|
| Status |
Public on Feb 21, 2012 |
| Title |
CB1190_pyruvate_rep3 |
| Sample type |
RNA |
| |
|
| Source name |
Pseudonocardia dioxanivorans strain CB1190 cells, pyruvate-grown
|
| Organism |
Pseudonocardia dioxanivorans CB1190 |
| Characteristics |
treatment: pyruvate (45 mM)
|
| Treatment protocol |
Cells were harvested by filtration and scraped from the filter into vials that were frozen at -80C.
|
| Growth protocol |
Cells were grown in AMS medium amended with pyruvate (45 mM) or 1,4-dioxane (4.7 mM) or glycolate (2 mM)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Nucleic acids were obtained following cell lysis with heating and bead-beating in the presence of SDS and phenol. Phenol/chloroform extraction, followed by column-based purification, was performed. Nucleic acids were treated with DNaseI and RNA was finally purified by RNeasy purification.
|
| Label |
biotin
|
| Label protocol |
cDNA was obtained from 5 ug of RNA following the Affymetrix protocol for RT. RNA template was degraded with NaOH treatment. cDNA was fragmented with DNaseI, and fragmented cDNA while terminally labeled with biotin.
|
| |
|
| Hybridization protocol |
Hybridization followed the procedure of the Affymetrix protocol for Modified FlexMidi_euk2v3 for P. aeruginosa Array.
|
| Scan protocol |
Chips were scanned using an Affymetrix GeneChip Scanner 3000 scanner.
|
| Data processing |
Primary data was generated with RMAExpress 1.05. Quantile normalization with background adjustment was performed across all arrays, and the PLM summarization method was used.
|
| |
|
| Submission date |
Oct 25, 2011 |
| Last update date |
Jul 11, 2013 |
| Contact name |
Ariel Grostern |
| E-mail(s) |
ariel.grostern@berkeley.edu
|
| Organization name |
UC Berkeley
|
| Department |
Civil & Environmental Engineering
|
| Lab |
Alvarez-Cohen
|
| Street address |
209 O'Brien Hall
|
| City |
Berkeley |
| State/province |
CA |
| ZIP/Postal code |
94720 |
| Country |
USA |
| |
|
| Platform ID |
GPL14784 |
| Series (1) |
| GSE33197 |
Analysis of gene expression in Pseudonocardia dioxanivorans strain CB1190 during growth with dioxane, glycolate or pyruvate |
|
| Relations |
| Reanalyzed by |
GSE48814 |
