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Status |
Public on Jun 20, 2013 |
Title |
Ecoli_wild-type_rep2_Anaerobic |
Sample type |
RNA |
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Source name |
Escherichia coli MG1655 K-12 WT
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Organism |
Escherichia coli str. K-12 substr. MG1655star |
Characteristics |
genotype: Wild-type phenotype: normal 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).
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Growth protocol |
Escherichia coli MG1655 K-12 WT and ∆fnr 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. RNA quality was determined by analysis with an Agilent 2100 bioanalyzer and quantity was determined using a NanoDrop.
|
Label |
Cy3
|
Label protocol |
Labeling was performed following Roche NimbleGen standard operating protocol. See www.nimblegen.com.
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Hybridization protocol |
Hybridzation was performed following Roche NimbleGen standard opperator protocol. See www.nimblegen.com.
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Scan protocol |
Scanning was performed using an Axon GenePix scanner at 5 µM resolution and PMT of 480.
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Description |
This sample is of wild-type Escherichia coli MG1655 K-12, anaerobic growth conditions. It is the second of two wild-type 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. 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.).
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Submission date |
Sep 27, 2012 |
Last update date |
Jun 20, 2013 |
Contact name |
Kevin S Myers |
E-mail(s) |
kmyers2@wisc.edu
|
Organization name |
University of Wisconsin - Madison
|
Department |
Great Lakes Bioenergy Research Center
|
Street address |
5127 WEI, 1552 University Ave
|
City |
Madison |
State/province |
WI |
ZIP/Postal code |
53726 |
Country |
USA |
|
|
Platform ID |
GPL14649 |
Series (2) |
GSE41189 |
Expression analysis of Escherichia coli MG1655 K-12 WT and ∆fnr mutant |
GSE41195 |
Genome-scale Analysis of E. coli FNR Reveals Complex Features of Transcription Factor Binding |
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