|
| Status |
Public on Jul 18, 2014 |
| Title |
GLBRCE1_SynH_Exp_rep318_1 |
| Sample type |
RNA |
| |
|
| Source name |
GLBRCE1, SynH, Exp
|
| Organism |
Escherichia coli |
| Characteristics |
strain: GLBRCE1
medium: SynH
growth phase: Exp
biological replicate: 318
technical replicate: 1
|
| Treatment protocol |
Cells (10 ml) for transcriptomic analysis were collected into tubes containing 1.25 ml ice-cold 5% (vol/vol) unbuffered phenol in ethanol (EP) and pelleted by centrifugation (10,000 g, 4°C, 3 min). To remove residual traces of hydrolysate, cell pellets were twice resuspended in ice-cold GMM plus 0.125 volume of EP, repelleted, then flash frozen in dry ice-ethanol, and stored at -80°C.
|
| Growth protocol |
Fermentations were carried out in 3 L bioreactors (Applikon Biotechnology) containing 2.45 L of ACSH or SynH media, and cultures were diluted into ACSH or SynH with initial OD at 0.2, grown anaerobically overnight, and then inoculated into bioreactors to a starting OD600 of 0.2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was obtained from cells pellets by lysozyme treatment and phenol-chloroform extraction, analyzed by agarose gel electrophoresis to confirm integrity, quantified using a Nanodrop spectrophotometer (Thermo Scientific), and stored at -80°C
|
| Label |
Cy3
|
| Label protocol |
cDNA labeling protocol was conducted according to the manufacturer’s instructions (Roche NimbleGen)
|
| |
|
| Hybridization protocol |
hybridization protocol was conducted according to the manufacturer’s instructions (Roche NimbleGen)
|
| Scan protocol |
Hybridized arrays were scanned with a NimbleGen MS 200 microarray scanner, and the probe signal intensities were determined using NimbleScan v 2.6 (Roche NimbleGen).
|
| Description |
Exp318_V1_T2
|
| Data processing |
Probe signal intensities were preprocessed using robust multichip averaging (RMA) in the program ArrayStar (DNASTAR), and the resulting gene expression signals were quantile-normalized across all samples using the normalize.quantiles function in the Bioconductor package for R.
|
| |
|
| Submission date |
Jun 25, 2014 |
| Last update date |
Jul 18, 2014 |
| Contact name |
Robert C Landick |
| E-mail(s) |
landick@bact.wisc.edu
|
| Phone |
(608) 265-8475
|
| Organization name |
University of Wisconsin - Madison
|
| Department |
Great Lakes Bioenergy Research Center
|
| Street address |
1550 Linden Dr
|
| City |
Madison |
| State/province |
WI |
| ZIP/Postal code |
53706 |
| Country |
USA |
| |
|
| Platform ID |
GPL14649 |
| Series (2) |
| GSE58806 |
Aromatic inhibitors derived from ammonia-pretreated lignocellulose hinder bacterial ethanologenesis by activating regulatory circuits controlling inhibitor efflux and detoxification (I) |
| GSE58927 |
Aromatic inhibitors derived from ammonia-pretreated lignocellulose hinder bacterial ethanologenesis by activating regulatory circuits controlling inhibitor efflux and detoxification |
|
