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View additional product information for Axiom™ 2.0 Reagent Kit - FAQs (901758)
9 product FAQs found
All human Axiom arrays (except the Axiom Genome-Wide Pan-African Array Set) require a total of 100 ng.
The Axiom Genome-Wide Pan-African Array Set requires a total of 300 ng or 100 ng per array.
Diploid plants and animals require 150 ng per array and polyploid plants and animals require 200 ng per array.
For Axiom Microbiome Arrays, a total of 50 ng of gDNA or 17.5 µL of cDNA reaction + 2.5 µL reduced TE buffer starting material is required per array.
Please refer to the Axiom 2.0 gDNA Sample Preparation Quick Reference for more details. Additionally, you can refer to pages 12-13 of the Axiom 2.0 Assay 96-Array Format Manual Workflow User Guide.
Quality recommendations:
- Starting gDNA must be double-stranded to support accurate concentration determination.
- gDNA must be of high purity.
- DNA should be free of DNA polymerase inhibitors. Examples of inhibitors include high concentrations of heme (from blood) and high concentrations of chelating agents (i.e., EDTA).
- The gDNA extraction/purification method should render DNA that is generally salt-free because high concentrations of particular salts can also inhibit enzyme reactions.
- DNA purity is indicated by OD260/OD280 and OD260/OD230 ratios. The OD260/OD280 ratio should be between 1.8 and 2.0 and the OD260/OD230 ratio should be greater than 1.5.
- DNA must not be degraded.
The approximate average size of gDNA may be assessed on a 1% agarose gel using an appropriate size standard control.
Approximately 90% of the DNA must be greater than 10 Kb in size. Control DNA can be run on the same gel for side-by-side comparison.
We recommend that DNA samples that do not meet these criteria be cleaned up as described under Genomic DNA Cleanup in the Axiom 2.0 Assay 96-Array Format Manual Workflow User Guide, pages 15-17.
Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.
The Axiom 2.0 reagent kits may be stored in a freezer at –25 degrees C to –15 degrees C, or, in a refrigerator at 2 degrees C to 8 degrees C to be used in subsequent experiments for up to 60 days after initial use. We recommend that the reagents should not exceed 3 freeze/thaw cycles.
Enzymes should never be thawed, but rather kept in the freezer -20 degreesC) until use, and then in a -20 degrees C portable cooler.
Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.
In addition to cell line gDNA, the Axiom 2.0 Reagent Kit also supports the following sample types as starting material in the target preparation assay:
- gDNA derived from fresh blood
- gDNA derived from saliva (collected using Oragene® DNA collection kits from DNA Genotek). Please note that this is not the same as a buccal swab, which is not an acceptable source due to bacterial contamination.
- Whole-genome amplified DNA (amplified from gDNA using Qiagen REPLI-g® Kits)
We recommend using Model BD 56 from BINDER (https://www.binder-world.com/us/products/standard-incubators/series-bd-avantgardeline/bd-56). This instrument has been validated for use with Axiom automated assays.
Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.
It is not recommended or supported to genotype Axiom 24 format arrays in the same batch as Axiom 96 arrays, even if they are the same array type.
Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.
The file sizes listed below are per array:
Axiom 96 DAT: 600MB
Axiom 96 CEL: 28MB
Axiom 96 ARR: 6kb
Axiom 96 JPG: 16MB
Axiom 96 AUDIT: 25kb
Axiom 384 DAT: 66 MB
Axiom 384 CEL: 3 MB
Axiom 384 ARR: 6 kb
Axiom 384 JPG: 2MB
Axiom 384 AUDIT: 26kb
Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.
The biggest risk is underestimation of the amount of input gDNA. You should quantify by PicoGreen assay to ensure you are adding the correct amount of starting DNA into the reaction. The contaminating RNA should not affect the assay. If a PicoGreen assay is not an option, you may need to clean up the sample to get a better assessment of the actual amount and quality of gDNA.
Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.
If gDNA preparation is suspected to contain inhibitors, the following cleanup procedure can be used:
1. Add 0.5 volumes of 7.5 M NH4OAc, 2.5 volumes of absolute ethanol (stored at -20 degrees C), to gDNA.
2. Vortex and incubate at -20 degrees C for 1 hr.
3. Centrifuge at 12,000 x g in a microcentrifuge at room temperature for 20 min.
4. Remove supernatant and wash pellet with 80% ethanol.
5. Centrifuge at 12,000 x g at room temperature for 5 min.
6. Remove the 80% ethanol and repeat the 80% ethanol wash one more time.
7. Resuspend the pellet in reduced EDTA TE Buffer (10 mM Tris-HCl pH 8.0, 0.1 mM EDTA).
Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.
Control Oligo B2 (3 nM) is a pre-labeled DNA spike-in control required for hybridization to the control probes on the array utilized for grid alignment by AGCC. A failure to include Control Oligo B2 in the hybridization cocktail will result in the inability of the software to apply a grid over the scanned image, leading to the unrecoverable loss of sample data from the array. The absence of the Control Oligo B2 also voids the customer's ability to submit an array replacement request.
Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.