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Status |
Public on Dec 31, 2011 |
Title |
phoP-F134-F335-35 h |
Sample type |
RNA |
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Source name |
phoP-F134-F335-35 h
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Organism |
Streptomyces coelicolor |
Characteristics |
strain: INB201 genotype/variation: delta phoP mutant time point: 35 h
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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.
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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.
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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).
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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.
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Scan protocol |
GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.
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Description |
Medium F134
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Data processing |
RMA (Bolstad, 2002) as implemented in the affy package of Bioconductor.
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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
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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 |
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|
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 |
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