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RAMA specifications

Information


Unique identifier OMICS_01982
Name RAMA
Alternative name Robust Analysis of MicroArrays
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.54.0
Stability Stable
Requirements
R(>=2.5.0)
Maintained Yes

Versioning


No version available

Documentation


RAMA citations

 (7)
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Resistance mechanisms and fitness of Salmonella Typhimurium and Salmonella Enteritidis mutants evolved under selection with ciprofloxacin in vitro

2017
Sci Rep
PMCID: 5567280
PMID: 28831084
DOI: 10.1038/s41598-017-09151-y
call_split See protocol

[…] RNA extraction from exponential cultures of the two parental strains (ST and SE) and three mutants (M1, M4, and M5) was performed according to Fàbrega et al.. The expression of acrA, acrB, tolC, ramA, marA, and soxS genes was analyzed by RT-PCR. The 16S rRNA gene was used as an internal control for normalization, and the parental strains were used as references for their derived mutants. The […]

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Lack of AcrB Efflux Function Confers Loss of Virulence on Salmonella enterica Serovar Typhimurium

2017
MBio
PMCID: 5516257
PMID: 28720734
DOI: 10.1128/mBio.00968-17
call_split See protocol

[…] manufacturer. Differences in expression were calculated by the threshold cycle (ΔΔCT) method as described previously (). 16S rRNA and gyrB were used as housekeeping genes for data normalization. The ramA-gfp reporter plasmid was obtained from reference . Plasmid was inserted into the AcrB D408A mutant by electroporation. Reporter induction assays were carried out as previously described (). […]

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In vitro characterization and inhibition of the interaction between ciprofloxacin and berberine against multidrug resistant Klebsiella pneumoniae

2016
PMCID: 5399161
PMID: 26932407
DOI: 10.1038/ja.2016.15
call_split See protocol

[…] C) using the RNeasy Protect Bacteria Mini Kit (Qiagen China, Shanghai, China) and lysozyme (Sigma, Sigma-Aldrich China, Shanghai, China) following the manufacturer's protocol. acrA, acrB, acrR, tolC, ramA and marA were detected via RT-PCR using primers to examine gene expression (). 16S ribosomal RNA was used as an internal control. The PrimeScript RT reagent kit (Takara Bio, Kyoto, Japan) was use […]

library_books

Modulation of Androgen Receptor Signaling in Hormonal Therapy Resistant Prostate Cancer Cell Lines

2011
PLoS One
PMCID: 3150397
PMID: 21829708
DOI: 10.1371/journal.pone.0023144

[…] Bioconductor [http://www.bioconductor.org]DAVID Database [http://david.abcc.ncifcrf.gov]Eisen Lab [http://rama.lbl.gov]Gene Ontology Omnibus (GEO)[ http://www.ncbi.nlm.nih.gov/geo/]Ingenuity Pathway Analysis [http://www.ingenuity.com/]Significance Analysis of Microarray Data [http://www-stat.stanford.edu/ […]

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Differential Gene Expression by RamA in Ciprofloxacin Resistant Salmonella Typhimurium

2011
PLoS One
PMCID: 3139621
PMID: 21811569
DOI: 10.1371/journal.pone.0022161
call_split See protocol

[…] ). LTL (ciprofloxacin MIC: 4 µg/ml) with a single point mutation in GyrA was derived from S. Typhimurium LT2 by in vitro-selection using ciprofloxacin . Strain LTL represented the control, expressing RamA constitutively. Experimental strain LTLramA::aph was constructed using λ red site-specific recombination, as previously described , in which the ramA gene was replaced with an aph cassette expres […]

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Bypass Mechanisms of the Androgen Receptor Pathway in Therapy Resistant Prostate Cancer Cell Models

2010
PLoS One
PMCID: 2957443
PMID: 20976069
DOI: 10.1371/journal.pone.0013500
call_split See protocol

[…] sitory (http://www.ncbi.nlm.nih.gov/geo/ under the GEO accession number GSE21596). Hierarchical clustering and data visualization was performed using Cluster and TreeView programs (Eisen Labs: http://rama.lbl.gov). Significance Analysis of Microarrays (SAM; http://www-stat.stanford.edu/~tibs/SAM) was used to determine which genes were statistically different between stimulated samples and non-stim […]

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