GeneTitan™ Wash Buffers A and B Module - FAQs

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.

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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

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

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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).

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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.

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

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

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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.

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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

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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

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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.

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

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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.

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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.

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

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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.

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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.

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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

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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.

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