioC-5_at 5.19748700061533
AFFX-BioDn-3_at 5.23543833492359
AFFX-BioDn-5_at 5.08778084240167
AFFX-Bsubtilis_dapB_at 12.6766574673925
AFFX-Bsubtilis_lys_at 8.16466075317542
AFFX-Bsubtilis_pheB_at 11.0252316401116
AFFX-Bsubtilis_thrC_at 11.5894251390740
AFFX-Bsubtilis_trpD_at 5.07134173882259
AFFX-CreX-3_at 6.20613040131099
AFFX-CreX-5_at 4.94969866083209
AFFX-DapX-3_at 11.9780637517651
AFFX-DapX-5_at 12.636182222032
AFFX-DapX-M_at 12.2563290551959

Total number of rows: 22779

Table truncated, full table size 719 Kbytes.




Supplementary file Size Download File type/resource
GSM769478.CEL.gz 965.0 Kb (ftp)(http) CEL
Processed data included within Sample table

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