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Genomic and RNA Profiling Core Facility

Houston, Texas

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Genomic and RNA Profiling Core
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TaqMan Low Density Arrays (TLDA Cards) and Array Fast Plates

TaqMan Low Density Arrays (TLDA Cards) and Array Fast Plates offered through the GARP core enable researchers to rapidly confirm or screen a targeted set of markers in challenging and limited sample inputs, including single cells, biofluids and FFPE samples. Diverse TaqMan chemistry permits the detection of mRNA, miRNA, lncRNA, germline SNPs and somatic mutations, all of which can be analyzed in array format. Coupling pre-amplification to a low-density array format allows high sensitivity and broad dynamic range from low input amounts, making this approach an ideal tool downstream of biomarker discovery from next generation sequencing and microarray studies.

The TaqMan Array functions as an array of reaction vessels for the PCR step. The wells of the TaqMan Array contain pre-loaded Taqman Gene Expression Assays that detect the real-time amplification of user- specified targets. Relative levels of gene expression are determined from the fluorescence data generated during PCR using the Applied Biosystems ViiA7 Real-Time PCR System. TLDA Cards are 384-well format and Array Fast Plates are 96-well fast format (10µL reaction). Life Technologies offers variety of pre-selected gene panel array plates and cards as well as custom plates/cards.

Recommended Total RNA Input Amount
Type Card Format Total RNA Input Minimum Concentration
TLDA Cards 1 sample/384-well (8 ports/sample) 0.8 - 1.6 µg 80 - 1600 ng/µL
2 samples/384-well (4 ports/sample) 0.4 - 0.8 µg 40 - 80 ng/µL
4 samples/384-well (2 ports/sample)
0.2 - 0.4 µg
20 - 40 ng/µL
8 samples/384-well (1 port/sample) 0.1 - 0.2 µg 10 - 20 ng/µL

*Please note, samples with expected low-expression levels for target genes require more total RNA starting input per assay. Expect up to 2.0ug total RNA required for 1-sample array cards (8 ports/sample) or 1-sample Array Fast Plates (96 wells/sample). Alternatively, a dynamic range test may be performed by GARP to determine the lowest input required for a particular project.

Please visit the Life Technologies website for a description of each of the TLDA card formats.

Each TLDA allows for reverse transciption product to be loaded to 8 ports, where the sample is then distributed over 24 wells (12 wells in duplicate). Depending on the TLDA card format, one sample can be loaded to 1-8 ports for distribution over 11-380 genes (plus 1-4 controls). When determining the amount of total RNA to start, estimate no less than 100-200ng total RNA per port. For example, if your card format allows for 63 assays (in triplicate) for two samples per card (i.e. 4 ports per samples), you will need to provide no less than 400-800ng total RNA for prep. A good rule of thumb is to divide the 8 available ports by the number of samples allowed per card. Please note, if the target genes are known to have low expression for your samples, more total RNA will need to be loaded per port. Please estimate up to 2.0 ug per sample for low expressing gene panels. Alternatively, a dynamic range test can be performed by GARP, using 2-4 samples, to determine the minimum total RNA input required for expression quantitation for a project.

Recommended Total RNA Input Amount for miRNA Cards
Card Type Total RNA Input Minimum Concentration
miRNA
TLDA Cards
Type A 1 - 350 ng* 0.3 - 117 ng/µL*
350 - 1000 ng (direct RT) 117 - 333 ng/µL (direct RT)
Type B 1 - 350 ng* 0.3 - 117 ng/µL*
350 - 1000 ng (direct RT) 117 - 333 ng/µL (direct RT)
Type A+B
2 - 700 ng*
0.3 - 117 ng/µL*
700 - 2000 ng (direct RT) 117 - 333 ng/µL (direct RT)

*Pre-Amplification Required

Although a profile can be generated with larger amounts of sample, preamplification is recommended for all samples.

Please note, samples with expected low-expression levels for target genes require more total RNA starting input per assay. Expect up to 2.0ug total RNA required for 1-sample array cards (8 ports/sample) or 1-sample Array Fast Plates (96 wells/sample). Alternatively, a dynamic range test may be performed by GARP to determine the lowest input required for a particular project.

Life Technologies offers miRNA TLDA cards from two species groups, Human or Rodent. Within each species group, there are three types of cards available to order, A, B and A+B. Primer sets specific to the probes loaded to the TLDA card types, A and B, are incorporated into the preamplification or direct reverse transcription reaction steps.

Please visit the Life Technologies website for a complete list of available pre-configured and custom arrays cards. Click here for miRNA array cards.

Recommended Total RNA Input Amount
Type Card Format Total RNA Input Minimum Concentration
Array Fast Plates 1 sample/96-well (96 wells/samples)
0.5 - 2.0 µg
50 - 200 ng/µL
2 samples/96-well (48 wells/sample) 0.25 - 0.5 µg 25 - 50 ng/µL
3 samples/96-well (32 wells/sample) 0.1 - 0.25 µg 10 - 25 ng/µL
6 samples/96-well (16 wells/sample) 0.05 - 0.1 µg 5.0 - 10.0 ng/µL
12 samples/96-well (8 wells/sample) 0.02 - 0.05 µg 2.0 - 5.0 ng/µL

*Please note, samples with expected low-expression levels for target genes require more total RNA starting input per assay. Expect up to 2.0ug total RNA required for 1-sample array cards (8 ports/sample) or 1-sample Array Fast Plates (96 wells/sample). Alternatively, a dynamic range test may be performed by GARP to determine the lowest input required for a particular project.

Please visit the Life Technologies website for a description of each of the Array Fast Plate formats.

Please visit the Life Technologies website for a description of each of the Gene-Specific Arrays.

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