|
| Status |
Public on Jun 14, 2011 |
| Title |
Wild type, M9 minimal medium, 1 |
| Sample type |
RNA |
| |
|
| Source name |
E. coli K12 MG1655, wild type cells in M9 minimal medium
|
| Organism |
Escherichia coli str. K-12 substr. MG1655 |
| Characteristics |
genotype: Wild type
growth condition: M9 minimal medium
biological replicate: 1
|
| Treatment protocol |
The cultures were inoculated into 100 mL of the fresh M9 minimal medium in either the presence or absence of 100 μg/ml adenine and continued to culture at 37 oC with constant agitation to mid-log phase.
|
| Growth protocol |
Glycerol stocks of E. coli strains were inoculated into M9 minimal medium supplemented with 2 g/L glucose and cultured overnight at 37 oC with constant agitation. The cultures were inoculated into 100 mL of the fresh M9 minimal medium in either the presence or absence of 100 μg/ml adenine and continued to culture at 37 oC with constant agitation to mid-log phase.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the RNeasy Plus Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA quality and concentration was determined by analysis with an Thermo NanoDrop 1000.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix) with a Dnase I fragmentation step.
|
| |
|
| Hybridization protocol |
Hybridization was performed by UCSD GeneChip Core, following affymetrix standard operating protocol. See www.affymetrix.com.
|
| Scan protocol |
Scan was performed with an Affymetrix 7G scanner by UCSD GeneChip Core, following affymetrix standard operating protocol. See www.affymetrix.com.
|
| Description |
E. coli K12 MG1655, wild type cells in M9 minimal medium, biological replicate 1
|
| Data processing |
The raw data (.CEL file) was normalized using GC RMA from the affy R package.
|
| |
|
| Submission date |
Jan 12, 2011 |
| Last update date |
Jun 14, 2011 |
| Contact name |
Bernhard Palsson |
| E-mail(s) |
[email protected]
|
| Phone |
858-534-5668
|
| Fax |
858-822-3120
|
| URL |
http://systemsbiology.ucsd.edu
|
| Organization name |
UCSD
|
| Department |
Bioengineering
|
| Lab |
Systems Biology Research Group
|
| Street address |
9500 Gilman Dr.
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92122 |
| Country |
USA |
| |
|
| Platform ID |
GPL3154 |
| Series (2) |
| GSE26588 |
Transcriptome analysis of E. coli MG1655 |
| GSE26591 |
Genome-scale reconstruction of the PurR regulon reveals its role in the adenine stimulon of Escherichia coli K-12 MG1655 |
|
