|
| Status |
Public on Sep 19, 2012 |
| Title |
Butanol_Challenge_Step_3-2 |
| Sample type |
other |
| |
|
| Channel 1 |
| Source name |
Butanol_Challenge_Step_3-2
|
| Organism |
Escherichia coli |
| Characteristics |
cell type: bacterial liquid culture
extracted molecule: plasmid DNA
|
| Growth protocol |
Genomic Library of E. coli was enriched via serial transfers. The cells were grown in M9 minimal media (5 g/L glucose), and in increasing concentration of n-butanol (0.5, 0.9, 1.3 and 1.7% v/v).
|
| Extracted molecule |
other |
| Extraction protocol |
other extracted using alkalyne lysis preparation. Plasmid DNA was clean and concentrated using Zymo Clean & Concentrated -5 kit
|
| Label |
Cy3
|
| Label protocol |
5 µg of plasmid DNA was digested with 5 U of AluI and 5 U of RsaI at 37°C 2h. 0.5 µg of fragmented plasmid DNA was labeled using Alexa Fluor Oligo CGH 2X reation mixes following manufacture's instructions.
|
| |
|
| Channel 2 |
| Source name |
Non-challenged Library
|
| Organism |
Escherichia coli |
| Characteristics |
cell type: bacterial liquid culture
extracted molecule: plasmid DNA
|
| Growth protocol |
Genomic Library of E. coli was enriched via serial transfers. The cells were grown in M9 minimal media (5 g/L glucose), and in increasing concentration of n-butanol (0.5, 0.9, 1.3 and 1.7% v/v).
|
| Extracted molecule |
other |
| Extraction protocol |
other extracted using alkalyne lysis preparation. Plasmid DNA was clean and concentrated using Zymo Clean & Concentrated -5 kit
|
| Label |
Cy5
|
| Label protocol |
5 µg of plasmid DNA was digested with 5 U of AluI and 5 U of RsaI at 37°C 2h. 0.5 µg of fragmented plasmid DNA was labeled using Alexa Fluor Oligo CGH 2X reation mixes following manufacture's instructions.
|
| |
|
| |
| Hybridization protocol |
Samples were for hybridization by adding lyophilized 10X Blocking Agent (supplied with Agilent Oligo aCGH Hybridization Kit), following manufacture's protocol. The samples were hybridazed in a Agilent's E. coli Gene Expression Microarray, 8x15K
|
| Scan protocol |
The arrays were scanned using the GenePix 4100A Microarray Scanner
|
| Description |
Sample 11
|
| Data processing |
The image analysis performed using GenePix Pro 6.0 Software (Molecular Devices), normalized with MIDAS (LOWESS method), with clustering analysis in MeV (CAST)
|
| |
|
| Submission date |
Dec 21, 2010 |
| Last update date |
Sep 19, 2012 |
| Contact name |
James Winkler |
| E-mail(s) |
jdwinkler@tamu.edu
|
| Organization name |
Texas A&M University
|
| Lab |
Kao Lab
|
| Street address |
3122 TAMU
|
| City |
College Station |
| State/province |
TX |
| ZIP/Postal code |
77843 |
| Country |
USA |
| |
|
| Platform ID |
GPL8984 |
| Series (1) |
| GSE26223 |
Genomic Library Enrichment for n-Butanol tolerance in E. coli. Samples vs Reference |
|
