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Agilent Feature Extraction specifications


Unique identifier OMICS_23697
Name Agilent Feature Extraction
Software type Pipeline/Workflow
Interface Command line interface, Graphical user interface
Restrictions to use None
Input data A microarray image.
Input format TIFF
Output data A text file.
Output format TXT
Biological technology Agilent Technologies
Operating system Windows
Programming languages C
Database management system MySQL, MSSQL Server, PostgreSQL
License Commercial
Computer skills Advanced
Version 12.0
Stability No
Free trial Yes
Registration required Yes
Maintained No


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Publication for Agilent Feature Extraction

Agilent Feature Extraction citations


Transcriptome Analysis of Circulating PBMCs to Understand Mechanism of High Altitude Adaptation in Native Cattle of Ladakh Region

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

[…] cows and sahiwal cows, the yield of crna was >1.65 μg and specific activity was >9.0 pmol cy3 per μg crna, indicating the good quality of crna obtained. the scanned images analysed using agilent feature extraction software showed successful hybridization of the crna samples. the microarray raw data files were subjected for quantile normalization to remove unwanted technical […]


The p53 activator overcomes resistance to ALK inhibitors by regulating p53 target selectivity in ALK driven neuroblastomas

PMCID: 5945735
PMID: 29760954
DOI: 10.1038/s41420-018-0059-0

[…] expression analysis protocol (agilent technology, v6.5, 2010). the hybridised array was immediately scanned with an agilent microarray scanner (agilent technologies) raw data were extracted using agilent feature extraction software (v11.0.1.1). the raw gene data were automatically summarised using the agilent feature extraction protocol to generate a raw data text file, thus providing […]


Derivative chromosomes involving 5p large rearranged segments went unnoticed with the use of conventional cytogenetics

PMCID: 5941813
PMID: 29760780
DOI: 10.1186/s13039-018-0374-4

[…] scanned using a microarray scanner with surescan high resolution technology (agilent, santa clara, usa). image quantification, array quality control and aberration detection were performed using the agilent feature extraction and dna analytics software (agilent, santa clara, usa) according to the manufacturer’s instructions. changes identified in the samples were visualized using the ucsc genome […]


The senescence associated secretory phenotype is potentiated by feedforward regulatory mechanisms involving Zscan4 and TAK1

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

[…] incubated for 17 h at 65 °c in an agilent hybridization oven. the hybridized arrays were washed, fixed and 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 […]


Identifying circRNA associated ceRNA networks in the hippocampus of Aβ1 42 induced Alzheimer's disease like rats using microarray analysis

PMCID: 5940119
PMID: 29706607
DOI: 10.18632/aging.101427

[…] were hybridized onto the arraystar rat circrna array (8x15k, arraystar). after washing the slides, the arrays were scanned using the agilent scanner g2505c. all data collection was performed using agilent feature extraction software (version kangchen bio-tech (shanghai, china) performed all microarray analyses., as previously described [], total rna was isolated using trizol […]


LncRNA ENST00113 promotes proliferation, survival, and migration by activating PI3K/Akt/mTOR signaling pathway in atherosclerosis

PMCID: 5916647
PMID: 29668625
DOI: 10.1097/MD.0000000000010473

[…] gene expression hybridization kit (agilent p/n 5188-5242) according to the manufacturer's protocols and the microarray was washed. agilent microarray scanner (agilent p/n g2565ba) was used and agilent feature extraction software (version was used to extract data. the microarray was performed by kangchen biotech (shanghai, china). by comparing the normalized expression levels […]

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Agilent Feature Extraction institution(s)
Johns Hopkins University School of Medicine, Oncology Biostatistics, Baltimore, MD, USA; Johns Hopkins School of Medicine, Baltimore, MD, USA; Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA; Johns Hopkins University School of Medicine, Baltimore, MD, USA; Johns Hopkins University School of Medicine, Baltimore, MD, USA; Johns Hopkins University School of Medicine, Baltimore, MD, USA
Agilent Feature Extraction funding source(s)
Supported by the bioinformatics and microarray core resources provided for by NCI grant P30 CA06973-44 and by NSF grant DMS034211.

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