BioPrime® Total for Agilent® aCGH
 | The BioPrime® Total for Agilent® aCGH system is a complete genomic DNA labeling kit for use in array comparative genomic hybridization applications (aCGH) on the Agilent® aCGH platform. Optimized and validated for the Agilent aCGH workflow, arrays, and scanners.
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Improved call rates and reduced channel bias
This complete, all-inclusive kit is optimized to work across the widest range of sample input material with no need for pre-amplification. Highly concentrated exo-Klenow fragment a component limited reaction allows for consistent, robust DNA yields. Optimized dye labeled nucleotide mix with new dNTP linkers, novel, application-specific Alexa Fluor® 3 and 5 dyes, and improved buffer chemistry reduce labeling variation and increase signal to noise on Agilent® arrays. Excitation and emission spectra of Alexa Fluor® 3 and 5 dyes are suited for Agilent® scanners with no need to change settings.
QC results for the BioPrime® Total for Agilent® aCGH Labeling kit, BioPrime® Total and Agilent Genomic DNA Enzymatic Labeling kit.
| DLRSpread | Signal-To-Noise Green | Signal-To-Noise Red | |
|---|---|---|---|
| BioPrime® Total for Agilent® aCGH | 0.19 ± 0.007 | 162 ± 0.67 | 107 ± 30 |
| BioPrime® Total | 0.195 ± 0.02 | 37 ± 4 | 62 ± 5 |
| Agilent Genomic DNA Enzymatic Labeling Kit | 0.13 ± 0.01 | 39 ± 2.0 | 36 ± 1.44 |
Table 1: QC results for the BioPrime® Total for Agilent® aCGH Labeling kit, BioPrime® Total and Agilent Genomic DNA Enzymatic Labeling kit.
Each labeling reaction started with 1µg of double digested MCF7 and normal breast DNA, and followed the standard conditions per Agilent CGH array recommendations. Labeled reactions using the Agilent Genomic DNA Enzymatic Labeling kit with GE Amersham Cy dyes were purified with Microcon (Millipore). Labeled DNA from BioPrime® Total for Agilent® aCGH Labeling kit and BioPrime® Total was purified using the included Purelink™ purification columns. Array data were collected from Agilent aCGH 4x44K arrays using Agilent array scanner, Feature Extraction and CGH Analytical Software. BioPrime® Total for Agilent® aCGH Labeling kit produced excellent DLRSpread value and higher signal-to-noise ratios. This indicated that the Invitrogen’s new kit had higher efficiency in labeling the DNA samples and that probe-to-probe noise remained low.
Each labeling reaction started with 1µg of double digested MCF7 and normal breast DNA, and followed the standard conditions per Agilent CGH array recommendations. Labeled reactions using the Agilent Genomic DNA Enzymatic Labeling kit with GE Amersham Cy dyes were purified with Microcon (Millipore). Labeled DNA from BioPrime® Total for Agilent® aCGH Labeling kit and BioPrime® Total was purified using the included Purelink™ purification columns. Array data were collected from Agilent aCGH 4x44K arrays using Agilent array scanner, Feature Extraction and CGH Analytical Software. BioPrime® Total for Agilent® aCGH Labeling kit produced excellent DLRSpread value and higher signal-to-noise ratios. This indicated that the Invitrogen’s new kit had higher efficiency in labeling the DNA samples and that probe-to-probe noise remained low.
Eliminate complicated volume-reduction steps
BioPrime® Total for Agilent® aCGH is supplied with Purelink™ purification which allows low elution, eliminating the need for complicated volume-reduction steps. The Purelink™ purification also reduces background due to dye bleed-through found in other purification systems.
Comparing PureLink™ (Invitrogen) and Microcon (Agilent) indicates that the majority of the free nucleotides are removed with PureLink™ purification. In addition PureLink™ also produces more higher molecular weight reaction products. The labeling data (not shown) further indicated that there is no purification bias for labeled and unlabeled nucleotides, as the DOL was not effected by two purification methods.
Comparing PureLink™ (Invitrogen) and Microcon (Agilent) indicates that the majority of the free nucleotides are removed with PureLink™ purification. In addition PureLink™ also produces more higher molecular weight reaction products. The labeling data (not shown) further indicated that there is no purification bias for labeled and unlabeled nucleotides, as the DOL was not effected by two purification methods.
Figure 1. TBE Urea Gel of Labeling Kinetics.
Reaction products were separated by electrophoresis in 6% TBE-Urea gels and visualized on a Typhoon scanner/imager (Applied Biosystems) using the fluorescein channel (MW markers) and Cy/AF channels (labeling reaction products).
Lane 1: Purelink™ Normal Lane 3: Microcon® Normal
Lane 2: Purelink™ MCF7 Lane 4: Microcon® MCF7
Lane 7: Purelink™ Normal Lane 9: Microcon® Normal
Lane 8: Purelink™ MCF7 Lane 10: Microcon® MCF7
Lane 5&6: BioVentures fluorescein labeled Map Marker
Simplified workflow
Convenient master mix formulation streamlines reaction set-ups increasing consistency. Complete kits include Alu I and RSA I and are batch tested to assure quality in performance from lot to lot.
Contains Alexa Fluor® 3 Oligo aCGH 2X reaction mix and Alexa Fluor® 5 Oligo aCGH 2x reaction mix, Exo-Klenow fragment (40 U/µl), 5 mM EDTA, TE Buffer, control DNA (Salmon Sperm), Alu I (10 U/µl), RSA I (10 U/µl). Store at -80°C for long term storage. The 2X Reaction Mixes may be stored at +4°C for up to 4 weeks and should be protected from light. Also contains Purelink™ Genomic DNA purification columns and purification buffers. Store at room temperature. All components are guaranteed for 6 months when properly stored.
Contains Alexa Fluor® 3 Oligo aCGH 2X reaction mix and Alexa Fluor® 5 Oligo aCGH 2x reaction mix, Exo-Klenow fragment (40 U/µl), 5 mM EDTA, TE Buffer, control DNA (Salmon Sperm), Alu I (10 U/µl), RSA I (10 U/µl). Store at -80°C for long term storage. The 2X Reaction Mixes may be stored at +4°C for up to 4 weeks and should be protected from light. Also contains Purelink™ Genomic DNA purification columns and purification buffers. Store at room temperature. All components are guaranteed for 6 months when properly stored.
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Application note
Genomic profiling of human embryonic stem cells by array comparative genomic hybridization (aCGH) using the BioPrime® Total for Agilent® aCGH kit
