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Product FAQ

Why does the protocol state to prepare a fragmentation master mix enough for 24 samples even if a smaller number of samples is processed?

Answer

It is critical to have correct size of the fragments for an optimal hybridization. The fragmentation reagent is very viscous and it is easier to get a correct proportion of enzyme when a larger volume is used. The recommendation is to always prepare a master mix for 24 samples even if a smaller number of samples are processed.

Answer Id: E14278

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Product FAQ

Can I perform the GeneChip Globin-Reduction kit protocol with less than 5 µg after concentration total RNA starting material?

Answer

The globin reduction method is optimized for use with 5 µg of total blood RNA. Starting with less than 5 µg is possible, but will lead to lower cRNA yields potentially leaving the user with insufficient material for hybridization.

Answer Id: E13487

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Product FAQ

What quality metrics can I examine to determine if dim or bright hybridizations have impacted my data?

Answer

Use either All_mean or PM mean to assay for hybridization intensity. All_mean is a probe-set metric. PM_mean is a probe-level metric, and is the mean of perfect match raw intensities prior to any transformations, such as normalization or probe summarization. PM_mean and All_mean can be compared to understand the effect that data processing steps have on the average intensity of an array because All_mean has been subject to any data transformations that have been performed during signal estimation and normalization. Apparent outliers only based on PM_mean can be ignored when corrected through data normalization in All_mean.

Answer Id: E14026

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Product FAQ

I have observed on occasion that multiple _at probe sets are mapped to the same gene but give different expression results. How do I reconcile the difference?

Answer

There are various reasons why this happens. With increasing knowledge of the genome, the unique probe sets (_at probe sets) that were initially designed may turn out to represent subclusters that have collapsed into a single cluster in a later design. Therefore, it may seem that multiple "unique" _at probe sets now correspond to a single gene. Different results from the probe sets could be observed due to the following reasons:

-They represent splice variants or may cross-hybridize to different members that belong to a highly similar gene family or transcripts with different poly-A sites.
-One probe set is more 5' than the other
-One probe set is better designed than the other

In these cases, it is important to use the resources available on the NetAffx Analysis Center to understand if any of the above scenarios apply. Other expression analysis techniques may also be used to confirm which probe set reflects the transcript level more accurately.

Answer Id: E13596

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Product FAQ

What are the fill volumes of the reagents in the CytoScan Reagent Kit?

Answer

We can only guarantee the volume that is indicated on the label. Since our assurance guarantee is only provided for the label volume we advise not planning experiments or standard operating procedures based on potential overage volumes.

Answer Id: E14192

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Product FAQ

What is the difference between the BLAST algorithm and the alignment algorithm used by the Probe Match tool?

Answer

Alignments by the Probe Match tool produce positive results only if every base in a probe sequence matches perfectly (that is, the aligned bases are identical) with those in the query (input) sequence without any gaps in the query sequence. This algorithm is different from the BLAST algorithm, because the BLAST algorithm allows mismatches and gaps within the query sequence to produce a positive alignment.

Answer Id: E13637

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Product FAQ

Can I track the samples that I have uploaded in the database?

Answer

If an xxCHP file has been previously published to the database, you will receive a warning indicating this sample already exists in the database. You can choose to overwrite the existing information or cancel to keep the existing information. It is important to back up and archive the ARR, CEL, CYCHP, and CHPCAR files at a minimum. This will allow you to maintain the ability to either reanalyze from the CEL file or revisualize the results using the CYCHP/CHPCAR files.

Answer Id: E13886

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Product FAQ

How do I know if my GeneChip Scanner 3000 has been enabled for high-resolution scanning that is needed for the HG-U133 2.0 Arrays?

Answer

a. GeneChip Scanner 3000 that were shipped after September 15, 2003 with serial number 502xxxxx are enabled for high-resolution scanning.

b. GeneChip Scanner 3000 that were shipped prior to September 15, 2003 with serial number 501xxxxx that have had the GeneChip Scanner 3000 High-Resolution Update installed by an instrument service engineer are enabled for high-resolution scanning. A sticker is applied to the rear of the scanner to indicate that the upgrade has been performed.

c. Contact 888 DNA-CHIP or your local Affymetrix technical support to inquire about a scanner upgrade.

Answer Id: E13777

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Product FAQ

What were the steps in designing the Axiom Genome-Wide BOS 1 Array?

Answer

We obtained information for more than 46 million SNPs from sequencing efforts coordinated by the Affymetrix Bovine Consortium (basic and applied researchers in the bovine community). From these, we selected SNPs to use based on physical coverage of the bovine genome and the number of breeds in which the SNPs were observed.

We then screened many millions of SNPs against approximately 400 samples from the Affymetrix Bovine Consortium and bovine HapMap samples (Texas A&M University). The result is a database of ~3 million validated SNPs, which means each has been demonstrated as a real, truly polymorphic SNP and has been proven to work in the assay. This implies that customers should be able to select SNPs from our database and create their own custom array, and that the SNPs chosen should perform at a very high level in the assay.

Finally, we selected a subset of more than 648,000 SNPs primarily based on genetic coverage for a selection of breeds and secondarily based on physical coverage of the bovine genome.

Answer Id: E14032

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Product FAQ

What is the HapMap concordance of genotyping calls?

Answer

The HapMap concordance of genotyping calls is greater than 99%.

Answer Id: E13855

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Product FAQ

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

Answer

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

Answer Id: E14134

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Product FAQ

In miRNA QC tool, is the Detection (True/False) based on the P-value, and does True mean Present?

Answer

Yes, the detection is based on the p-value. True does mean present, relative to the p- value.

For example: if a miR has low signal and high p-value, it will probably be FALSE. But if a miR has low signal (but still above background) and low p-value, it might be TRUE. Refer to the miRNA QC Tool User's Guide for more detail.

Answer Id: E14084

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Product FAQ

What is DABG, PLIER?

Answer

DABG stands for "detection above background" and is a detection metric generated by comparing Perfect Match probes to a distribution of background probes. This comparison yields a p-value which is then combined into a probe set level p-value using the Fischer equation. PLIER stands for "Probe Logarithmic Intensity Error" and is a model-based signal estimator which benefits from multi-array analysis.

For more information on DABG, see the
"Exon Array Background Correction" (https://tools.thermofisher.com/content/sfs/brochures/exon_background_correction_whitepaper.pdf) white paper; for more information on PLIER, refer to the PLIER Technical Note. (https://tools.thermofisher.com/content/sfs/brochures/plier_technote.pdf)

Answer Id: E13534

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Product FAQ

How can you tell the difference between a silver and aluminum thermal cycler block?

Answer

Look at the serial number on the block. An “A” in the serial number indicates the block is aluminum; an “S” indicates it is silver. Also, an aluminum block has a honeycomb appearance between the wells, whereas a silver block is smooth.

Answer Id: E13899

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Product FAQ

Do the Affymetrix miRNA Arrays require pre-hybridization?

Answer

No.

Answer Id: E14069

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