ImaGene protocols

View ImaGene computational protocol

ImaGene statistics

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ImaGene specifications

Information


Unique identifier OMICS_00841
Name ImaGene
Software type Package/Module
Interface Graphical user interface
Restrictions to use License purchase required
Operating system Unix/Linux, Mac OS, Windows
License Commercial
Computer skills Medium
Version 9.0
Stability Stable
Maintained Yes

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ImaGene in pipelines

 (7)
2016
PMCID: 4726345
PMID: 26797113
DOI: 10.1038/srep19411

[…] benelux) using 1000 ng, 1–2% cy5 or cy3 labeled crna per channel as described. slides were scanned on an agilent g2565ba scanner at 100% laser power, 30% pmt., after automatic data extraction using imagene 8.0 (biodiscovery), the mean spot intensities were normalized using quantile normalization and the two dye-swapped profiles per sample were merged by averaging the fold changes. quality […]

2015
PMCID: 4534052
PMID: 26265132
DOI: 10.1186/s12864-015-1772-1

[…] station (tecan, austria) and microarray slides were scanned using the agilent g2565ba microarray scanner system (agilent technologies, inc., usa). image analysis was carried out using the imagene 9.0 software (biodiscovery, inc., usa). the data were pre-processed using the robust multi-array average expression measure []. one control array was removed after performing qc using […]

2014
PMCID: 4427718
PMID: 26109882
DOI: 10.2478/intox-2014-0010

[…] and processing, the arrays were scanned using the agilent g2565ba microarray scanner system (agilent technologies, santa clara, ca) and quantification of the signals was performed using imagene 9.0 software (biodiscovery, hawthorne, ca, usa). raw data were provided in an imagene text file format., the quality of the affymetrix.cel files was checked by utilizing the r packages affy, […]

2013
PMCID: 3865091
PMID: 24358208
DOI: 10.1371/journal.pone.0082565

[…] by mirbase v.16, in addition to many proprietary probes. samples were labeled with cy3, while the red channel was used for quality control and reference purposes. images were analyzed using imagene 8.0 (biodiscovery, hawthorne, ca). mirna microarray data analysis was implemented in r environment using the linear models for microarray data (limma) and the weighted gene correlation […]

2011
PMCID: 3818864
PMID: 21342469
DOI: 10.1111/j.1751-7915.2010.00232.x

[…] minnesota comprising 7629 genes. after 16 h of hybridization and three subsequent washing steps the arrays were scanned with an affymetrix array scanner 417., raw data collection was performed using imagene (as described in ). further statistical and bioinformatical analyses were performed using the r language ( http://www.r‐project.org) and packages from the bioconductor project (limma, marray, […]


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ImaGene in publications

 (496)
PMCID: 5928217
PMID: 29740411
DOI: 10.3389/fmicb.2018.00763

[…] strands of the intergenic regions (igr) (sinorhizobium meliloti rm1021 sm14koli; ). probes in the igr were separated by approximately 50–100 nt. the analysis of microarray images was performed with imagene 6.0 software (biodiscoveries). lowess normalization and significance test (p-value adjustment based on fdr) were performed with the emma software (). the m-value represents the logarithmic […]

PMCID: 5911652
PMID: 29686437
DOI: 10.5114/reum.2018.74742

[…] capture probes targeting all micrornas for human registered in the mirbase 18.0., and scanned using microarray scanner system (agilent technologies, usa). the image analysis was carried out using imagene 9 software (exiqon). the quantified signals were background corrected (normexp with offset value 10) and normalized using the global lowess (locally weighted scatterplot smoothing) regression […]

PMCID: 5829249
PMID: 29487324
DOI: 10.1038/s41598-018-22057-7

[…] using a powerscanner confocal laser scanner (tecan trading ag, switzerland) and the 16-bit images were generated with powerscanner software variant 1.2 at 10 μm/pixel resolution and processed using imagene 9.0 software (biodiscovery inc, ca). elaboration and analysis of image raw fluorescence intensity (fi) data was performed using in-house developed software and r scripts. signals […]

PMCID: 5827990
PMID: 29482503
DOI: 10.1186/s12885-018-4145-8

[…] station (tecan, switzerland). microarray slides were scanned using a ls reloaded scanner (tecan, switzerland) for microarray image analysis, and the data generated were further analyzed using imagene ver. 9.0 (biodiscovery, usa) and genespring gx ver. 11.0 (agilent technologies, usa) software. loess normalization was performed to adjust microarray data for variation. gene expression fold […]

PMCID: 5811468
PMID: 29479354
DOI: 10.3389/fimmu.2018.00195

[…] washes, the immunoblots on the membrane were developed with chemiluminescent substrate reagent kit (invitrogen) and were exposed to x-ray film. cytokine array tif file images were analyzed using imagene 8.0 software (biodiscovery, inc.). after uploading images into the software, a grid file was manually over imposed on them to assign spot gene identities. in the next step, spot finding […]


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