|
| Status |
Public on Jan 15, 2014 |
| Title |
WT 1313_acetate 15 |
| Sample type |
RNA |
| |
|
| Source name |
WT 1313, acetate
|
| Organism |
Acetivibrio thermocellus DSM 1313 |
| Characteristics |
strain/background: DSM 1313
genotype/variation: wild type
treatment: acetate
|
| Treatment protocol |
The wild type and mutants were grown in rich medium with 5 mM added acetate and controls were grown without acetate. The cells were grown to an OD of 0.3-0.4 in rich medium and centrifuged at 4 deg C for 5 min; immediately flash frozen in liquid N2. Total RNA was isolated for comparison of acetate treatment.
|
| Growth protocol |
Clostridium thermocellum DSM1313 and mutant strains were grown at 55 deg C in the 100 ml volume in 250 ml anaerobic bottles in rich medium as described by Tripathi et al., 2010, which is based on DSM122 medium.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Briefly, samples were harvested by centrifugation and the TRIzol reagent (Invitrogen, Carlsbad, CA) was used to extract total cellular RNA. Each total RNA preparation was treated with RNase-free DNase I (Ambion, Austin, TX) to digest residual chromosomal DNA and subsequently purified with the Qiagen RNeasy Mini kit in accordance with the instructions from the manufacturer. Total cellular RNA was quantified at OD260 and OD280 with a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE) and the RNA quality was checked with Agilent Bioanalyzer (Agilent, CA). The purified RNA with good quality from each sample was used as the template to generate ds-cDNA using Invitrogen ds-cDNA synthesis kit (Invitrogen, CA).
|
| Label |
Cy3
|
| Label protocol |
The labeling was performed following NimbleGen company's protocols.
|
| |
|
| Hybridization protocol |
The hybridization was performed following NimbleGen company's protocols.
|
| Scan protocol |
The scanning was performed following NimbleGen company's protocols.
|
| Data processing |
Statistical analysis was done with JMP Genomics 6.0 software (SAS Institute, Cary, NC). The data were subsequently normalized using the Loess normalization algorithm within JMP Genomics. An analysis of variance (ANOVA) was performed to determine differential expression levels between conditions and time points using the FDR testing method (p < 0.05).
|
| |
|
| Submission date |
Jan 14, 2014 |
| Last update date |
Jan 15, 2014 |
| Contact name |
Dawn Marie Klingeman |
| E-mail(s) |
[email protected]
|
| Phone |
+18655763435
|
| Organization name |
Oak Ridge National Lab
|
| Department |
Biosciences Division
|
| Lab |
RNA Profiling
|
| Street address |
1 Bethel Valley Rd building 15056 Rm 366 MS 6038
|
| City |
Oak Ridge |
| State/province |
TN |
| ZIP/Postal code |
37831-6342 |
| Country |
USA |
| |
|
| Platform ID |
GPL18170 |
| Series (1) |
| GSE54082 |
Elimination of hydrogenase post-translational modification blocks H2 production and increases ethanol yield in Clostridium thermocellum |
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