Agilent feature extraction software version 9.5

Manufactured by Agilent Technologies

Agilent Feature Extraction software (version 9.5) is a tool designed for the analysis of microarray data. It extracts numerical intensity values from microarray images, which can then be used for further analysis.

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Lab products found in correlation

Rneasy kit, by Qiagen (2 mentions) Whole human genome microarray, by Agilent Technologies (1 mentions) Trizol, by Thermo Fisher Scientific (1 mentions) Agilent dna microarray scanner g2505b, by Agilent Technologies (1 mentions) Surehyb hybridization chamber, by Agilent Technologies (1 mentions) Genespring gx, by Agilent Technologies (1 mentions) Agilent dna microarray scanner, by Agilent Technologies (1 mentions)

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Feature Extraction software (941 citations) Agilent Feature Extraction software (343 citations) Feature Extraction software version 9.5 (37 citations) Feature Extraction 9.1 (20 citations) Agilent Feature Extraction (19 citations) Agilent Feature Extraction Software version 9.5.1 (14 citations) Feature Extraction software 9.5.3 (13 citations) Agilent Feature Extraction software 9.3.2.1 (11 citations) Feature Extraction version 9.5 (5 citations) Feature Extraction version software (2 citations)

4 protocols using agilent feature extraction software version 9.5

Transcriptome Analysis of lncRNA RP11 Knockdown

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lncRNA RP11 expression was knocked down in HPA-v using anti-lncRNA against lncRNA RP11 (SH1 and SH2). After differentiation was induced as previously described, total RNA was isolated from differentiated cells using an RNeasy kit (Qiagen). After RNA quality determination and RT, microarray analysis for detection of gene expression was performed using a Whole Human Genome Microarray (Agilent Technologies) according to the manufacturer’s protocol. Data were extracted using the Agilent Feature Extraction software (version 9.5). Differentially expressed genes between the SH1/SH2 and control groups were identified, and an intersection was made. Differentially intersecting genes were identified via analyzing the fold change and the Student’s t-test P value. For fold change analysis, a cutoff value of 2 was used. Next, all candidate genes were mapped to gene ontology (GO) terms in the database (http://www.geneontology.org/). Pathway analysis is a functional analysis that maps genes to the Kyoto Encyclopedia of Genes and Genomes (KEGG; http://www.genome.jp/kegg) pathways.

Lin Y., Zhang Y., Xu L., Long W., Shan C., Ding H., You L., Zhao C, & Shi Z. (2021). High expression of an unknown long noncoding RNA RP11-290L1.3 from GDM macrosomia and its effect on preadipocyte differentiation. Endocrine Connections, 10(2), 191-204.

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Transcriptional Profiling of Plasmodium falciparum Asexual and Gametocyte Stages

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Total RNA was extracted from tightly synchronized PfAP2-G2::KO and WT parasites every 6 hours, starting at 3 hpi, throughout the 48 hour asexual life cycle. A separate timecourse was designed to collect RNA from gametocytes starting at Day 1 and every 12 hours for the following 7 days. RNA was extracted from parasite-infected RBCs collected at each time point using TRIzol (ThermoFisher Scientific), following the manufacturer’s protocol. cDNA synthesis and DNA microarray analysis was carried out as previously described (Painter et al. 2013 ). Two-channel Agilent DNA microarrays (AMADID 037237) were hybridized, washed, and scanned on an Axon 4200A scanner. Signal intensities for each gene were extracted from the scanned image using Agilent Feature Extraction Software version 9.5. Detailed microarray protocols can be found at http://llinaslab.psu.edu/protocols/. The data were analyzed by Significance Analysis of Microarrays (SAM) (Tusher et al. 2001 (link)) for the significantly (>1.5 log2FC, 0.30 local FDR) changing genes between the WT and ap2-g2 KO lines using two-class paired t-test throughout the timecourse. No data was available for TP6 due to technical reasons. All heat maps were clustered using Cluster 4.0 and was visualized using Java Tree View.

Singh S., Santos J.M., Orchard L.M., Yamada N., van Biljon R., Painter H.J., Mahony S, & Llinás M. (2021). The PfAP2-G2 transcription factor is a critical regulator of gametocyte maturation. Molecular microbiology, 115(5), 1005-1024.

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Microarray-based Transcriptome Analysis

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Total RNA (350 ng) from each sample (90 LM, 90 SM) was individually labeled with Cy3 using the Low RNA Input Linear Amplification Kit PLUS, One-Color (ref 5188–5339, Agilent Technologies, Massy, France) following the manufacturer’s instructions. Microarray hybridizations were carried out at 65°C for 17 hours in Agilent’s SureHyb Hybridization Chambers containing 600 ng of Cy3-labeled cRNA sample. Slides were disassembled and washed in Gene Expression Wash Buffer 1 for 1 minute at room temperature and then in Gene Expression Wash Buffer 2 for 1 minute at 37°C. Microarrays were scanned at 5 µm/pixel resolution using the Agilent DNA Microarray Scanner G2505B, and images were analyzed with Agilent Feature Extraction Software (Version 9.5), using the GE2-v5_95_Feb07 FE extraction protocol. These MIAME compliant microarray data have been deposited into the GEO repository (http://www.ncbi.nlm.nih.gov/geo/) and are publicly available through GEO Series accession no. GSE33957.

Herault F., Vincent A., Dameron O., Le Roy P., Cherel P, & Damon M. (2014). The Longissimus and Semimembranosus Muscles Display Marked Differences in Their Gene Expression Profiles in Pig. PLoS ONE, 9(5), e96491.

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Whole Genome RNA Expression Profiling

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Quality-checked total RNAs (0.5 μg) successfully obtained from 55 patients were reverse transcribed to first-strand cDNA using Moloney Murine Leukemia Virus reverse transcriptase and T7 primer, and the Cy3-labeled cRNAs were generated by the Quick Amp Labeling Kit One-Color® (Agilent Technologies). The labelled cRNA was purified by RNeasy Kit® (Qiagen, Valencia, CA), and a total of 1.65 μg of cRNA was hybridized to Whole Human Genome Oligo 4×44K (Agilent Technologies) according to the manufacturer's recommendations. The microarrays were scanned using an Agilent DNA Microarray Scanner® and analyzed with Agilent Feature Extraction software version 9.5® (Agilent Technologies). Expression levels were normalized to the 75th percentile expression value of the entire spot using GeneSpring GX® (Agilent Technologies).

Kawabata-Iwakawa R., Iwasa N., Satoh K., Colinge J., Shimada M., Takeuchi S., Fujiwara H., Eguchi H., Oishi T., Sugiyama T., Suzuki M., Hasegawa K., Fujiwara K, & Nishiyama M. (2024). Prediction of response to promising first-line chemotherapy in ovarian cancer patients with residual peritoneal tumors: practical biomarkers and robust multiplex models. International journal of clinical oncology, 29(9).

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