Feature extraction software v10

Manufactured by Agilent Technologies

Sourced in United States

Feature Extraction software v10.7 is a laboratory data analysis tool designed to extract and quantify relevant information from complex data sets. The software provides a suite of algorithms and processing capabilities to aid researchers and scientists in their data analysis workflows.

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Feature Extraction software (941 citations) Feature Extraction (73 citations) Feature Extraction v10.7 (36 citations) Agilent Feature Extraction Software v10.7.3.1 (22 citations) Agilent Feature Extraction software (v10.7) (19 citations) Feature Extraction (v10.7) software (7 citations) Agilent Feature Extraction Software (v10.5). (2 citations) Feature Extraction software (v10.0), (2 citations)

89 protocols using feature extraction software v10

Microarray Transcriptional Profiling of Mouse Colon

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Total RNA was isolated using the protocol described above. RNA integrity was verified using a Bioanalyser 2100 with RNA 6000 Nano chips (Agilent Technologies, Palo Alto, CA, USA). Transcriptional profiling was performed on mouse colon samples using the SurePrint G3 Mouse GE 8 × 60 K Microarray kit (design ID: 028005, Agilent Technologies). Cyanine-3 (Cy3)-labeled cRNAs were prepared with 100 ng of total RNA using a One-Color Low Input Quick Amp Labeling kit (Agilent Technologies), following the recommended protocol. The specific activities and cRNA yields were determined by using a NanoDrop ND-1000 (Thermo Fisher Scientific, Waltham, MA, USA). For each sample, 600 ng of Cy3-labeled cRNA (specific activity > 11.0 pmol Cy3/μg of cRNA) were fragmented at 60 °C for 30 min and hybridized to the microarrays for 17 h at 65 °C in a rotating hybridization oven (Agilent Technologies). After hybridization, the microarrays were washed and then immediately dried. After washing, the slides were scanned using a G2565CA Scanner System (Agilent Technologies) at a resolution of 3 μm and a dynamic range of 20 bits. The resulting TIFF images were analyzed using the Feature Extraction Software v10.7.3.1 (Agilent Technologies) according to the GE1_107_Sep09 protocol. The microarray data were submitted to GEO under accession number GSE67577.

Lamas B., Richard M.L., Leducq V., Pham H.P., Michel M.L., Da Costa G., Bridonneau C., Jegou S., Hoffmann T.W., Natividad J.M., Brot L., Taleb S., Couturier-Maillard A., Nion-Larmurier I., Merabtene F., Seksik P., Bourrier A., Cosnes J., Ryffel B., Beaugerie L., Launay J.M., Langella P., Xavier R.J, & Sokol H. (2016). CARD9 impacts colitis by altering gut microbiota metabolism of tryptophan into aryl hydrocarbon receptor ligands. Nature medicine, 22(6), 598-605.

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Profiling Cervical Neoplasia Copy Number

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DNA copy number profiling was performed using Agilent Sure Print G3 Human comparative genomic hybridization (CGH) Microarray 180K. The genomic DNA from cervical neoplasia and matched normal genomes were hybridized onto the array as described elsewhere [26 (link)]. Background correction and normalization form array images were done using the Agilent Feature Extraction Software v10.7.3.1. The RankSegmentation statistical algorithm in NEXUS software v7.5 (Biodiscovery Inc.) was used to define copy number alterations of each sample. The microarray dataset has been deposited in Gene Expression Omnibus (GEO; http://www.ncbi.nlm.nih.gov/geo/) with the accession of GSE60067.

Jung S.H., Choi Y.J., Kim M.S., Baek I.P., Lee S.H., Lee A.W., Hur S.Y., Kim T.M., Lee S.H, & Chung Y.J. (2015). Progression of naive intraepithelial neoplasia genome to aggressive squamous cell carcinoma genome of uterine cervix. Oncotarget, 6(6), 4385-4393.

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Transcriptomic Analysis of Human Cells

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Transcriptomic analysis was performed using the SurePrint G3 Human GE v2 8×60K Microarray (Agilent Technologies, ID: 039494) according to the manufacturer’s protocol and to previously published [17 (link)]. Cyanine-3 labeled cRNAs were prepared using the One-Color Low Input Quick Amp Labeling kit (Agilent Technologies).
The slides were scanned using a G2565CA Scanner System (Agilent Technologies), and using a scan protocol with a resolution of 3 μm and a dynamic range of 20 bit. The resulting .tiff images were analyzed with the Feature Extraction Software v10.7.3.1 (Agilent Technologies) and using the GE2_107_Sep09 protocol. Original dataset was normalized using quantile method implemented in Limma’s package. Probes with bad detection p-values (<0.01) in half of the samples of a biological group were discarded. Ranked gene lists were obtained using statistical score of paired eBayes implemented in Limma’s package. Gene set enrichment analyses were performed using the Blood Transcription Modules [45 (link)] added with a selection of molecular signatures from C2 database provided by GSEA software [46 (link), 47 (link)]. Network analyses were performed using Cytoscape 2.8.3 and the plugin Enrichment Map dedicated to gene set enrichment analyses.
All datasets can be accessed in the ArrayExpress database (www.ebi.ac.uk/arrayexpress) under accession number E-MTAB-2858.

Rosenzwajg M., Churlaud G., Mallone R., Six A., Derian N., Chaara W., Lorenzon R., Long A., Buckner J., Afonso G., Pham H.P., Hartemann A., Yu A., Pugliese A., Malek T.R, & Klatzmann D. (2015). Low-dose interleukin-2 fosters a dose-dependent regulatory T cell tuned milieu in T1D patients. Journal of autoimmunity, 58, 48-58.

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Microarray Data Normalization and Annotation

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Agilent Feature Extraction software v. 10.7.3.1 (Agilent technologies) was used to analyse acquired array images. Data were then within-array normalized by Loess normalization method and between-array normalized by Quantile normalization. The normalized values were used to calculate log₂ transformed Cy5/Cy3 ratios. Replicate probes were collapsed calculating the median. Missing expression values were imputed by k-nearest neighbours averaging (k = 10). Date pre-processing was performed using the R (R Core team 2012) package limma[16] (link). Microarray data were deposited to the Gene Expression Omnibus (GSE53515).
All the 42,164 probes of the Agilent SurePrint G3 array were re-annotated using GENCODE v.16 gene annotation database (www.gencodegenes.org) [11] (link). The genomic coordinates of the probes in the Agilent array were matched to the genomic coordinates of the lncRNAs from the GENCODE v.16, to identify the probes covering lncRNAs. LncRNAs were included if 55 base pairs overlapped with the 60-mer array probes.

Tørring P.M., Larsen M.J., Kjeldsen A.D., Ousager L.B., Tan Q, & Brusgaard K. (2014). Long Non-Coding RNA Expression Profiles in Hereditary Haemorrhagic Telangiectasia. PLoS ONE, 9(3), e90272.

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Comprehensive Genomic Profiling of Breast Tumors

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DNA copy number profiling was performed using the Agilent Sure Print G3 Human comparative genomic hybridization (CGH) Microarray 180 K. The genomic DNA of breast tumor tissues and matched normal genomes was hybridized onto the array according to the manufacturer's instructions. Background correction and normalization for array images was performed using Agilent Feature Extraction Software v10.7.3.1. The RankSegmentation statistical algorithm in NEXUS software v7.5 (Biodiscovery Inc., El Segundo, CA) was used to define the CNAs of each sample; a log2 ratio larger than 0.3 was identified as gain and lower than −0.3 as loss. The a-CGH results from patients 3 and 12 were of poor quality and deemed inappropriate for analysis, so the copy number alterations for these samples were generated from whole-exome sequencing data. The inference of chromothripsis was manually curated by examining cases with > 10 identifiable shifts in the copy number profiles per chromosome.

Kim S.Y., Jung S.H., Kim M.S., Baek I.P., Lee S.H., Kim T.M., Chung Y.J, & Lee S.H. (2015). Genomic differences between pure ductal carcinoma in situ and synchronous ductal carcinoma in situ with invasive breast cancer. Oncotarget, 6(10), 7597-7607.

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Microarray Analysis of Stimulated Cells

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For Microarray analysis cells were prepared as above and stimulated 4 hours, lysed and mRNA extracted using a microRNeasy (Qiagen) kit. RNA quality was verified by Bioanalyser 2100 (Agilent). Samples from five separate donors were submitted for microarray analysis (Agilent; G3 gene-expression chip). TIFF image files were processed using Agilent’s Feature Extraction software (v10.7.3.1) using protocol GE2_107_Sep09. Data was imported into GeneSpring and Log(2) ratios calculated as Cy3(sample)/Cy5(reference). ANOVA was used to compare the three groups (RNA40, R848 and control) for differentially expressed genes and, at the same time, a fold change analysis conducted. The Benjamini-Hochberg multiple testing correction was applied and a corrected p-value of <0.01 taken to be significant. All analysis was carried out in GeneSpring GX v11.5.

Colak E., Leslie A., Zausmer K., Khatamzas E., Kubarenko A.V., Pichulik T., Klimosch S.N., Mayer A., Siggs O., Hector A., Fischer R., Klesser B., Rautanen A., Frank M., Hill A.V., Manoury B., Beutler B., Hartl D., Simmons A, & Weber A.N. (2014). RNA and Imidazoquinolines are sensed by distinct TLR7/8 ectodomain sites resulting in functionally disparate signaling events. Journal of immunology (Baltimore, Md. : 1950), 192(12), 5963-5973.

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Array Comparative Genomic Analysis of Tracheal Tumors

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For Array Comparative Genomic analysis, an 180 K oligonucleotide microarray with even whole genome coverage and median probe spacing of approximately 16 kb was used (Oxford Gene Technology, UK). Genomic DNA isolated from the cells of primary tracheal tumor patient and a sex-matched pooled reference DNA isolated from healthy controls (Promega, WI, USA) were labeled with Cy3 and Cy5 respectively (Enzo Life Sciences, NY, USA). Hybridization and slide washing (Oligo aCGH/ChIP-on-Chip Wash Buffer Kit, Agilent Technologies, DE, USA) were performed according to the manufacturers' recommendations. Scanning of the array slide was performed on a microarray scanner with 3 µm resolution and initial data analysis was performed with the Feature Extraction software v 10.7.3.1 (Agilent Technologies) followed by analysis with the CytoSure Interpret Software v 4.3 (Oxford Gene Technology).

Lim M.L., Ooi B.N., Jungebluth P., Sjöqvist S., Hultman I., Lemon G., Gustafsson Y., Asmundsson J., Baiguera S., Douagi I., Gilevich I., Popova A., Haag J.C., Rodríguez A.B., Lim J., Liedén A., Nordenskjöld M., Alici E., Baker D., Unger C., Luedde T., Vassiliev I., Inzunza J., Ährlund-Richter L, & Macchiarini P. (2014). Characterization of Stem-Like Cells in Mucoepidermoid Tracheal Paediatric Tumor. PLoS ONE, 9(9), e107712.

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RNA Extraction and Microarray Analysis

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Total RNA from fresh-frozen samples was isolated using TRIzol reagent (Invitrogen). The RNA quantity was determined using the NanoDrop ND-1000 spectrometer (Thermo Scientific), and RNA integrity numbers (RIN) were measured with an RNA 6000 Kit on the 2100 Bioanalyzer (Agilent Technologies) according to the manufacturer's protocol. Microarrays from Agilent Technologies (Agilent SurePrint G3 Human Gene Expression 8×60K v2) were used for mRNA profiling. Total RNA (100μg) was labelled with Cy3 and hybridized on the arrays according to the manufacturer's recommendations. Arrays were scanned using Agilent Microarray Scanner (Agilent Technologies). The raw signal data were pre-processed with Agilent's Feature Extraction Software (v10.7.3.1).

Østrup O., Dagenborg V.J., Rødland E.A., Skarpeteig V., Silwal-Pandit L., Grzyb K., Berstad A.E., Fretland Å.A., Mælandsmo G.M., Børresen-Dale A.L., Ree A.H., Edwin B., Nygaard V, & Flatmark K. (2017). Molecular signatures reflecting microenvironmental metabolism and chemotherapy-induced immunogenic cell death in colorectal liver metastases. Oncotarget, 8(44), 76290-76304.

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Microarray-based Gene Expression Analysis

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A total of 30-ng of RNA was amplified by WTA2 kit (Sigma-Aldrich) and 2.5-µg of complementary DNA was labeled with Kreatech ULS labeling kit (Kreatech Diagnostics). Labeled samples were purified with QIAquick polymerase-chain-reaction (PCR) purification columns (Qiagen) and quantitated on a Nanodrop spectrophotometer (NanoDrop Technologies). The labeled DNA was hybridized using Agilent Human 8×60K microarrays chips (Agilent Technologies) at 65°C for 20h followed by routine washing. The microarrays were scanned on an Agilent SureScan scanner to detect Cy5 fluorescence. Gridding and analysis of images were performed using Agilent Feature Extraction software v10.7.3.1.

Rai M.F., Tycksen E.D., Sandell L.J, & Brophy R.H. (2017). Advantages of RNA-seq Compared to RNA Microarrays for Transcriptome Profiling of Anterior Cruciate Ligament Tears. Journal of orthopaedic research : official publication of the Orthopaedic Research Society, 36(1), 484-497.

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Microarray Data Quality Control

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Fluorescence intensity data was obtained with Agilent Feature Extraction Software v. 10.7.3.1, using recommended protocol GE1_107_Sep09. Quality control was done by inspecting the reports on the Agilent Spike-in control probes.

Roca C.P., Gomes S.I., Amorim M.J, & Scott-Fordsmand J.J. (2017). Variation-preserving normalization unveils blind spots in gene expression profiling. Scientific Reports, 7, 42460.

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