Scanned images were then analyzed using feature extraction software ver. As with the hmsc and dermal fibroblast data, the slides used in the gse16444 series were scanned with an agilent g2565ba scanner according to the microrna microarray system protocol, and the raw data were obtained with the agilent feature extraction software v. Contains three subtables, storing the feature extraction parameters, microarray level statistics, and featurelevel data. The surescan microarray scanner is a key component of agilents complete microarray solution. Microarray scanners microarray scanner systems biocompare. The scanned tiff images were analyzed numerically and background corrected using the agilent feature extraction software version 10. Agilent oligonucleotide arraybased cgh for genomic dna. Microarray scanners this information can help determine whether overexpression of a certain gene is involved in causing a specific disease, rendering the microarrays and scanners powerful tools in. Agilent g2565ca microarray scanner system scan control software 8. Signal data were collected with dedicated agilent feature extraction software v9. Whether performing gene expression studies, array cgh. Agilent surescan 2600d microarray scanner used microscopes.
The package is written in r, opensource software for statistical computing, and. An ontime batch mode interfaces feature extraction 9. The signal level of the feature shown is 8 counts and 58 counts over background in the red and green channels, respectively, on the agilent microarray scanner. G2565 series microarray scanner software and accessories. The hybridized microarrays were scanned agilent g2565ba microarray scanner and quantified using feature extraction software agilent technologies. Data from all 72 scans were extracted using agilent feature extraction software version 6. It measures the fluorescence intensity of two dyes simultaneously from labeled sample nucleic acid bound to microarrays.
If you will be using a 3rd party microarray scanner other than the axon genepix, the scanner s software will need this file to process the images. A comparative study of rnaseq and microarray data analysis. Validation of the agilent 244k oligonucleotide arraybased. New stringent twocolor gene expression workflow enables more. After hybridization, wash processes were performed according to the manufacturers instructions, and hybridized microarrays were scanned using an agilent microarray scanner g2505b and software g2565ba. Reverse transcription and cdna amplification steps for nimblegen microarrays were carried out with an ovation pico wta system sl nugen using 30 ng of total rna because of the small amount of total rna obtained from the. Agilent technologies dna microarray scanner g2505 c g2505c with software.
This note lists the specifications of the glass on which the active. Agimicrorna includes functions that wrap around already existing bioconductor functions as well as new specific functions that have been collected and integrated into a library to facilitate the preprocessing and differential expression analysis of agilent microrna microarray data in a systematic and easy way. Microarray scanners microarray scanner systems microarray scanners are widely used in functional biology, cellomics, gene expression and drug discovery research. Surescan microarray scannerg4900da from agilent technologies. Fluorescently labeled targets were hybridized to agilent rice oligo microarrays for 17 h at 65c. Eriocitrin ameliorates dietinduced hepatic steatosis with. If you will be using a 3rd party microarray scanner other than the axon genepix, the scanners software will need this file to process the images. Processing of agilent microrna array data bmc research. On september 29th, agilent launched a major web update for our line of genomics products. Agilent is one of the major producers of microrna arrays, and microarray data are commonly analyzed by using r and the functions and packages collected in the bioconductor project.
Features special to this model are highlighted yellow. Preprocessing and differential expression analysis of agilent microrna arrays using the agimicrorna bioconductor library. This technology provides for rapid, highquality, automated, handsoff scanning of microarrays. Maqc study data generation plan agilent technologies gene. Oct 31, 20 phosphorylated satb1 is associated with the progression and prognosis of glioma. Agilent dna microarray scanner part number g2565ba. Development and validation of a high density sunflower. Prior to this, agilent slide had a single barcode on the. Arrays were scanned at 5 um resolution on an agilent dna microarray scanner g2565ba, agilent technologies using the default settings for mirna microarray v2.
A method for quantifying the performance of a dna microarray. Agilent microarray scanner agilent pn g2565ba hybridization chamber, stainless agilent pn g2534a hybridization chamber gasket slides 1 microarray slide, 5 slidesbox 2 microarraysslide, 5 slidesbox 4 microarraysslide, 5 slidesbox. However, an analytical package that integrates the specific. When buying a microarray scanner, important features to consider are sensitivity, resolution, scan area, rapidity of scan, and ease of use. Hybridized microarray slides were scanned with an agilent dna microarray scanner g2505c and data was analyzed with the agilent scancontrol version 8. The microarray scanner is a sophisticated laserinduced fluorescence scanner designed to read microarrays deposited on standard 1 in. Microarray design files available for download agilent. Surescan microarray scanner high sensitivity and resolution.
Dynamic autofocus continually adjusts scanner s focus, keeping features in focus at all times. Hardware and software features agilent g2565ca microarray scanner system scan control software 8. Agilent technologies dna microarray scanner g2505 c g2539ac micro array. Surescan microarray scanner software and accessories. Oneway analysis of variance anova was performed to identify differentially expressed probes p microarray scanner agilent g2565ba, and features were extracted using the afe image analysis tool ver sion a. Agilent oligonucleotide arraybased cgh for genomic dna analysis protocol 1 before you begin procedural notes 10 safety notes 11 agilent oligo cgh microarray kit contents 12 required equipment 18 required reagents 21 required hardware and software 25 make sure that you read and understand the information in this chapter and. With improved feature resolution, it delivers exceptional flexibility to analyze any microarray. Images provided by the scanner were analyzed using agilent s software feature extraction version 9. Jan 26, 2011 arrays were scanned at 5 um resolution on an agilent dna microarray scanner g2565ba, agilent technologies using the default settings for mirna microarray v2.
Agilent technologies g250560502 dna microarray scanner. New stringent twocolor gene expression workflow enables. Three scanners the agilent dual laser dna microarray scanner part number g2565ba and two instruments labeled scanner y and scanner z. The agilent surescan scanner is an advanced microarray scanner system for.
Notice that the feature is clearly distinguished on the agilent microarray scanner, but is barely distinguishable on the brand y scan, and is not detectable at all on the brand z scan. Twocolor microarray based gene expression analysis 11 required equipment description company and part no. For rnaseq singleend sequencing for 50 base pair reads the rna was isolated using trizol reagent including a dnase i roche, mannheim, germany digestion step. Illumina iscan microarray scanner computer pc with software new. The microarray scanner plays a pivotal role in the dna microarray. Phosphorylated satb1 is associated with the progression and. Agilent g2565ba surescan dna microarray scanner g2505b w.
This system comes with the computer and installed agilent scan control software suite, carousel, 5 new chip cassettes and all. Jan 15, 2014 the hybridized microarrays were scanned agilent g2565ba microarray scanner and quantified using feature extraction software agilent technologies. Agilents feature extraction is a software that locates and places microarray grids. Maqc study data generation plan agilent technologies.
Such pipelines for rnaseq data should include mapping of reads, counting and differential gene expression analysis or preprocessing, normalization and differential gene expression in case of. Jan 26, 2011 the main research tool for identifying micrornas involved in specific cellular processes is gene expression profiling using microarray technology. The feature extraction files were imported into microsoft access, microsoft excel, and spotfire decisionsite. Agilent g2565ba microarray scanner iet refurbished. Agilent microarray scanner bundle agilent pn g2565ba hybridization chamber, stainless agilent pn g2534a hybridization chamber gasket slides, 5pack alternative packaging sizes are available 1x microarrays or 2x microarrays or 4x microarrays or 8x microarrays agilent pn g253460003 or agilent pn g253460002 or agilent pn g253460011 or. Agilent microarray scan control software installed agilent feature extraction software installed agilent installation qualification tool software installed declaration of conformity the microarray scan control software 9. The mircury lna array microarray slides were scanned using the agilent g2565ba microarray scanner system agilent technologies, inc. Discover more about how the surescan dx scanner provides a complete microarray solution, offering outstanding sensitivity and resolution. Agilent g5761a surescan dx microarray scanner system. This tabdelimited text file lists the location of each probe in the design from front, bottom orientationalong with its accession number, gene name, performance score, and other information. Surescan dx microarray scanner by agilent technologies, inc.
After washing, all microarray slides were scanned on an agilent microarray scanner g2565ba with 5. Agilent technologies was used to extract data and analyze the acquired array images. Three scanners the agilent dual laser dna microarray scanner part number g2565ba and two instruments. The surescan dx microarray scanner is a sophisticated laserinduced fluorescence scanner designed to read microarrays printed on standard 25. Jan 22, 2010 as with the hmsc and dermal fibroblast data, the slides used in the gse16444 series were scanned with an agilent g2565ba scanner according to the microrna microarray system protocol, and the raw data were obtained with the agilent feature extraction software v. Agilent microarray bar codes is automatically paired with microarray images. The software automatically finds and places microarray grids, rejects outlier pixels, accurately determines feature intensities and ratios, flags outlier pixels, and calculates statistical confidences. Pdf preprocessing and differential expression analysis of. The scanner is equipped with new optics, electronics, and software and is part of an improved microarray platform that provides greater transcript definition and chromosomal definition, as well as expression measurements that more accurately reflect the range of gene activity in biological systems.
Background pipeline comparisons for gene expression data are highly valuable for applied real data analyses, as they enable the selection of suitable analysis strategies for the dataset at hand. The average signal intensities were corrected for median background intensity and transferred with genbank descriptors to a microsoft excel data spreadsheet microsoft, redmond, wa. Data analysis software 2 perpetual licenses of agilent feature extraction included. Agilent technologies microarray scanner approved for in vitro diagnostics in china. The glass slides were scanned using an agilent g2565ba microarray scanner.
A methodical microarray design enables surveying of. The surescan dx microarray scanner is part of the surescan dx microarray scanner system solution from agilent technologies. Microarray scanning and data analysis slides were scanned in an agilent microarray scanner g2565ba according to the manufacturers protocol. The agilent g2565ba microarray scanner system and agilent feature extraction software version 9. The agilent surescan dx microarray scanner is ceivd marked for diagnostic use in the eu, iceland, korea, norway, singapore, and switzerland. From mid2002, agilent barcodes are positioned one on each side. Scanning was performed with the agilent g2565ba microarray scanner. After hybridization, microarrays were washed 1 minute at room.
File format used for the storage and exchange of microarray data and metainformation. Information on thirdparty microarrays can be entered and assigned through setup screens. The agilent g2565ba microarray scanner is designed to read agilent microarrays as well as most common glass slides. Phosphorylated satb1 is associated with the progression. Images provided by the scanner were analyzed using agilents software feature extraction version 9.
Data were acquired using the agilent g2565ba microarray scanner system and agilent feature extraction software version 9. The integrity of total rna was checked using an agilent 2100 bioanalyzer agilent. Arrays were scanned using an agilent technologies g2565ba microarray scanner system and feature extraction 10. The quantified signals were background corrected normexp with offset value 10 and normalized using the. Captured images were transformed to data with feature extraction software, version 9. The microarray images generated by the scanner were analyzed with agilent feature extraction software version 8. Product dna microarray scanner, model g2565ba special features. Microarray and deep sequencing crossplatform analysis of. Nov 12, 20 hybridized microarray slides were scanned with an agilent dna microarray scanner g2505c and data was analyzed with the agilent scancontrol version 8.
Agilent microarray scanner including feature extraction software v8. A crossplatform comparison of affymetrix and agilent. Agilent microrna microarray agilent microrna assays integrate eight individual microarrays on a single glass slide. The end result is an automated, handsoff precision microarray scan followed by automated feature extraction. The surescan microarray scanner is a laser induced fluorescence scanner designed to read microarrays printed on a standard 1 inch x 3 inch glass slides. Dna microarray scanner g2565ba table contains all key specifications for the dna microarray scanner, model ba. Gse75471 osmyc2responsive genes in osmyc2overexpressing. Output format of agilent feature extraction and agilent genomic workbench agw software.
Three nominally identical oligo microarrays each microarray used in the study was an agilent human oligo 1a microarray kit cat. Data was extracted using the agilent feature extraction software 7. Microarray profiling and coexpression network analysis of. The surescan dx scanner measures the fluorescence intensity. Microarray analysis of differentially expressed fetal. The mircury lna microrna array slides were scanned using the agilent g2565ba microarray scanner system agilent technologies, inc. Surescan microarray scanner from agilent technologies. Agilent microarray scanner and feature extraction software. Pdf preprocessing and differential expression analysis.
Data analysis software 2 perpetual licenses of agilent feature extraction included approximate scanner dimensions height. Slides were washed and scanned using an agilent g2565ba scanner. Another custom analytical software package, agilent cgh analytics, version 3. Oneway analysis of variance anova was performed to identify differentially expressed probes p lna microrna array analysis software, exiqon. Phosphorylated satb1 is associated with the progression and prognosis of glioma. Refurbished agilent g2565ba microarray scanner pn g2505b complete with 48 position carousel, feature extraction and analysis software, and pc data system. Industry experts, and our own experts reorganized and improved the content so that you find the trusted answers that you need for genomics products like. Agilent g2565ba microarray scanner pn g2505b complete with agilent scanner control software a. Number g4110a and was printed on 1inch by 3inch 25. The surescan dx microarray scanner system has been validated for use with agilent g3 gene expression and cytogenetic.
Microarray data were saved in the gene expression omnibus database. Trade up your existing agilent c microarray scanner and save. Agilents dna microarray scanner with surescan highresolution technology is the key component of. Preprocessing and differential expression analysis of. Scan protocol, images were scanned at 2um resolution in an agilent dna microarrays scanner g2565ba, agilent technologies and were with feature extraction 9. Agilent g2565ba microarray scanner bar code and glass. Agilent s feature extraction software reads and processes up to 100 raw microarray image files in an automated, walkaway mode. Sensitivity and reliability of this technology is validated by mirqc and other studies.
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