|
| Status |
Public on Mar 04, 2014 |
| Title |
Ecoli_DH1_0%1-4-butanediol rep1 |
| Sample type |
RNA |
| |
|
| Source name |
Escherichia coli DH1 in M9 medium
|
| Organism |
Escherichia coli DH1 |
| Characteristics |
genotype/variation: wild type
agent: no treatment
|
| Treatment protocol |
Cells were grown to mid log and then treated with either 0% or 6% 1,4 Butanediol for one hour before sample collection.
|
| Growth protocol |
All cultures were grown in M9 minimal media (per liter: 200 ml 5x M9 salts, 2 ml 1M MgSO4, 50 ml 20% glucose, 20 ml 5% Casamino acids, 100 μl 0.5% Thiamine, 100 μl 1M CaCl2) and with appropriate antibiotics
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cultures were harvested, centrifuged (8,000 x g, 4°C, 5 min) and the pellet stored at -80°C. total RNA was isolated using the Qiagen RNeasy Mini Kit and RNA integrity and quantity were verified via gel electrophoresis and NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies, Wilmington, DE) respectively
|
| Label |
Cy3
|
| Label protocol |
Direct Rapid Labeling and cDNA synthesis protocols (Ouellet, 2009, A Rapid and Inexpensive Labeling Method for Microarray Gene Expression Analysis. BMC Biotechnology) were used to prepare triplicate samples for hybridization
|
| |
|
| Hybridization protocol |
Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.
|
| Scan protocol |
Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
|
| Description |
This sample is of wild-type E. coli DH1 grown in M9 defined medium and represents one of three technical replicates
|
| Data processing |
Data summarization, normalization, and analysis were performed using ArrayStar (DNASTAR) with the RMA algorithm.
|
| |
|
| Submission date |
Mar 03, 2014 |
| Last update date |
Mar 04, 2014 |
| Contact name |
Aindrila Mukhopadhyay |
| E-mail(s) |
amukhopadhyay@lbl.gov
|
| Organization name |
Lawrence Berkeley National Laboratory
|
| Department |
Physical Biosciences Division
|
| Street address |
1 Cyclotron Road
|
| City |
Berkeley |
| State/province |
CA |
| ZIP/Postal code |
94712 |
| Country |
USA |
| |
|
| Platform ID |
GPL14649 |
| Series (1) |
| GSE55496 |
Study of 1,4 Butanediol response in Escherichia coli DH1 |
|
