|
| Status |
Public on Mar 31, 2012 |
| Title |
PF2-12_R2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
PF2-12
|
| Organism |
Escherichia coli K-12 |
| Characteristics |
strain: BW25113
wt or mutant: PF2-12
growth medium: liquid culture
|
| Growth protocol |
E. coli K-12 strain BW25113 was evolved in chemostats. The cells were grown in M9 minimal media (5 g/L glucose) with increasing concentrations of n-butanol.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the RNeasy Mini Kit (QIAGEN). The SuperScript indirect cDNA labeling system (Invitrogen) was used to generate cDNA.
|
| Label |
Cy3
|
| Label protocol |
Cy3- and Cy5-dUTP dyes (GE Healthcare) were used to label 0.5 µg of cDNA samples by following the manufacturer’s protocol.
|
| |
|
| Channel 2 |
| Source name |
wild-type
|
| Organism |
Escherichia coli K-12 |
| Characteristics |
strain: BW25113
wt or mutant: WT @ 0.8%But
growth medium: liquid culture
|
| Growth protocol |
E. coli K-12 strain BW25113 was evolved in chemostats. The cells were grown in M9 minimal media (5 g/L glucose) with increasing concentrations of n-butanol.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the RNeasy Mini Kit (QIAGEN). The SuperScript indirect cDNA labeling system (Invitrogen) was used to generate cDNA.
|
| Label |
Cy5
|
| Label protocol |
Cy3- and Cy5-dUTP dyes (GE Healthcare) were used to label 0.5 µg of cDNA samples by following the manufacturer’s protocol.
|
| |
|
| |
| Hybridization protocol |
Samples were for hybridization by adding lyophilized 10X Blocking Agent (supplied with the Agilent Oligo aCGH Hybridization Kit) following the manufacturer's protocol. The samples were hybridized in Agilent's E. coli Gene Expression Microarray, 8x15K.
|
| Scan protocol |
The arrays were scanned using the GenePix 4100A Microarray Scanner.
|
| Description |
Biological replicate 2 of 3.
|
| Data processing |
The image analysis was performed using GenePix Pro 6.0 Software (Molecular Devices). Data were normalized with MIDAS (LOWESS method), with clustering analysis in MeV (CAST).
|
| |
|
| Submission date |
Jun 15, 2011 |
| Last update date |
Mar 31, 2012 |
| Contact name |
Luis Humberto Reyes |
| E-mail(s) |
lhr2006@tamu.edu
|
| Phone |
(979) 571-9493
|
| Organization name |
Texas A&M University
|
| Department |
Chemical Engineering
|
| Lab |
Katy Kao Lab
|
| Street address |
3122 TAMU
|
| City |
College Station |
| State/province |
Texas |
| ZIP/Postal code |
77843-3122 |
| Country |
USA |
| |
|
| Platform ID |
GPL8984 |
| Series (1) |
| GSE30005 |
Transcriptome analysis of isolated Escherichia coli mutants using VERT for the study of n-butanol tolerance |
|
