GeneTitan™ miRNA Array Holding Buffer - FAQs

View additional product information for GeneTitan™ miRNA Array Holding Buffer - FAQs (901582)

20 product FAQs found

How long can I store my GeneChip miRNA 3.1 Array Strip after wash/stain, but before scanning?

The array strip may be stored at 4 degrees C in GeneTitan miRNA Array Holding Buffer (Cat. No. 901582) for up to 24 hours prior to scanning with negligible impact on data. Please equilibrate the array strip to room temperature before scanning.

Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.

What signal and fold-change concordance can I expect between Affymetrix miRNA 4.0 and miRNA 4.1 Arrays and miRNA 3.0 and miRNA 3.1 Arrays?

You should expect high signal and fold-change concordance for transcripts with identical probes on the miRNA 4.0 and miRNA 4.1 Arrays and the miRNA 3.0 and miRNA 3.1 Arrays. The snoRNA, scaRNA, and precursor miRNA probe sets were reselected, and for some probe sets in these categories, the probes are not identical between the two array designs. Because the probes selected may be different, one may observe changes in the probe set signal summary for a given target. This is possible as different probe sequences will have varying affinity to the target and may show a higher or lower absolute probe signal depending on the GC content of the probes. However, fold changes are typically well-correlated to the legacy probe set unless there is cross-hybridization in the legacy probe set. Our expectation is that more unique and specific probes result in more specific hybridization to the intended target, and therefore a better performing probe set. Target preparation replicates of human brain and lung samples were pooled and hybridized to four miRNA 3.0 Arrays and four miRNA 4.0 Arrays. The Pearson product moment correlation was calculated from the median signal of matched probe sets and from the median fold change of detected matched probe sets on the miRNA 3.0 Array compared to the miRNA 4.0 Array. Probe sets were defined as detected if the median DABG p-value of the four miRNA 3.0 Array brain replicates was less than 0.06. Two subsets of matched probe sets were used for miRNA 3.0 Array to miRNA 4.0 Array signal and fold change correlation: All human probe sets including those that do not necessarily share identical probe sequences and human probe sets for which the probe sequences are identical on both the miRNA 3.0 and miRNA 4.0 Arrays.

Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.

Do we have to use any Affymetrix Reagents with our assay?

GeneChip Hybridization Control Kit 30 reactions
GeneTitan Hybridization, Wash, and Stain Kit for miRNA Array Plates 96 reactions
GeneTitan Hybridization Module for miRNA Plates 96 reactions
Affymetrix FlashTag Biotin HSR RNA Labeling Kit 10 reactions
Affymetrix FlashTag Biotin HSR RNA Labeling Kit 30 reactions

Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.

What kind of dynamic range can I expect from Affymetrix miRNA Array Plates?

Affymetrix miRNA Array Plate provides a similar dynamic range to GeneChip miRNA Array.

Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.

How do results from GeneChip miRNA Cartridge Array compare to Affymetrix miRNA Array Plates?

When evaluating non-control probe sets in common to both arrays, we observed very high signal and fold-change correlation for GeneChip miRNA Cartridge Arrays compared to Affymetrix miRNA Array Plates (Pearson correlation coefficients of 0.97-0.98 for signal correlation and Pearson correlation coefficients of 0.96-0.98 for fold-change correlation).

Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.

What is the tolerance around hybridization time when working with Affymetrix miRNA Array strips?

We recommend maintaining consistency in array processing protocols to minimize introduction of variability. Our recommended hybridization time for Thermo Fisher Scientific miRNA Array Strip is 20 hrs.

Thermo Fisher Scientific miRNA Array Strip should be hybridized no less than 20 hrs and no longer than 24 hrs. We strongly encourage maintaining consistent hybridization times to avoid false positives with respect to differential expression due to hybridization time.

Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.

Where can I get a list of miRNAs represented on Thermo Fisher Scientific miRNA Arrays?

You can get the list by downloading the annotation files that will be available on the website.

Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.

What are the proper storage conditions for Thermo Fisher Scientific miRNA Arrays?

The arrays should be stored at 2-8 degrees C.

Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.

What is the shelf life for Thermofisher Scientific miRNA Arrays?

This product has 12 months of shelf life with a minimum shelf life of 3 months. Minimum shelf life is defined as the minimum amount of time from date of order shipment to array expiration date. If users receive products with shorter than expected minimum shelf life, we will replace the products at no cost to the user-subject to terms and conditions.

Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.

What is the recommended temperature for hybridization for Thermo Fisher Scientific  miRNA Arrays?

The following hybridization temperatures should be used with each version of ThermoFisher Scientific miRNA Array:

- GeneChip miRNA Arrays 48 degrees C

- Thermo Fisher Scientific miRNA Array Plates 48 degrees C

- Thermo Fisher Scientific miRNA Array Strips 48 degrees C

Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.

Which fluidics script is required with GeneChip miRNA Array?

The following fluidics scripts should be used with each version of GeneChip miRNA Array:

- GeneChip miRNA Array FS450_0003
- GeneChip miRNA 2.0 Array FS450_0003
- GeneChip miRNA 3.0 Array FS450_0002
- GeneChip miRNA 4.0 Array FS450_0002

Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.

What data analysis software solutions are offered?

We provideTranscriptome Analysis Console Software for normalization, summarization,  differential expression analysis and visualization free of charge. Due to the presence of multiple organisms on the miRNA arrays, the chromosomal location feature in Transcriptome Analysis Console Software will not give accurate results.

For analysis in Transcriptome Analysis Console Software, array type-specific configuration and annotation files are required. Use the “Download Array Type Files” button in the Preferences tab to download and install array type-specific library files.

Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.

Where can I find the library files for Affymetrix miRNA Arrays ?

Access the library files on www.thermofisher.com/us/en/home/life-science/microarray-analysis/microarray-data-analysis/genechip-array-library-files.html.

Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.

Why do I need to use GeneChip 20X Hybridization Controls?

The Hybridization Controls are high-quality controls for monitoring array hybridization, washing, and staining for reproducible results.

20X Hybridization Controls are composed of a mixture of biotinylated and fragmented cRNA of bioB, bioC, and bioD from E. coli and cre from P1 bacteriophage in staggered concentrations. The premixed controls are ready to be added directly to the hybridization cocktail. Probes for detecting these controls are present on GeneChip miRNA Array, ThermoFisher Scientific miRNA Array Strip, and Thermofisher Scientific miRNA Array Plate.

The 20X Hybridization Controls are spiked into the hybridization cocktail, independent of RNA sample preparation, and are thus used to evaluate sample hybridization efficiency on eukaryotic gene expression arrays. As the 20X Hybridization Controls are used to troubleshoot potential array and array processing issues, a failure to include the 20X Hybridization Controls in the hybridization cocktail will void the customer's ability to submit an array replacement request.

Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.

Can I use the human, mouse, and rat .ps files to limit my data output in Partek Express and Partek Genomics Suite?

No, Partek Express and Partek Genomics Suite do not use the .ps file when analyzing data. We will notify you when this has been resolved.

Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.

Can I analyze my Affymetrix miRNA Array Strip data using Partek Express?

Yes, Partek Express version 1.12.1121 supports the analysis of miRNA Array Strips.

Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.

Why do your miRNA Array Strips and miRNA Array Plates have different hybridization, wash, and stain kits compared to your 3' IVT Array Strips and 3' IVT Array Plates and Gene ST Array Strips and Gene ST Array Plates?

IMPORTANT: The hybridization, wash, and stain protocol for Affymetrix miRNA Array Strips and Array Plates is different from the 3' IVT and the Gene ST Array Strips and Array Plates protocols. Additional reagents have been added to these kits to help ensure adequate washing after the stain has been introduced to the array.

Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.

Which assay do you recommend for use with Affymetrix GeneChip miRNA Arrays?

Affymetrix only supports use of the Affymetrix FlashTag Biotin HSR RNA Labeling Kit for preparing targets to be applied to GeneChip miRNA Array, Affymetrix miRNA Array Strip, and Affymetrix miRNA Array Plate. This product may be ordered through Affymetrix using Cat. No.s 901910 for the 10- reaction kit and 901911 for the 30-reaction kit.

Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.

Why are there more data headers and columns in my miRNA 4.0/4.1 or newer annotation files?

The miRNA 4.0/4.1 annotations contain additional data fields to help ease the integration and correlation of small non-coding RNA data contained on Affymetrix miRNA 4.0 and 4.1 Arrays (and newer) with the content from our other expression products such as GeneChip Human Genome U133 Plus 2.0 Array, GeneChip Human Gene 2.0 ST Array, and GeneChip Human Transcriptome Array 2.0. These additional fields include:

- Genomic context (where the miRNA is located in the genome)
- Clustered miRNA (miRNA that are located 10 KB from one another)
- Predicted miRNA targets
- Validated miRNA targets

Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.

Why can I not see the miRBase identifier for probe sets in Affymetrix Expression Console Software charts and graphs?

We have changed the naming convention for probe sets on our miRNA arrays to be consistent with other array designs. Probe set IDs on Affymetrix miRNA 4.0 and 4.1 Arrays (and newer) will be a unique number. The probe set name will have the accession number and an Affymetrix suffix (e.g., “_st”). While the transcript ID is no longer contained in the probe set name, it is included in the annotation file.

Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.