GeneSpring GX protocols

View GeneSpring GX computational protocol

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GeneSpring GX specifications

Information


Unique identifier OMICS_00853
Name GeneSpring GX
Alternative name Genespring
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
Stability Stable
Maintained Yes

Versioning


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Documentation


Maintainer


  • person_outline Spectrum Mill Team <>

Additional information


https://www.genomics.agilent.com/en/Microarray-Data-Analysis-Software/GeneSpring-GX/?cid=AG-PT-130&tabId=AG-PR-1061

GeneSpring GX in pipelines

 (77)
2018
PMCID: 5784595
PMID: 29368634
DOI: 10.1186/s13567-018-0504-3

[…] (part number g2505c)., the agilent feature extraction software (version 11.0.1.1) was used to extract the array images. quantile normalization and subsequent data processing were performed with the genespring gx v11.5.1 software package (agilent technologies). after quantile normalization of the raw data, the genes that that were flagged in detected (“all targets value”) in at least two […]

2018
PMCID: 5824024
PMID: 29385670
DOI: 10.14348/molcells.2018.2257

[…] these samples were processed and hybridized on agilent sureprint g3 mouse ge 8x 60k array covered by the gasket 8-plex slide (agilent technologies, usa), then data were processed and analyzed using genespring gx12.6 (agilent technologies, usa). the methods and data processing procedures are described elsewhere (), and raw data is available on ncbi’s gene expression omnibus (geo) as gse105772., […]

2018
PMCID: 5833785
PMID: 29382826
DOI: 10.1038/s41419-017-0032-5

[…] calculated and local background was subtracted with the agilent feature extraction software package. all data normalization and selection of upregulated and downregulated genes was performed using genespring gx 7.3 (agilent technologies). the averages of normalized ratio were calculated by dividing the average of the test channel signal intensity by the control channel signal intensity. […]

2018
PMCID: 5960261
PMID: 29785339
DOI: 10.7717/peerj.4704

[…] surgery were defined as the surgery group, and samples obtained from the sham surgery group were defined as the control group., the raw signal intensities were normalized with the quantile method by genespring gx v11.5, and low intensity genes were filtered. the probe quality control was determined using principal component analysis (pca) in genespring. the statistical software r (version 3.4.1; […]

2017
PMCID: 5299406
PMID: 28181499
DOI: 10.1038/srep41772

[…] scanned with an agilent’s high-resolution microarray scanner, and image data were processed by using agilent feature extraction software, version 10.7.3.1. all data were subsequently uploaded into genespring gx, version 12.6 for data analysis. each gene expression array dataset was normalized to the in silico pool for the macrophages cultured with rbcs. statistically significant differences […]


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GeneSpring GX in publications

 (2091)
PMCID: 5955995
PMID: 29769561
DOI: 10.1038/s41598-018-25736-7

[…] the signal intensities were checked from the digit images using agilent feature extractor software version 9.5 (agilent technologies). the microarray raw data files in.txt format were imported to genespring gx 13.1 (agilent technologies) and subjected for quantile normalization which is highly effective in reducing variation between arrays. normalized data was analysed for statistically […]

PMCID: 5945636
PMID: 29748542
DOI: 10.1038/s41598-018-25333-8

[…] ensure that the change in gene expression was statistically significant and that false positives were <5%). functional annotations of genes from the gene ontology consortium were retrieved with genespring gx 7.3. genes were based on searches of david (http://david.abcc.ncifcrf.gov/) and medline (http://www.ncbi.nlm.nih.gov/) databases., qrt-pcr was performed using the stepone™ real-time pcr […]

PMCID: 5940223
PMID: 29738527
DOI: 10.1371/journal.pone.0196929

[…] (agilent). the rna was hybridized to a mouse mirna release 16.0 8×60 k array (agilent) and a sureprint g3 mouse ge 8×60 k array (agilent), respectively, according to the manufacturer’s protocols. genespring gx (agilent) and ingenuity pathway analysis (ipa) software (ingenuity systems, redwood city, ca, usa) were employed to process the output data from the microarrays., according […]

PMCID: 5935736
PMID: 29728568
DOI: 10.1038/s41598-018-25302-1

[…] access number e-mexp-1343 data. background adjustment and standardization were performed using bioconductor’s mas5 package in statistical software r. hierarchical clustering was performed in genespring gx (agilent technologies, santa clara, ca, usa) for genes whose expression was enhanced 1.5-fold compared to cd4+cd25−cd45rbhigh t cells (naïve cd4+ t cells), or expression decreased […]

PMCID: 5928226
PMID: 29712904
DOI: 10.1038/s41467-018-04010-4

[…] scanned using the agilent dna microarray scanner (g2565ba), with data extracted with the agilent feature extraction software (v11.0.1.1). resulting single channel raw data were analyzed with agilent genespring gx software (v12.1). raw datasets were imported and log2-transformed according to the recommended default procedure and were subsequently quantile normalized. entities showing technical […]


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