|
| Status |
Public on Jul 20, 2011 |
| Title |
F.pla_benzene, rep 1 |
| Sample type |
RNA |
| |
|
| Source name |
1 mM benzene as electron donor and 56 mM ferric citrate as electron acceptor
|
| Organism |
Ferroglobus placidus DSM 10642 |
| Characteristics |
strain: DSM 10642
electron donor: benzene
electron donor type: aromatic hydrocarbon
|
| Growth protocol |
Ferroglobus placidus DSM 10642 was grown in strict anaerobic conditions (80:20 N2/CO2) in medium previously described (Tor et al., Env. Micro. 2001, 3(4) p281) with 1 mM benzene as electron donor and Fe(III) citrate as electron acceptor. Cultures were incubated at 85C in the dark.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cultures (100 ml in 156 ml serum bottles) were divided into 50 ml conical tubes (Falcon), and cells were pelleted with centrifugation at 3,000 xg for 15 min. Pellets were then immediately frozen in liquid nitrogen and stored at –80°C.
Total RNA was extracted according to the HG protocol described in Holmes et al., ISME Journal, 2011.
|
| Label |
Cy3
|
| Label protocol |
Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
|
| |
|
| Hybridization protocol |
Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.
|
| Scan protocol |
Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
|
| Description |
F. placidus grown with 1 mM benzene. First biological replicate of three.
|
| Data processing |
The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).
|
| |
|
| Submission date |
Jul 19, 2011 |
| Last update date |
Jul 20, 2011 |
| Contact name |
Dawn E Holmes |
| E-mail(s) |
dholmes@microbio.umass.edu
|
| Phone |
4135772439
|
| Organization name |
University of Massachusetts Amherst
|
| Department |
Microbiology
|
| Lab |
Lovley
|
| Street address |
639 N Pleasant St Morrill IVN 422C
|
| City |
Amherst |
| State/province |
Massachusetts |
| ZIP/Postal code |
01003 |
| Country |
USA |
| |
|
| Platform ID |
GPL11378 |
| Series (4)
|
| GSE30796 |
Anaerobic Oxidation of Benzene by the Hyperthermophilic Archaeon Ferroglobus placidus |
| GSE30798 |
Anaerobic Oxidation of Benzene by the Hyperthermophilic Archaeon Ferroglobus placidus (Benzene vs. Acetate) |
| GSE30799 |
Anaerobic Oxidation of Benzene by the Hyperthermophilic Archaeon Ferroglobus placidus (Benzene vs. Phenol) |
| GSE30801 |
Anaerobic Oxidation of Benzene by the Hyperthermophilic Archaeon Ferroglobus placidus (Benzene vs. Benzoate) |
|
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