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Status |
Public on Jun 27, 2015 |
Title |
Ecoli_WTnsrR_rep3 |
Sample type |
RNA |
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Source name |
Escherichia coli MG1655 K-12 wild-type nsrR
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Organism |
Escherichia coli str. K-12 substr. MG1655 |
Characteristics |
genotype: nsrR deletion, leu::GUGnsrR-kan
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Growth protocol |
The cultures were grown aerobically at 37ÂșC in L broth to mid-exponential phase (OD650nm = ~0.6).
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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.
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Hybridization protocol |
Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.
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Scan protocol |
Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
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Description |
This sample is of Escherichia coli MG1655 K-12 containing a wild-type nsrR (GUGnsrR). It is the third of three WT strain biological replicates used in this experiment, each from separate cultures.
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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.).
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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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