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Feature extraction 10

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Feature Extraction 10.5.1.1 is a software application designed for the analysis of microarray data. The software provides core functionality for extracting, processing, and analyzing feature data from microarray experiments.

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Lab products found in correlation

Agilent microarray scanner, by Agilent Technologies (26 mentions) Low input quick amp labeling kit, by Agilent Technologies (25 mentions) Cydye, by Agilent Technologies (16 mentions) Agilent scanner, by Agilent Technologies (12 mentions) Trizol reagent, by Thermo Fisher Scientific (11 mentions) Rneasy mini kit, by Qiagen (10 mentions) Agilent sureprint g3 human v2 ge 8 60 k microarray, by Agilent Technologies (8 mentions) Dna microarray scanner, by Agilent Technologies (7 mentions) Mirna complete labeling and hyb kit, by Agilent Technologies (7 mentions) Genespring gx 12, by Agilent Technologies (6 mentions) Gene expression hybridization kit, by Agilent Technologies (5 mentions) Bioanalyzer, by Agilent Technologies (5 mentions) Nd 1000 spectrophotometer, by Thermo Fisher Scientific (4 mentions) 2100 bioanalyzer, by Agilent Technologies (4 mentions) Gene expression wash buffer kit, by Agilent Technologies (4 mentions) Microarray scanner, by Agilent Technologies (3 mentions) Agilent low input quick amp labeling kit, by Agilent Technologies (3 mentions) Scan control a 8, by Agilent Technologies (3 mentions) Microrna spike in kit, by Agilent Technologies (3 mentions) Gene expression wash buffer, by Agilent Technologies (3 mentions)

Close spelling variants of this product

Feature Extraction software 10.7 (213 citations) Feature Extraction (73 citations) Feature Extraction software version 10.7 (66 citations) Feature Extraction version 10.7.3.1 (23 citations) Agilent Feature Extraction software 10.7 (22 citations) Agilent Feature Extraction software (version 10.7.3.1) (16 citations) Agilent feature extraction software version 10.10 (15 citations) Agilent Feature Extraction 10.7.3.1 software (8 citations) Feature Extraction Software Ver. 10.7.3.1 (8 citations) Agilent Feature Extraction software (version 10.7). (6 citations)

101 protocols using feature extraction 10

1

Microarray profiling and data analysis

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Microarray profiling was performed using Agilent SurePrint Microarray (Agilent Technologies, Santa Clara, CA, USA) at 65 °C for 17 h After washing and drying by nitrogen gun blowing, microarrays were scanned with an Agilent microarray scanner (Agilent Technologies, Santa Clara, CA, USA) at 535 nm for Cy3. Scanned images were analyzed by Feature Extraction 10.7.3.1 software (Agilent Technologies, Santa Clara, CA, USA), an image analysis and normalization software was used to quantify signal and background intensity for each feature. Raw signal data was normalized by quantile normalization for differential expressed genes discovery. For functional assay, enrichment tests for gene ontology (GO) and KEGG pathway were performed for DEGs by clusterProfiler.
Huang K.S., Wang Y.T., Byadgi O., Huang T.Y., Tai M.H., Shaw J.F, & Yang C.H. (2022). Screening of Specific and Common Pathways in Breast Cancer Cell Lines MCF-7 and MDA-MB-231 Treated with Chlorophyllides Composites. Molecules, 27(12), 3950.
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2

Two-Color Microarray-Based Gene Expression Analysis

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“Two-Color Microarray-Based Gene Expression Analysis” protocol (www.agilent.com) was employed as previously described (Iacobas et al., 2008 (link)). The samples (n = 4 each, 2 mm coronal slice at mid-septal nucleus level at d 3) were hybridized to an Agilent rabbit gene expression microarray (Catalog # G2519F-020908, one glass slide formatted with four high-definition 44K arrays) at 65°C for 17 h. The hybridized chip was washed at room temperature with gene expression wash pack, stabilization solution, and drying solution. We next scanned the chip using an Agilent G2565A dual laser scanner at 5 μm resolution. The tiff images, obtained by Scan Control 8.3 (Agilent), were analyzed with (Agilent) Feature Extraction 10.7.3.1. All spots affected by local corruption or with the median foreground fluorescence less than twice the median background fluorescence were removed from the analysis (Iacobas et al., 2008 (link)),
Zia M.T., Vinukonda G., Vose L., Bhimavarapu B.B., Iacobas S., Pandey N.K., Beall A.M., Dohare P., LaGamma E.F., Iacobas D.A, & Ballabh P. (2014). Postnatal glucocorticoid-induced hypomyelination, gliosis, neurologic deficits are dose-dependent, preparation-specific, and reversible. Experimental neurology, 263, 200-213.
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3

Comparative Genomic Hybridization of Patient DNA

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Genomic DNA extracted from patient TSB together with sex-matched control DNA was fragmented by AluI and RsaI enzyme digestion. DNA labeling was conducted using an Agilent SureTag DNA Labeling Kit. Different fluorescence dyes were used for DNA labeling of patient DNA (Cy5-dUTP) and control DNA (Cy3-dUTP). The labeled products were mixed and hybridized onto Agilent SurePrint G3 human 1 × v1M microarray for 40 hours at 65 °C. DNA processing, microarray handling and scanning were conducted following the Agilent oligonucleotide comparative genomic hybridization (CGH) protocol (version 6.0). The microarray scanning profiles were processed by Agilent Feature Extraction 10.7.3.1. The extracted data were analyzed and plotted by Agilent Workbench 7.0. ADM-2 was selected as the statistical algorithm with the threshold set at 6.0 and Fuzzy Zero turned on.
Huang J., Zhou S., Niu X., Hu B., Li Q., Zhang F., Zhang X., Cai X., Lou Y., Liu F., Xu C, & Wang Y. (2017). Generation of special autosomal dominant polycystic kidney disease iPSCs with the capability of functional kidney-like cell differentiation. Stem Cell Research & Therapy, 8, 196.
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4

Microarray Analysis of Mouse Islet Transcriptome

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Total RNA was extracted using an RNeasy Micro Kit (QIAGEN) from isolated mouse islets. Cy3-Labeld cRNA was synthesized employing the Agilent Low Input Quick Amp Labeling Kit, one color (Agilent Technologies, Santa Clara, CA, USA). After hybridization of cRNA samples with a Gene Expression Hybridization Kit (Agilent), the microarray slide was scanned on a DNA microarray scanner (Agilent). Image data were processed by Feature Extraction 10.7.3.1 (Agilent). Data analyses were performed using the GeneSpring software GX12.1 (Agilent). Pathway analysis was performed according to the PAGE method15 (link). Microarray data have been deposited in the ArrayExpress database at EMBL-EBI (www.ebi.ac.uk/arrayexpress) under accession number E-MTAB-5799.
Yamamoto J., Imai J., Izumi T., Takahashi H., Kawana Y., Takahashi K., Kodama S., Kaneko K., Gao J., Uno K., Sawada S., Asano T., Kalinichenko V.V., Susaki E.A., Kanzaki M., Ueda H.R., Ishigaki Y., Yamada T, & Katagiri H. (2017). Neuronal signals regulate obesity induced β-cell proliferation by FoxM1 dependent mechanism. Nature Communications, 8, 1930.
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5

Profiling miRNA Expression via Microarray

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Human miRNA microarrays (Agilent Technologies), containing 3523 markers that represent 1,205 human and 142 human viral miRNAs, were used for miRNA expression profiling according to the manufacturer protocol. For samples meeting the quality control standards, 200 ng of total RNA was labeled using the miRNA Complete Labeling and Hybridization Kit (Agilent). Labeled RNA was hybridized in Agilent Human miRNA Microarray Release 16.0. Slides were washed and scanned according to the manufacturer’s instructions. Images were quantified using Feature Extraction 10.7.3.1 (Agilent).
Qin L.X., Zhou Q., Bogomolniy F., Villafania L., Olvera N., Cavatore M., Satagopan J.M., Begg C.B, & Levine D.A. (2014). Blocking and Randomization to Improve Molecular Biomarker Discovery. Clinical cancer research : an official journal of the American Association for Cancer Research, 20(13), 3371-3378.
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6

Rare CNV Identification from Microarray Data

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The microarray scanning profiles were processed by Agilent Feature Extraction 10.7.3.1. The extracted data were analyzed and plotted by Agilent Workbench 7.0. ADM-2 was selected as statistical algorithm with the threshold of 6.0 and the Fuzzy Zero turning on. Each CNV was called by at least four consecutive probes with log2 Ratio (fluorescence value ratio of subject-associated Cy5 to control-associated Cy3) consistent with deletion or duplication. The CNV records archived in Database of Genomic Variants were used as references to exclude common CNVs in human populations and help identified rare CNVs that may cause the clinical conditions in our pedigree.
Guan J., Wang D., Cao W., Zhao Y., Du R., Yuan H., Liu Q., Lan L., Zong L., Yang J., Yin Z., Han B., Zhang F, & Wang Q. (2016). SIX2 haploinsufficiency causes conductive hearing loss with ptosis in humans. Journal of Human Genetics, 61(11), 917-922.
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7

Microarray-Based Comparative Genomic Hybridization

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Comparative genomic hybridization based on microarrays was performed in a commercial whole-genome 180 K platform containing 180,000 oligonucleotide probes (Agilent Technologies; design 22060), using DNA from the tumor sample. Reference DNA was a commercially available human pool of samples from multiple anonymous healthy donors (Promega Corporation). Technical procedures are described in Torrezan et al. [11 (link)]. Hybridization and washing were performed as recommended by the manufacturer. Scanned images were processed using Feature Extraction 10.7.3.1 software (Agilent Technologies), and array CGH analysis was conducted with Nexus Copy Number software 7.0 (Biodiscovery). We used the FASST2 segmentation algorithm, according to the following settings: minimum of five consecutive probes (effective resolution of ~70 Kb for CNA calling), significance threshold set at 10−8, and threshold log2 Cy3/Cy5 of 0.33 and −0.3 for gains for loss, respectively, and 1.2 and −1.1 for high copy number gains and homozygous losses, respectively. All copy number alterations are reported in the Database of Genomic Variants [12 ].
Ferreira E.N., Barros B.D., de Souza J.E., Almeida R.V., Torrezan G.T., Garcia S., Krepischi A.C., Mello C.A., Cunha I.W., Pinto C.A., Soares F.A., Dias-Neto E., Lopes A., de Souza S.J, & Carraro D.M. (2016). A genomic case study of desmoplastic small round cell tumor: comprehensive analysis reveals insights into potential therapeutic targets and development of a monitoring tool for a rare and aggressive disease. Human Genomics, 10, 36.
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8

Microarray CNV Detection Pipeline

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The microarray scanning profiles were processed by Agilent Feature Extraction 10.7.3.1. The extracted data was analyzed and plotted by Agilent Workbench 7.0. ADM-2 was selected as statistical algorithm with the threshold of 6.0 and the Fuzzy Zero turning on. Each CNV was called by at least four consecutive probes with log2Ratio (fluorescence value ratio of miPSC-associated Cy5 to donor-associated Cy3) consistent with deletion or duplication.
Chen Y., Guo L., Chen J., Zhao X., Zhou W., Zhang C., Wang J., Jin L., Pei D, & Zhang F. (2014). Genome-wide CNV analysis in mouse induced pluripotent stem cells reveals dosage effect of pluripotent factors on genome integrity. BMC Genomics, 15, 79.
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9

Genome-Wide Array-CGH Profiling

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We performed comparative genomic hybridization based on microarrays (array-CGH) in a commercial whole-genome 180 K platform containing 180,000 oligonucleotide probes (design 30864, Agilent Technologies, Palo Alto, California) using as reference DNA a commercially available human pool of healthy individuals (Promega). Purification, cohybridization of labelled test and reference DNA samples and washing were carried out according to the manufacturer’s instructions. Scanned images were processed using the Feature Extraction 10.7.3.1 software (Agilent Technologies, Palo Alto, California).
Maschietto M., Tahira A.C., Puga R., Lima L., Mariani D., da Silveira Paulsen B., Belmonte-de-Abreu P., Vieira H., Krepischi A.C., Carraro D.M., Palha J.A., Rehen S, & Brentani H. (2015). Co-expression network of neural-differentiation genes shows specific pattern in schizophrenia. BMC Medical Genomics, 8, 23.
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10

Microarray-Based Copy Number Variation Analysis

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In Family 1, Affymetrix 6.0 chips and Agilent 1 M microarrays were hybridized as previously described (10 (link)) (Santa Clara, CA). Agilent 244 k arrays were performed on individual CDH12. Birdsuite (broadinstitute.org) and Agilent Feature Extraction (10.7.3.1), respectively, were used to generate CNV calls. Clinical microarrays were obtained on 2-II-1 [ClariSure CGH, Quest Diagnostics (Madison, NJ)], 2-II-2 and 2-II-3 [GenomeDx v5, GeneDx (Gaithersburg, MD)].
Longoni M., Russell M.K., High F.A., Darvishi K., Maalouf F.I., Kashani A., Tracy A.A., Coletti C.M., Loscertales M., Lage K., Ackerman K.G., Woods S.A., Ward-Melver C., Andrews D., Lee C., Pober B.R, & Donahoe P.K. (2014). Prevalence and penetrance of ZFPM2 mutations and deletions causing congenital diaphragmatic hernia. Clinical genetics, 87(4), 362-367.
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