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View additional product information for TaqMan™ Array, Plate 96 - FAQs (4391524)
30 product FAQs found
We recommend that for standard (20 µL) TaqMan Array Plates, you use either the Universal Master Mix (I or II) or the Gene Expression MasterMix. For fast (10 µL) TaqMan Array Plates, use the Fast Universal Master Mix. The Fast Advanced Master Mix can also be used for either plate type, but we recommend following the protocol in this manual (https://assets.thermofisher.com/TFS-Assets/LSG/manuals/MAN0025706_TaqManFastAdvMM_UG.pdf).
We recommend storing TaqMan Array Plates (TAP) at room temperature (15-30 degrees C). TaqMan Array Plates are stable for 2 years from the manufacturing date. The expiration date is listed on the packaging.
Find additional tips, troubleshooting help, and resources within our Real-Time PCR and Digital PCR Instruments Support Center.
By default, custom TaqMan Array plates have FAM as a reporter dye for all the assays on the plate. Therefore, you do not need to change anything on the plate you have designed.
Find additional tips, troubleshooting help, and resources within our TaqMan Primers and Probes Support Center.
The 18s assay (Hs99999901_s1) is a manufacturing control that is added to all TaqMan Custom and TaqMan Flexible Content array plates. It cannot be removed or swapped out for a different assay. Although the 18s assay will detect in all eukaryotic species, we recommend that you determine whether it will be a suitable endogenous control for your experiments. It may be necessary to include 1-2 additional assays to serve as the endogenous control for your experiment. If you want a TaqMan array plate layout that does not include 18s, you can order a TaqMan Specialty array plate using the online Specialty Configurator Tool (https://specialty-taqman-arrays.com).
Yes, once you are in the Custom Array Configurator, you can add any predesigned TaqMan Gene Expression assay you want to the TaqMan Flexible Content panel array plate prior to ordering.
Yes, the Custom Array Configurator will allow you to configure replicate wells on the TaqMan Flexible Content panel array plate. The tool will provide a warning that there are repeats, but once you confirm the layout is correct, the plate layout can be ordered.
The online Custom Assay Configurator will allow you to edit as many target assays on the TaqMan Flexible Content panel array plate as you want to. The manufacturing control is the only assay that cannot be changed. If you want to make changes to the manufacturing control or candidate endogenous controls on the array plate, please use the Specialty Configurator Tool (https://specialty-taqman-arrays.com) to order a Specialty TaqMan array plate.
If you are placing the order, the online Custom Array Configurator allows you to order the preamp pool for the array plate when you finalize your order. On the "Custom Array Summary" page, there is a button to "Add Custom Preamp Pool (Optional)". Click this button before adding the array plates to your cart to order a custom preamp pool for your plates.
If you are reordering the preamp pool for a previous array plate order, you can contact genomicorders@thermofisher.com and provide the sales order number, part number, and lot number for the previous array plate to ensure the correct preamp pool is ordered.
The minimum amount of TaqMan Array plates needed to submit an order is based on the plate type:
• Inventoried TaqMan array plates: 1 plate
• TaqMan Flexible Content panel array plates: 6 plates
• Custom TaqMan array plates: 6 plates
• Specialty TaqMan array plates: 10-20 plates (depends on assay format and configuration). Please contact our Specialty Plates team at Specialty_Plates@thermofisher.com for details.
We recommend using our Plastics Selection Tool to verify which plates are compatible with your instrument model, https://www.thermofisher.com/us/en/home/life-science/pcr/pcr-plastics/plastics-selection-guide.html.
Based on our testing, the 96-well TaqMan Array Plates can be used on the following non-Applied Biosystem real-time PCR instruments:
• Standard (0.2mL) 96-well Plates: Bio-Rad IQ5
• Fast (0.1mL) Plates: Bio-Rad CFX Connect and Bio-Rad CFX96 Touch
Custom TaqMan Array Plates allow you to choose from any of our predesigned TaqMan Gene Expression Assays to configure your panel from scratch. They are only available in Standard 96-well or Fast 96-well plate formats, and there are 9 different layouts to select from.
Specialty TaqMan Array Plates allow you to expand your selection outside of our predesigned TaqMan Gene Expression Assays. They are available in Standard 96-well, Fast 96-well, and 384-well plate formats. If you want to configure a panel that contains the following assay types or custom plate layouts, we recommend ordering a Specialty TaqMan Array Plate:
• Custom TaqMan assays
• Predesigned TaqMan SNP Genotyping assays, TaqMan Copy Number assays, TaqMan miRNA assays (Classic or Advanced), and TaqMan Mutation Detection assays
• TaqMan assays manufactured by our Specialty Oligos group (e.g. Assays with nonstandard oligo concentrations, assays with extra oligos, assays with TAMRA or QSY probes, assays with oligos containing degenerate nucleotides)
• Duplexed TaqMan assays
• A combination of TaqMan assay types on one plate (i.e., TaqMan SNP Genotyping assays and TaqMan Gene Expression assays)
• A predesigned TaqMan Array Plate layout without the manufacturing control
• A plate layout that is not supported by the Custom Array Configurator for Custom TaqMan Array Plates
Beginning in April 2016, TaqMan documentation files for TaqMan Array Plates (assay information files (AIF), experimental setup files, and plate layout files) can be downloaded from the Thermo Fisher Scientific website at https://www.thermofisher.com/taqmanfiles. To obtain your TaqMan documentation files:
• Select the appropriate product type.
• Enter the information being requested for the product type.
• Fixed TaqMan array plates: Enter the Part number and Batch number
• TaqMan Flexible Content panel array plates/Custom TaqMan array plates: Enter the Sales Order number and Batch number
• Click Submit.
Please review the following possible causes and solutions:
-The sample evaporated. Check the seal of the adhesive film for leaks.
- The well is empty because of inaccurate pipetting. Check the calibration of the pipettes, and pipette at least 5 µL of sample.
- The well is assigned a sample or target in the plate document or experiment, but the well is empty. Ensure that the plate document or experiment is set up correctly. Then try excluding the well and reanalyzing the data.
A small ΔRn can mean that the PCR efficiency was poor. Ensure that the reagents were used at the correct concentration. Alternatively, the quantity of the cDNA may be low (a low copy number of the target). In this case, we recommend that you increase the quantity of the cDNA in the reaction.
Most likely fluorescence did not stabilize to the buffer conditions of the reaction mix.
Note: This condition does not affect PCR or the final results.
We recommend that you try the following:
- Reset the lower value of the baseline range.
- Use an automatic baseline.
- Use the relative threshold algorithm (Crt). See Introduction to Gene Expression Getting Started Guide (Pub. No. 4454239).
Please review the following possible causes and solutions:
- The reagents were not mixed properly. We suggest increasing the length of time that you mix the reagents and confirming your mixing process by running a replicate assay.
- Pipetting was inaccurate. We recommend that you check the pipette calibration, and pipette at least 5 µL of sample to prepare the reaction mix.
- The threshold was not set correctly. Set the threshold above the noise level and where the replicates are tightest. Please see your real‑time PCR system user documentation for more information about setting the threshold.
- There was a low concentration of the target of interest. Rerun the assay with more cDNA template.
Please review the following possible causes and solutions:
- The endogenous control is not consistently expressed across the samples. Please ensure that the endogenous control is consistently expressed in your sample type.
- The sample concentrations vary. We recommend that you quantify and normalize the PCR samples before running the assay.
- Pipetting was inaccurate. We recommend that you check the pipette calibration, and pipet at least 5 µL of sample to prepare the reaction mix.
Most likely the reagents are contaminated with gDNA, amplicon or plasmid clones. We recommend that you clean your workspace and equipment, then rerun the assay using new reagents. We also recommend that you run no-RT controls to rule out genomic DNA contamination, and treat the sample with DNase.
Most likely the ROX dye was not set as the passive reference. Set ROX dye as the passive reference, then reanalyze the data.
Most likely incorrect dyes were selected for each target. We suggest checking the dyes selected for each target, then reanalyzing the data.
The sample evaporated. We recommend that you check the seal of the adhesive film for leaks before running the plate on the real-time PCR instrument.
It is possible that there was precipitation in the buffers. Before preapring reactions, we recommend that you mix the Master Mix thoroughly to produce a homogenous solution.
It as also possible that the reagents have degraded. Ensure that the kits and reagents have been stored according to the instructions on the packaging and that they have not expired.
Please review the following possible causes and solutions:
- The gene is not expressed in the sample. First, confirm that the gene is expressed in the sample type or tissue type at ncbi.nlm.nih.gov/unigene. If the gene is expressed, confirm the results by rerunning the sample using the same assay and/or rerunning the experiment using more of the sample. Avoid preparing PCR reaction mixes with more than 20% reverse transcription reaction. You can also run the experiment using an alternative assay, if available, that detects a different transcript or more than one transcript from the same gene.
Note: If the recommended actions do not resolve the problem, the result may be correct.
- The sample does not have enough copies of the target RNA. To confirm the results, we suggest rerunning the sample using the same assay and/or rerunning the assay using more of the sample. Avoid PCR reaction mix with more than 20% from the reverse transcription reaction.
Note: If the recommended actions do not resolve the problem, the result may be correct.
- One or more of the reaction components was not added. Please check your pipetting equipment and/or technique.
- Incorrect dyes were selected for each target. We recommend checking the dyes selected for each target, then reanalyze the data.
Please review the following possible causes and solutions:
- The baseline was set improperly. See your real‑time PCR system user guide for procedures on setting the baseline. We recommend switching from an automatic baseline to a manual baseline (or vice versa) and/or increasing the upper or lower value of the baseline range.
- The sample quality was poor. We recommend performing a quality check on the sample, then re-extracting the sample if needed.
- There were different concentrations caused my imprecise pipetting. Please follow accurate pipetting practices.
- The reagents or equipment are contaminated. Please ensure that your workspace and equipment are cleaned properly.
Most likely little or no MasterMix is present in the reaction due to inaccurate pipetting. Please follow accurate pipetting practices when setting up reactions.
Please review the following possible causes and solutions:
- The baseline was set too high and some samples have Ct values lower than the baseline stop value. We recommend that you switch from manual to automatic baselining, or move the baseline stop value to a lower Ct. The baseline stop value should be set to a Ct 2 cycles before the amplification curve crosses the threshold. Please see your real‑time PCR system user guide for procedures on setting the baseline.
-No baseline can be set because the amplification signal is detected too early in the PCR cycles. Diluting the sample can increase the Ct value.
The dried-down assays on the TaqMan Array Plate were reconstituted at different rates, causing a dip in the early cycles of the baseline. We recommend that you use the relative threshold algorithm (Crt), which may correct for a variable baseline. If your instrument does not have the relative threshold algorithm, you can use the Relative Quantification app on Thermo Fisher Connect.
Please review the following possible causes and solutions:
-Genomic DNA (gDNA) contamination occured. We recommend that you improve sample extraction methods and use DNase to ensure minimal gDNA contamination of the RNA.
For custom assays, we recommend that you design an assay that spans an exon-exon boundary. Please see the Custom TaqMan Assays Design and Ordering Guide (Pub. No. 4367671).
- The cDNA template or amplicon is contaminated. In this case, please follow established PCR good laboratory practices.
Please review the following possible causes and solutions:
- Contamination occurred. We recommend that you run a no-RT control to confirm that there was genomic DNA (gDNA) contamination. We also recommend the use DNase to ensure minimal gDNA contamination of the RNA.
For custom assays, we recommend that you design an assay that spans an exon-exon boundary. Please see the Custom TaqMan Assays Design and Ordering Guide (Pub. No. 4367671).
- Too much cDNA template was added to the reaction. We recommend that you quantitate the RNA before the reverse transcription (RT) reaction. After the RT reaction, adjust the concentration of cDNA before adding it to the reaction.
- The cDNA template or the amplicon is contaminated. Follow established PCR good laboratory practices.
Please review the following possible causes and solutions:
- One or more of the reaction components was not added. Ensure that the cDNA, the assay and the Master Mix were added to the reaction plate. The passive reference fails if the Master Mix is missing.
- Incorrect dyes were selected for each target. Check the dyes selected for each target, then reanalyze the data.
- The annealing temperature was too high for the primers and/or probe. Ensure that the correct annealing and extension temperatures are set, and that the real-time PCR instrument is calibrated and maintained regularly.
- Inappropriate reaction conditions were used. Ensure that the properties and the thermal protocol are correct, then troubleshoot the real-time PCR optimization.
- The template is degraded. Determine the quality of the template, then rerun the assay with fresh template if needed. We recommend that you use use RNase-free reagents and an RNase inhibitor.
- Inhibitors are present in the reaction. To check for inhibitors, we recommend that you run a serial dilution of your sample with an expressing assay (for example, an endogenous control). If an inhibitor is present, the high concentration samples yield higher-than-expected Ct values because the samples are not diluted.
- The baseline and/or threshold was improperly set. See your real-time PCR system user guide for procedures on setting the baseline and threshold. Some possible solutions to this issue are switching from an automatic baseline to a manual baseline (or vice versa), and/or lowering the threshold value to fall within the appropriate range.
- The reverse transcription failed. We recommend checking the RNA integrity and concentration, checking for RNase activity, following the recommended thermal profile, and/or repeating the reverse transcription using new reagents.
- (Custom TaqManGene Expression Assays only) The design or synthesis of the custom assay failed. Ensure that the sequence you submitted is correct. We also recomend that you check for an alternative trascript or splice variant.
- (Custom TaqManGene Expression Assays only) The assay is designed in a variable regions of the gene transccript. Ensure that the location that is targeted by the assay is not within the 5' untranslated region (UTR), which can be highly variable
between transcripts. If the assay is designed within the 5' UTR, we recommend that you select a different assay that is within the coding region of the transcript. Otherwise, select an assay for an alternative transcriptor splice variant.