|
| Status |
Public on Aug 15, 2013 |
| Title |
feco3.H.NO3.M3.X32363 |
| Sample type |
RNA |
| |
|
| Source name |
FeCO3.H2.NO3.Batch M3
|
| Organism |
Thiobacillus denitrificans ATCC 25259 |
| Characteristics |
strain: ATCC 25259
|
| Treatment protocol |
Exposure conditions are shown in Table 1 (Beller et al 2013), Group V.
|
| Growth protocol |
Wild-type T. denitrificans (ATCC strain 25259) was cultivated at 30oC under strictly anaerobic conditions with exposure conditions described in (Beller et al, 2013).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the MasterPure Complete DNA and RNA Purification Kit (EpiCentre) using a modified protocol and RNAprotect (Qiagen).
|
| 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 |
Sample name constructed with pattern:
electron-donor1.electron-donor2.electron-acceptor.batch.chip
32363_532
|
| 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 |
Apr 24, 2013 |
| Last update date |
Aug 15, 2013 |
| Contact name |
Anu Chakicherla |
| E-mail(s) |
chakicherla1@llnl.gov
|
| Organization name |
Lawrence Livermore National Lab
|
| Street address |
7000 East Avenue, Mail Stop: L-446
|
| City |
Livermore |
| State/province |
CA |
| ZIP/Postal code |
94551 |
| Country |
USA |
| |
|
| Platform ID |
GPL3977 |
| Series (1) |
| GSE46339 |
Genome-enabled studies of anaerobic, nitrate-dependent Fe(II) oxidation in the chemolithoautotrophic bacterium Thiobacillus denitrificans |
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