|
| Status |
Public on Sep 25, 2014 |
| Title |
Agrobacterium tumefaciens_in_low_Fe_rep1 |
| Sample type |
RNA |
| |
|
| Source name |
Agrobacterium tumefaciens C58 AB7 No Fe
|
| Organism |
Agrobacterium fabrum str. C58 |
| Characteristics |
strain: C58
treatment: Low Fe
|
| Growth protocol |
Agrobacterium tumefaciens C58 low Fe was grown to mid-log phase (O.D.600nm 0.6~0.8) at 28°C in AB7 without Fe media (AB7 Fe-).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the RNeasy Mini kit (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA concentration was measured by SpectorPhotometer(NonoDrop).
cDNA were synthesized from the reverse transcription of Total RNA using the Life Technologies SuperScript II Double-Strand Synthesis Kit
|
| Label |
Cy3
|
| Label protocol |
Labeling was performed by NimbleGen Labelling kit following their standard operating protocol. See www.nimblegen.com.
|
| |
|
| Hybridization protocol |
Hybridization was performed using the NimbleGen Hybridization kit and 4-Chip Workstation following their standard operating protocol. See www.nimblegen.com.
|
| Scan protocol |
Scanning was performed by GenePix 4100A, following their standard operating protocol. See http://www.moleculardevices.com/systems/microarray-scanners/genepix-4100a-microarray-scanner.
|
| Description |
This sample is the first one which is grown under low Fe condition
|
| 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 NimbleGen Deva software, version 1.2 (Roche NimbleGen, Inc.).
|
| |
|
| Submission date |
Sep 24, 2014 |
| Last update date |
Sep 25, 2014 |
| Contact name |
Hui-Hsien Chou |
| E-mail(s) |
hhchou@iastate.edu
|
| Phone |
515-294-9242
|
| Organization name |
Iowa State University
|
| Department |
Genetics, Development and Cell Biology
|
| Lab |
Complex Computation Lab
|
| Street address |
503 Science II
|
| City |
Ames |
| State/province |
IA |
| ZIP/Postal code |
50011 |
| Country |
USA |
| |
|
| Platform ID |
GPL19222 |
| Series (2) |
| GSE61737 |
Agrobacterium tumefaciens C58 whole-genome tiling microarray design and validation |
| GSE61738 |
Prokaryote whole-genome tiling microarray design and validation |
|
