|
| Status |
Public on Jun 27, 2015 |
| Title |
Ecoli_AUGnsrR_rep1 |
| Sample type |
RNA |
| |
|
| Source name |
Escherichia coli MG1655 K-12 AUGnsrR
|
| Organism |
Escherichia coli str. K-12 substr. MG1655 |
| Characteristics |
genotype: nsrR deletion, leu::AUGnsrR-kan
|
| Growth protocol |
The cultures were grown aerobically at 37ºC in L broth to mid-exponential phase (OD650nm = ~0.6).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the RNeasy Mini kit (Qiagen) and the RNAprotect reagent (Qiagen). Contaminating DNA was removed by on-column DNase digestion by the RNase-Free DNase Set (Qiagen), and RNA purity was checked by UV absorbance and by agarose gel electrophoresis.
|
| Label |
Cy3
|
| Label protocol |
Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
|
| |
|
| 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 Escherichia coli MG1655 K-12 containing a modified nsrR (AUGnsrR). It is the first of three AUGnsrR strain 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., 2003, Biostatistics 4:249), quantile normalization (Bolstad et al., 2003, Bioinformatics 19:185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).
|
| |
|
| Submission date |
Jun 26, 2015 |
| Last update date |
Jun 27, 2015 |
| Contact name |
Stephen Spiro |
| E-mail(s) |
stephen.spiro@utdallas.edu
|
| Phone |
001-972-883-6896
|
| Organization name |
University of Texas at Dallas
|
| Department |
Molecular and Cell Biology
|
| Lab |
Spiro Lab
|
| Street address |
800 West Campbell Road
|
| City |
Richardson |
| State/province |
TX |
| ZIP/Postal code |
75080 |
| Country |
USA |
| |
|
| Platform ID |
GPL14649 |
| Series (1) |
| GSE70325 |
Inefficient translation of nsrR constrains behavior of the NsrR regulon in Escherichia coli |
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