|
| Status |
Public on Dec 15, 2014 |
| Title |
WT_Photosynthetic_Rep3 |
| Sample type |
RNA |
| |
|
| Source name |
WT cells grown photosynthetically on SIS
|
| Organism |
Cereibacter sphaeroides |
| Characteristics |
strain: 2.4.1
|
| Growth protocol |
R. sphaeroides strains that were grown in 500 ml cultures in roux bottles photosynthetically (bubbling with 95% N2, 5% CO2) on Sistrom's minimal media (SIS) (or SIS media with succinate replaced with acetate) and harvested at exponential phase. Some cells were grown in the dark under anaerobic respiratory conditions (bubbling with 95% N2, 5% CO2) with pyruvate provided as the main carbon source and DMSO as electron acceptor.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from R. sphaeroides cells by hot acid phenol extraction.
|
| Label |
biotin
|
| Label protocol |
Synthesized cDNA was labeled with BioArray™ Terminal labeling kit with biotin-ddUTP
|
| |
|
| Hybridization protocol |
not provided
|
| Scan protocol |
not provided
|
| Description |
Gene expression data from WT cells obtained under photosynthetic conditions.
|
| Data processing |
Microarray datasets were normalized by Robust Multichip Average (RMA) to log2 scale with background adjustment and quantile normalization. Statistical analysis of normalized data to identify differentially expressed genes was done using the limma package. Correction for multiple testing was done using Benjamini-Hochberg correction. All analyses were conducted in the R statistical programming environment.
|
| |
|
| Submission date |
Jun 16, 2014 |
| Last update date |
Dec 15, 2014 |
| Contact name |
Timothy J Donohue |
| E-mail(s) |
tdonohue@bact.wisc.edu
|
| Phone |
608-265-8465
|
| Organization name |
University of Wisconsin - Madison
|
| Department |
Bacteriology
|
| Lab |
Timothy Donohue
|
| Street address |
1552 University Avenue
|
| City |
Madison |
| State/province |
WI |
| ZIP/Postal code |
53726 |
| Country |
USA |
| |
|
| Platform ID |
GPL162 |
| Series (2) |
| GSE58554 |
Global analysis of photosynthesis transcriptional regulatory networks [Expression profiling] |
| GSE58717 |
Global analysis of photosynthesis transcriptional regulatory networks |
|
