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Genepix pro 6.0 analysis software

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Genepix Pro 6.0 is a microarray image analysis software designed for use with Molecular Devices' GenePix microarray scanners. The software provides tools for image acquisition, feature extraction, and data analysis of microarray experiments.

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Lab products found in correlation

Genepix 4000b microarray scanner, by Molecular Devices (6 mentions) Proscanarray ht, by PerkinElmer (1 mentions) Innoscan 1100 al, by Innopsys (1 mentions)

Spelling variants of this product

GenePix Pro 6.0 (276 citations) GenePix Pro (33 citations) GenePix software (26 citations) Genepix 6.0 software (22 citations) GenePix Pro software (21 citations) Analysis 6.4 software (5 citations) Genepix Pro 6.0 analysis (3 citations)

9 protocols using genepix pro 6.0 analysis software

1

Microarray Image Analysis Protocol

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Processed slides were scanned and analyzed as described at 10 μm resolution with a Genepix 4000B microarray scanner (Molecular Devices) using 350 gain. Image analysis was carried out with Genepix Pro 6.0 analysis software (Molecular Devices). Spots were defined as circular features with a variable radius as determined by the Genepix scanning software. Local background subtraction was performed.
Leviatan Ben-Arye S., Schneider C., Yu H., Bashir S., Chen X., von Gunten S, & Padler-Karavani V. (2019). Differential Recognition of Diet-Derived Neu5Gc-Neoantigens on Glycan Microarrays by Carbohydrate-Specific Pooled Human IgG and IgA Antibodies. Bioconjugate chemistry, 30(5), 1565-1574.
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2

Amine-Functional Glycan Array Profiling

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Amine-functional glycans were printed in replicates of three onto NHS-activated glass slides at a 100 mM concentration as previously described (Liang et al., 2011 (link); Shivatare et al., 2013b (link)). Printed slides were incubated for 1hr at 80% humidity followed by o/n desiccation. Slides were blocked with ethanolamine (50 mM ethanolamine in borate buffer, pH 9.2). Antibodies, 10 µg, were pre-complexed with DyLight 649-AffiniPure mouse antihuman IgG-Fc (5 µg, Jackson) for 1 hr at 4°C. The sample was added to glycan array and incubated at 1 hr at 4°C. The slides were washed sequentially in PBS 0.05% Tween-20, PBS and then water. Arrays were scanned on a ProScanArray HT (PerkinElmer) confocal slide scanner. Image analysis was carried out with Genepix Pro 6.0 analysis software (Molecular Devices Corporation, Union City, CA). Error bars represent the average percentage error for all data points reported. The oligosaccharide probes and array data are shown in Table S5.
Falkowska E., Le K.M., Ramos A., Doores K.J., Lee J.H., Blattner C., Ramirez A., Derking R., van Gils M.J., Liang C.H., Mcbride R., von Bredow B., Shivatare S.S., Wu C.Y., Chan-Hui P.Y., Liu Y., Feizi T., Zwick M.B., Koff W.C., Seaman M.S., Swiderek K., Moore J.P., Evans D., Paulson J.C., Wong C.H., Ward A.B., Wilson I.A., Sanders R.W., Poignard P, & Burton D.R. (2014). Broadly neutralizing HIV antibodies define a glycan-dependent epitope on the pre-fusion conformation of the gp41 protein on cleaved Envelope trimers. Immunity, 40(5), 657-668.
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3

Microarray Data Normalization Protocol

Cited 2 times
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Slides were scanned at 5 μm resolution with an InnoScan 1100 AL fluorescence scanner (Innopsys, Carbonne, France). Image analysis was carried out with Genepix Pro 6.0 analysis software (Molecular Devices Corporation, Union City, CA) as previously described [14 (link),15 (link)]. Spots were defined as circular features with a diameter of 90 μm. Local background subtraction (median background) was performed and the background-subtracted median pixel intensity feature was used. To minimize the impact of noise on our comparisons, spots with intensity lower than 150 (1/2 the typical background signal when analyzing IgM and IgG at 1:50) were considered too low to be measured accurately and were set to 150. The average of duplicate spots was calculated to obtain a normalized value to the reference samples. A log-transformed (base 2) was applied for each slide, and the final data value was obtained from the normalized average of data from both wells for a given macaque sample. Full microarray data can be found in the Supplemental Table S1.
Nanno Y., Sterner E., Gildersleeve J.C., Hering B.J, & Burlak C. (2019). Profiling Natural Serum Antibodies of Nonhuman Primates with a Carbohydrate Antigen Microarray. Xenotransplantation, 27(2), e12567.
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4

Microarray Image Analysis Protocol

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Processed slides were scanned and analyzed as described at 10 μm resolution with a Genepix 4000B microarray scanner (Molecular Devices) using 300 gain. Image analysis was carried out with Genepix Pro 6.0 analysis software (Molecular Devices). Spots were defined as circular features with a variable radius as determined by the Genepix scanning software. Local background subtraction was performed.
Amon R., Grant O.C., Leviatan Ben-Arye S., Makeneni S., Nivedha A.K., Marshanski T., Norn C., Yu H., Glushka J.N., Fleishman S.J., Chen X., Woods R.J, & Padler-Karavani V. (2018). A combined computational-experimental approach to define the structural origin of antibody recognition of sialyl-Tn, a tumor-associated carbohydrate antigen. Scientific Reports, 8, 10786.
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5

Microarray Image Analysis Protocol

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Processed slides were scanned and analyzed as described at 10 μm resolution with a Genepix 4000B microarray scanner (Molecular Devices) at 350 gain. Image analysis was carried out with Genepix Pro 6.0 analysis software (Molecular Devices). Spots were defined as circular features with a variable radius using with local background subtraction.
Amon R., Ben-Arye S.L., Engler L., Yu H., Lim N., Berre L.L., Harris K.M., Ehlers M.R., Gitelman S.E., Chen X., Soulillou J.P, & Padler-Karavani V. (2017). Glycan microarray reveal induced IgGs repertoire shift against a dietary carbohydrate in response to rabbit anti-human thymocyte therapy. Oncotarget, 8(68), 112236-112244.
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6

Microarray Image Analysis Protocol

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Processed slides were scanned and analyzed as described at 10 μm resolution with a Genepix 4000B microarray scanner (Molecular Devices) at 350 gain. Image analysis was carried out with Genepix Pro 6.0 analysis software (Molecular Devices). Spots were defined as circular features with a variable radius using with local background subtraction.
Bashir S., Leviatan Ben Arye S., Reuven E.M., Yu H., Costa C., Galiñanes M., Bottio T., Chen X, & Padler-Karavani V. (2018). Presentation Mode of Glycans Affect Recognition of Human Serum anti-Neu5Gc IgG Antibodies. Bioconjugate chemistry, 30(1), 161-168.
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7

Microarray Image Analysis Protocol

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Processed slides were scanned and analyzed described4 (link),5 (link) at 10 μm resolution with a Genepix 4000B microarray scanner (Molecular Devices) using 350 gain. Image analysis was carried out with Genepix Pro 6.0 analysis software (Molecular Devices). Spots were defined as circular features with a variable radius as determined by the Genepix scanning software. Local background subtraction was performed.
Shanthamurthy C.D., Jain P., Yehuda S., Monteiro J.T., Leviatan Ben-Arye S., Subramani B., Lepenies B., Padler-Karavani V, & Kikkeri R. (2018). ABO Antigens Active Tri- and Disaccharides Microarray to Evaluate C-type Lectin Receptor Binding Preferences. Scientific Reports, 8, 6603.
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8

Glycan Array Profiling of Monoclonal Antibodies

Cited 1 time
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Abs were assessed for glycan reactivity with amine functional glycans printed onto NHS-activated glass slides as previously described (Shivatare et al., 2016 (link)). Briefly, amine-functionalized glycans were printed in replicates of three onto NHS-activated glass slides at a concentration of 100 mM. Printed slides were allowed to react in an atmosphere of 80% humidity for 2 hour followed by desiccation overnight, and stored at room temperature in a desiccator until use. The slides were blocked with ethanolamine (50mM ethanolamine in borate buffer, pH9.2) just before use. Monoclonal antibodies (10 μg in 50μl PBS) were pre-complexed with R-Phycoerythrin-AffiniPure goat anti-human IgG, Fcγ (5 μg, Jackson Immuno Research Inc.) for 1 hr at 4°C. Thes e samples were added to the glycan array and incubated at 4°C for 6 h. Furt her, the slides were sequentially washed in PBST (0.05% Tween-20), PBS and water. Arrays were scanned on an ArrayWorx microarray reader. Image analysis was carried out with Genepix Pro 6.0 analysis software (Molecular Devices Corporation, Union City, CA) with image resolution set to 5 μm per pixel. The spots were defined as circular features with maximum diameter of 100 μm. The data was recoded as fluorescence intensity (a.u.) for all data points and is represented as average fluorescent intensity with standard deviation.
Andrabi R., Su C.Y., Liang C.H., Shivatare S.S., Briney B., Voss J.E., Nawazi S.K., Wu C.Y., Wong C.H, & Burton D.R. (2017). Glycans function as anchors for antibodies and help drive HIV broadly neutralizing antibody development. Immunity, 47(3), 524-537.e3.
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9

Quantitative Protein Binding Assay

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Processed slides were scanned and analyzed as described at 10 μm resolution with a GenePix 4000B microarray scanner (Molecular Devices) using 350 gain. Image analysis was carried out with GenePix Pro 6.0 analysis software (Molecular Devices). Spots were defined as circular features with a variable radius as determined by the GenePix scanning software. Local background subtraction was performed. Apparent KD was calculated according to non-linear fit with one-site specific binding using GraphPad Prism 8.0.
Amon R., Rosenfeld R., Perlmutter S., Grant O.C., Yehuda S., Borenstein-Katz A., Alcalay R., Marshanski T., Yu H., Diskin R., Woods R.J., Chen X, & Padler-Karavani V. (2020). Directed Evolution of Therapeutic Antibodies Targeting Glycosylation in Cancer. Cancers, 12(10), 2824.
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