Scan protocol, images were scanned at 2um resolution in an agilent dna microarrays scanner g2565ba, agilent technologies and were with feature extraction 9. 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 technologies dna microarray scanner g2505 c g2505c with software. Agilent technologies was used to extract data and analyze the acquired array images. Data analysis software 2 perpetual licenses of agilent feature extraction included. Hybridized microarray slides were scanned with an agilent dna microarray scanner g2505c and data was analyzed with the agilent scancontrol version 8. Maqc study data generation plan agilent technologies gene.
Sensitivity and reliability of this technology is validated by mirqc and other studies. An ontime batch mode interfaces feature extraction 9. 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. The average signal intensities were corrected for median background intensity and transferred with genbank descriptors to a microsoft excel data spreadsheet microsoft, redmond, wa. 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. 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. New stringent twocolor gene expression workflow enables more. Microarray design files available for download agilent. 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. 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. 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. Microarray and deep sequencing crossplatform analysis of.
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. This note lists the specifications of the glass on which the active. Agilent g2565ba microarray scanner pn g2505b complete with agilent scanner control software a. Jan 26, 2011 the main research tool for identifying micrornas involved in specific cellular processes is gene expression profiling using microarray technology. 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. The microarray scanner plays a pivotal role in the dna microarray. The hybridized microarrays were scanned agilent g2565ba microarray scanner and quantified using feature extraction software agilent technologies. Surescan dx microarray scanner by agilent technologies, inc. Agilent g5761a surescan dx microarray scanner system.
Surescan microarray scanner from agilent technologies. Features special to this model are highlighted yellow. After hybridization, microarrays were washed 1 minute at room. Agilent oligonucleotide arraybased cgh for genomic dna. Agilent dna microarray scanner part number g2565ba. Fluorescently labeled targets were hybridized to agilent rice oligo microarrays for 17 h at 65c. Surescan microarray scannerg4900da from agilent technologies. Scanning was performed with the agilent g2565ba microarray scanner. The mircury lna microrna array slides were scanned using the agilent g2565ba microarray scanner system agilent technologies, inc. 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. Captured images were transformed to data with feature extraction software, version 9. File format used for the storage and exchange of microarray data and metainformation.
Gse75471 osmyc2responsive genes in osmyc2overexpressing. Dynamic autofocus continually adjusts scanner s focus, keeping features in focus at all times. Prior to this, agilent slide had a single barcode on the. It measures the fluorescence intensity of two dyes simultaneously from labeled sample nucleic acid bound to microarrays. 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. 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. Microarray scanners microarray scanner systems biocompare. Whether performing gene expression studies, array cgh. Agilent microrna microarray agilent microrna assays integrate eight individual microarrays on a single glass slide. The surescan microarray scanner is a key component of agilents complete microarray solution. Contains three subtables, storing the feature extraction parameters, microarray level statistics, and featurelevel data.
The software automatically finds and places microarray grids, rejects outlier pixels, accurately determines feature intensities and ratios, flags outlier pixels, and calculates statistical confidences. After washing, all microarray slides were scanned on an agilent microarray scanner g2565ba with 5. 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. Jan 15, 2014 the hybridized microarrays were scanned agilent g2565ba microarray scanner and quantified using feature extraction software agilent technologies. Phosphorylated satb1 is associated with the progression and. The glass slides were scanned using an agilent g2565ba microarray scanner. When buying a microarray scanner, important features to consider are sensitivity, resolution, scan area, rapidity of scan, and ease of use. Surescan microarray scanner high sensitivity and resolution. On september 29th, agilent launched a major web update for our line of genomics products. G2565 series microarray scanner software and accessories.
Agilent g2565ca microarray scanner system scan control software 8. Hardware and software features agilent g2565ca microarray scanner system scan control software 8. Data from all 72 scans were extracted using agilent feature extraction software version 6. Agilent technologies microarray scanner approved for in vitro diagnostics in china. Oneway analysis of variance anova was performed to identify differentially expressed probes p lna microrna array analysis software, exiqon. The surescan dx microarray scanner is part of the surescan dx microarray scanner system solution from agilent technologies. The package is written in r, opensource software for statistical computing, and. Microarray profiling and coexpression network analysis of. Validation of the agilent 244k oligonucleotide arraybased. The agilent g2565ba microarray scanner is designed to read agilent microarrays as well as most common glass slides. Oct 31, 20 phosphorylated satb1 is associated with the progression and prognosis of glioma. The microarray scanner is a sophisticated laserinduced fluorescence scanner designed to read microarrays deposited on standard 1 in. 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. The agilent surescan dx microarray scanner is ceivd marked for diagnostic use in the eu, iceland, korea, norway, singapore, and switzerland.
Data were acquired using the agilent g2565ba microarray scanner system and agilent feature extraction software version 9. A comparative study of rnaseq and microarray data analysis. The quantified signals were background corrected normexp with offset value 10 and normalized using the. Phosphorylated satb1 is associated with the progression. The end result is an automated, handsoff precision microarray scan followed by automated feature extraction. The integrity of total rna was checked using an agilent 2100 bioanalyzer agilent. The surescan dx microarray scanner system has been validated for use with agilent g3 gene expression and cytogenetic. The microarray images generated by the scanner were analyzed with agilent feature extraction software version 8. However, an analytical package that integrates the specific. Arrays were scanned at 5 um resolution on an agilent dna microarray scanner g2565ba, agilent technologies using the default settings for mirna microarray v2.
Output format of agilent feature extraction and agilent genomic workbench agw software. 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. The surescan dx scanner measures the fluorescence intensity. Preprocessing and differential expression analysis of. The agilent g2565ba microarray scanner system and agilent feature extraction software version 9. A crossplatform comparison of affymetrix and agilent. Agilent surescan 2600d microarray scanner used microscopes. Eriocitrin ameliorates dietinduced hepatic steatosis with. Signal data were collected with dedicated agilent feature extraction software v9. Dna microarray scanner g2565ba table contains all key specifications for the dna microarray scanner, model ba. 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. Agilent technologies dna microarray scanner g2505 c g2539ac micro array.
A methodical microarray design enables surveying of. Information on thirdparty microarrays can be entered and assigned through setup screens. Microarray and deep sequencing crossplatform analysis of the. The scanned tiff images were analyzed numerically and background corrected using the agilent feature extraction software version 10. The surescan dx microarray scanner is a sophisticated laserinduced fluorescence scanner designed to read microarrays printed on standard 25. Data was extracted using the agilent feature extraction software 7.
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. Preprocessing and differential expression analysis of agilent microrna arrays using the agimicrorna bioconductor library. Another custom analytical software package, agilent cgh analytics, version 3. Agilents dna microarray scanner with surescan highresolution technology is the key component of. The agilent surescan scanner is an advanced microarray scanner system for. Trade up your existing agilent c microarray scanner and save. The mircury lna array microarray slides were scanned using the agilent g2565ba microarray scanner system agilent technologies, inc. Three scanners the agilent dual laser dna microarray scanner part number g2565ba and two instruments labeled scanner y and scanner z. Three scanners the agilent dual laser dna microarray scanner part number g2565ba and two instruments. Pdf preprocessing and differential expression analysis.
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. 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. Agilent microarray bar codes is automatically paired with microarray images. From mid2002, agilent barcodes are positioned one on each side. Surescan microarray scanner software and accessories.
Agilent technologies g250560502 dna microarray scanner. New stringent twocolor gene expression workflow enables. This technology provides for rapid, highquality, automated, handsoff scanning of microarrays. 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. Contains three subtables, storing the feature extraction parameters, microarraylevel statistics, and featurelevel data. Product dna microarray scanner, model g2565ba special features.
This system comes with the computer and installed agilent scan control software suite, carousel, 5 new chip cassettes and all. Twocolor microarray based gene expression analysis 11 required equipment description company and part no. Agilents feature extraction is a software that locates and places microarray grids. The feature extraction files were imported into microsoft access, microsoft excel, and spotfire decisionsite. Maqc study data generation plan agilent technologies. Images provided by the scanner were analyzed using agilents software feature extraction version 9. With improved feature resolution, it delivers exceptional flexibility to analyze any microarray. 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 g2565ba microarray scanner bar code and glass. Microarray data were saved in the gene expression omnibus database.
A method for quantifying the performance of a dna microarray. Slides were washed and scanned using an agilent g2565ba scanner. Microarray scanning and data analysis slides were scanned in an agilent microarray scanner g2565ba according to the manufacturers protocol. Arrays were scanned using an agilent technologies g2565ba microarray scanner system and feature extraction 10. 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. 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. Agilent g2565ba surescan dna microarray scanner g2505b w. Refurbished agilent g2565ba microarray scanner pn g2505b complete with 48 position carousel, feature extraction and analysis software, and pc data system. To speak with a representative, please fill out the contact form below or call us directly. Data analysis software 2 perpetual licenses of agilent feature extraction included approximate scanner dimensions height. Microarray analysis of differentially expressed fetal.
Pdf preprocessing and differential expression analysis of. Phosphorylated satb1 is associated with the progression and prognosis of glioma. Microarray scanners microarray scanner systems microarray scanners are widely used in functional biology, cellomics, gene expression and drug discovery research. 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. Agilent g2565ba microarray scanner iet refurbished. 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. Discover more about how the surescan dx scanner provides a complete microarray solution, offering outstanding sensitivity and resolution. The microarray images were analyzed using agilent feature extraction software, version 8.