|
| Status |
Public on Oct 17, 2013 |
| Title |
Ecoli_darcA_rep1_Anaerobic |
| Sample type |
RNA |
| |
|
| Source name |
Escherichia coli MG1655 K-12 ∆fnr
|
| Organism |
Escherichia coli str. K-12 substr. MG1655 |
| Characteristics |
genotype: darcA
phenotype: lacking ArcA protein
accession: NC_000913
|
| Treatment protocol |
Cells were treated with a stop solution of Phenol and Ethanol, spun down and flash frozen and stored at -80°C (Khodursky et al, 2003).
|
| Growth protocol |
Escherichia coli MG1655 K-12 WT and ∆arcA were grown to mid-log phase (O.D.600nm 0.3) anerobically (95% N2, 5% CO2) at 37°C in MOPS +0.2% glucose media (Neidhardt et al, 1974, Lazazzera et al, 1993).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using a hot phenol method (ref). RNA quality was determined by gel electrophoresis and quantity was determined using a NanoDrop.
|
| Label |
Cy3
|
| Label protocol |
Labeling was performed following Roche NimbleGen standard operating protocol. See www.nimblegen.com.
|
| |
|
| Hybridization protocol |
Hybridzation was performed following Roche NimbleGen standard opperator protocol. See www.nimblegen.com.
|
| Scan protocol |
Scanning was performed using an Axon GenePix scanner at 5 µM resolution and PMT of 480.
|
| Description |
This sample is of ∆arcA Escherichia coli MG1655 K-12, anaerobic growth conditions. It is the first of three ∆arcA biological replicates used in this experiment, each from separate cultures.
|
| Data processing |
The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).
|
| |
|
| Submission date |
Apr 26, 2013 |
| Last update date |
Oct 17, 2013 |
| Contact name |
Dan Park |
| E-mail(s) |
danmpark85@gmail.com
|
| Organization name |
UW Madison
|
| Street address |
440 Henry Mall
|
| City |
Madison |
| State/province |
WI |
| ZIP/Postal code |
53701 |
| Country |
USA |
| |
|
| Platform ID |
GPL14649 |
| Series (2) |
| GSE46412 |
Expression analysis of Escherichia coli MG1655 K-12 WT and ∆arcA mutant |
| GSE46415 |
The response regulator ArcA uses a diverse binding site architechture to globally regulate carbon oxidation in E. coli |
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