|
| Status |
Public on Feb 17, 2012 |
| Title |
AMB-1 WT rep4 |
| Sample type |
RNA |
| |
|
| Source name |
Magnetospirillum magneticum str. AMB-1 wild-type
|
| Organism |
Paramagnetospirillum magneticum AMB-1 |
| Characteristics |
genotype/variation: wild-type
motility: non-motile
growth conditions: MG
|
| Treatment protocol |
All strains grown identically, excepting the addition carbenicillin for strains carrying plasmids.
|
| Growth protocol |
All strains were grown to mid-exponential phase (OD400 0.04 to 0.08) in 50 mL conical tubes in magnetospirillum growth media (MG) amended with 1/100 volume Wolfe's vitamin solution and 1/100 volume 3mM ferric 9mM malate. For ΔctrA deletion strains complemented with CtrA alleles, carbenicillin was added to 20ug/mL.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the Trizol reagent as directed, DNase treated, and purified using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA). RNA quality and concentration was determined by analysis with NanoDrop. cDNA was reverse transcribed using the Invitrogen Super Script RT III kit as directed and purified using a Qiagen PCR Clean Up kit.
|
| Label |
cy3
|
| Label protocol |
0.5µg cDNA was fluorescently-labeled with Cy3 using the Nimblegen One Color DNA Labeling kit as directed.
|
| |
|
| Hybridization protocol |
Hybridization was performed by Fred Hutchinson Cancer Research Center, according to the standard operating protocol of NimbleGen Systems Inc., Madison, WI, USA.
|
| Scan protocol |
Scanning was performed by Fred Hutchinson Cancer Research Center, according to the standard operating protocol of NimbleGen Systems Inc., Madison, WI, USA.
|
| Description |
WT 3B2B
Nimb4PA04_3B2B_330326_532.pair
|
| 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 |
Feb 08, 2012 |
| Last update date |
Feb 17, 2012 |
| Contact name |
Arash Komeili |
| E-mail(s) |
komeili@berkeley.edu
|
| Phone |
510-642-2140
|
| Organization name |
UC Berkeley
|
| Department |
Plant and Microbial Biology
|
| Lab |
Komeili
|
| Street address |
111 Koshland Hall #3102
|
| City |
Berkeley |
| State/province |
CA |
| ZIP/Postal code |
94720 |
| Country |
USA |
| |
|
| Platform ID |
GPL15199 |
| Series (1) |
| GSE35625 |
Expression analysis of Magnetospirillum magneticum AMB-1 WT, ΔMAI, ΔctrA, ΔdivK, and ΔctrA complemented with CtrA D51E, CtrA D51A, and an empty vector control |
|
