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Product FAQ

What are the GeneChip Operating Software (GCOS) and GCOS Server Software (GCOS Server) products?

Answer

The GeneChip Operating Software (GCOS) is an operating system software that controls our instruments, acquires data, and executes gene expression analysis. In addition, GCOS contains an embedded database that manages both experiment information and data. Stratagene Array Assist Lite, Affymetrix GeneChip Sequence Analysis Software (GSEQ), Affymetrix GeneChip Genotyping Analysis Software (GTYPE), Affymetrix GeneChip Targeted Genotyping Analysis Software (GTGS) use data from the GCOS Database for gene expression cluster/statistical analysis, sequencing analysis and genotyping data analysis, respectively.

GCOS desktop version (client) can be conveniently upgraded to GCOS Server. With GCOS Server, customers benefit from increased systems flexibility, streamlined user interface integration, enhanced automation, and robust data handling and security. Using either an Oracle or SQL based server, researchers can perform a variety of data management tasks and data queries. Plus, extensive security features are available to allow users secure access to their data.

Answer Id: E13556

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Product FAQ

Can PCR plates and thermal cyclers be used for the incubation steps in FlashTag HSR labeling?

Answer

Yes.

Answer Id: E14066

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Product FAQ

When should data analyzed with RMA be re-analyzed using SST-RMA?

Answer

You should re-analyze your data if comparing with RT-PCR or RNA-Seq data using fold change values for filtering.

Answer Id: E14024

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Product FAQ

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

Answer

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

Answer Id: E14132

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Product FAQ

Are there any specific concerns for running FlashTag HSR labeling?

Answer

All materials (tubes, tips, etc.) should be nuclease-free, and all reagents should be prepared with nuclease-free components.

Answer Id: E14067

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Product FAQ

How were the 900 genes that are cancer-related chosen for the OncoScan Arrays?

Answer

Key opinion leaders in the Oncology field as well as papers were consulted when choosing the 900 cancer-related genes for the array.

Answer Id: E14277

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Product FAQ

What are the positive and negative controls?

Answer

Positive controls are probe sets designed against putative exons of about 100 housekeeping genes shown to be expressed at detectable levels across a variety of tissues. Since the extent of alternative splicing and transcript expression is not known for all tissues, not all exons are expected to be expressed in all tissues.

Negative controls are putative introns of the same 100 housekeeping genes chosen for positive controls. These probe sets may be expressed in certain tissues through intron retention. They are not true negative controls. Overall, the positive and negative control probe sets provide a medium-size dataset with expected high and low signal values, respectively. This data set is useful to estimate overall data quality though the Pos_vs_neg_auc value.

Answer Id: E14025

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Product FAQ

What is the basic component in the DNA Labeling Reagent?

Answer

The key labeling molecule in the DNA Labeling Reagent is Biotin Allonamide Triphosphate.

Answer Id: E14191

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Product FAQ

What are the instrumentation and software requirements for Human Genome U133 Plus 2.0 Array?

Answer

For array hybridization, washing, staining and scanning, the following instrumentation is required:

-GeneChip Scanner 3000 7G
-GeneChip Fluidics Station 450
-GeneChip Hybridization Oven 640

Data acquisition and analysis of Human Genome U133 Plus 2.0 Arrays requires the following software:

-GeneChip Command Console Software
-Expression Console Software

Answer Id: E13776

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Product FAQ

How many SNPs are tiled on the Axiom Genome-Wide BOS 1 Array?

Answer

Approximately 648,000 SNPs are tiled on the array.

Answer Id: E14031

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Product FAQ

What is the dynamic range of OncoScan CNV & Oncoscan CNV Plus Assay Kit?

Answer

OncoScan CNV & Oncoscan CNV Plus Assay Kit can detect copy number changes up to 50 copies. As the number of copies increases, the user should bin the calls. For example, copy numbers of 20-50 should be considered as one bin. The recommended bins are: 0, 1, 2, 3, 4, 5-6, 7-10, 11-20, 20-50.

Answer Id: E13854

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Product FAQ

What is the shelf life for Thermofisher Scientific miRNA Arrays?

Answer

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.

Answer Id: E14133

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Product FAQ

What can I do to reduce the analysis time required to generate probe set level signal when working with GeneChip Exon Arrays?

Answer

Two primary factors can affect the length of analysis time: 1) the number of arrays analyzed at one time, and 2) the number of probe sets to be included in the analysis. Reducing the size of either one of these two factors will increase the analysis speed.

Answer Id: E13533

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Product FAQ

What thermal cycler can be used for the CytoScan Assay?

Answer

The ABI 9700 (silver or gold-plated silver block only; do not use an aluminum block) and the ABI 2720 (pre-PCR room only) thermal cyclers have been validated for the CytoScan Assay.

Answer Id: E13898

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Product FAQ

Can I label my samples in advance and hybridize arrays later?

Answer

Yes, store at -20 degrees C for up to two weeks.

Answer Id: E14068

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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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Product FAQ

What is the maximum number of freeze/thaw cycles recommended for the CytoScan Reagent kit?

Answer

The CytoScan Reagent kit has been validated for less than or equal to 5 freeze/thaw cycles.

Answer Id: E14279

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Product FAQ

What is the difference between GeneChip miRNA 4.0 Cartridge Array, miRNA 4.1 Array Strip, and Affymetrix miRNA 4.1 Array Plate?

Answer

The arrays have the exact same design and contain the same number of probes and probe sets.

Answer Id: E14120

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Product FAQ

What procedure is used to generate the genome alignment data?

Answer

Genome alignments are currently provided for Human/Mouse/Rat/Drosophila/C elegans arrays. We align the target sequences against the genome sequence downloaded from the UCSC website using BLAT. While some of the target sequences do not align, perhaps due to the draft nature of several genomes, some targets align at multiple locations on the genome. We apply a filter to select the best hit for each target sequence.
We use the following procedure:

Calculate a score for each alignment as follows:

score=matches - (mismatches+5*qbaseinsert)
where matches = number of bases that match (including both repeat and non-repeat regions)
mismatches = number of bases that do not match in the alignment
qbaseinsert = number of bases inserted in the query

It is therefore possible that some of the scores are negative.

Pcgood=score*100/target size

The pcgood metric is provided on the website and in the download files.

Select the alignment with the best score.

Derive genomic coordinates for the probes (25-mers) from the "best" target sequence alignment.

We use the genomic coordinates for each probe (25-mer) from above and search for transcripts (RefSeq and GenBank mRNA alignments to the genome from UCSC genome database) that overlap with the alignment of the probes. In the NetAffx summary report, we provide the transcript whose genomic alignment overlaps with the maximum number of probes from that particular probe set. We also provide the total number of probes from the probe set that overlap with the transcript as measure of the ability of the probe set to detect the corresponding transcript.

Answer Id: E13479

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Product FAQ

How many SNP and CN probes are included on CytoScan Optima Array?

Answer

CytoScan Optima Array has a total of 315,608 features covering control, CN, and SNP probes. There are a total of 18,018 non polymorphic CN probes and 148,450 SNP markers on the Optima Suite.

Answer Id: E13840

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Product FAQ

How can I test if blocking of cDNA synthesis is specific for globin mRNA transcripts isolated using the GeneChip Globin-Reduction Kit?

Answer

The specificity of the method can be tested by using the GeneChip Globin Reduction RNA Controls kit which contains two control samples, Jurkat RNA and Jurkat RNA + Globin RNA. These controls mimic blood RNA samples not affected by excess globin message (for example, an erythrocyte lysis fractionation method) and affected by excess globin (for example, a PAXgene blood RNA sample) respectively. Besides providing additional possibilities for validation of the globin reduction procedure, target preparation starting from Jurkat RNA (which is free of globin transcripts) can be performed with and without integrated globin reduction.

Thus, specificity can be confirmed by comparing the expression profiles obtained from each sample. If non-globin transcripts are unaffected by the globin reduction procedure, no significant differences in the expression profiles derived is expected. For more information on the GeneChip Globin Reduction RNA Controls kit, please refer to the GeneChip Globin-Reduction Kit handbook (http://media.affymetrix.com/support/downloads/manuals/globin_reduction_protocol_manual.pdf).

Answer Id: E13488

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Product FAQ

What has been used as reference RNA for FlashTag labeling?

Answer

Ambion FirstChoice Total RNA samples have been used as reference RNA.

Answer Id: E14057

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Product FAQ

Why is the bgrd_mean (background) value sometimes higher than that of PM_mean (signal)?

Answer

The mean of the background probe signal values is based on background probes defined in the background probe file, which are by default the anti-genomic probes. Anti-genomic probes consist of about 1,000 probes for each level of GC content (0 to 25) with no homology to most studied organisms. This set has a higher GC content than the average probe on the array, and therefore can have relatively higher signal values than the mean of all probes (PM_mean).

Answer Id: E14027

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Product FAQ

When performing the CytoScan Assay, what can cause faint or absent bands on the PCR gel?

Answer

Several things can cause this problem. To troubleshoot this problem, first determine if the positive control worked properly. Common reasons for this failure include incomplete digestion of genomic DNA or inefficient ligation of adaptors, ligation samples that are not properly diluted or mixed, and degraded DNA (if only the positive control worked). See the troubleshooting section of the CytoScan Assay User Manual (Cat. No. 703038) for more information

Answer Id: E13966

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Product FAQ

What are the 10 CytoScan assay processing steps listed in order?

Answer

The 10 assay processing steps, as listed in the CytoScan Assay User Manual (Cat. No. 703038) are the following:

1. Genomic DNA Preparation
2. NSP1 Restriction Enzyme Digestion
3. Ligation
4. PCR
5. PCR Product Purification
6. Quantitation
7. Fragmentation
8. Labeling
9. Hybridization
10. Wash, Stain, Scanning

Answer Id: E13962

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Product FAQ

What 3'/5' ratio for control genes, for example GAPDH and Actin, should I anticipate to obtain on GeneChip probe arrays?

Answer

In addition to the conventional probe sets designed to be within the most 3' 600 bp of a transcript, additional probe sets in the 5' region and middle portion (M) of the transcript have also been selected for certain housekeeping genes, including GAPDH and Actin. Signal intensity ratio of the 3' probe set over the 5' probe set is often referred to as the 3'/5' ratio. This ratio gives an indication of the integrity of your starting RNA, efficiency of first strand cDNA synthesis, and/or in vitro transcription of cRNA. The signal of each probe set reflects the sequence of the probes and their hybridization properties. A 1:1 molar ratio of the 3' to 5' transcript regions will not necessarily give a signal ratio of 1.

There is no single threshold cutoff to assess sample quality for all of the diverse organisms and tissues. This is due to the presence of different isoforms of these house-keeping genes and their different expression patterns in various tissues and organisms. Although we routinely refer to a threshold ratio of less than 3 for the most common tissues, such as mammalian liver and brain, this may not be applicable to all situations. It may be more appropriate to document the 3'/5' ratios within a particular study and flag the results that deviate, therefore representing an unusual sample that deserves further investigation.

Answer Id: E13597

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Product FAQ

In the Command Console Software, what is sample/array registration?

Answer

It is the process of associating a sample record to a physical array or set of physical arrays. With this feature, users can link a sample to a single array, a sample to an array set (such as the GeneChip HG-U133A and B Arrays, or the GeneChip Human Mapping 500K Array Set), or a sample to an array type in replicate (one sample run on multiple arrays of the same type).

Answer Id: E14243

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Product FAQ

How many single nucleotide polymorphism (SNP) and copy number (CN) probes are included on the CytoScan HD Array?

Answer

CytoScan HD Array includes a total of approximately 6.5 million probes: 1 probe per allele in triplicate for 750,000 SNPs probes and 1.9 million non-polymorphic probes.

Answer Id: E13834

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Product FAQ

What quality control tools are available for the Axiom Genome-Wide BOS 1 Array?

Answer

Dish QC (DQC) is the recommended QC metric for Axiom Genome-Wide Arrays in Genotyping Console Software. The default threshold is greater than or equal to 0.82 for each sample. It operates by measuring signal at a collection of sites in the genome that are known not to vary from one individual to the next. Because the metric monitors non-polymorphic locations, at each position it is known which of the two channels in the assay should contain signal and which should be just background. DQC is a measure of the extent to which the distribution of signal values is separated from background values, with 0 indicating no separation and 1 indicating perfect separation.

Answer Id: E14044

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Product FAQ

What does the "_s_at" extension represent in the HG-U133 probe set name?

Answer

The primary goal in probe set selection is to select a probe set unique to a single transcript or common among a small set of similar transcript variants. A probe set name is appended with the "_s_at" extension when all the probes exactly match multiple transcripts. The probe set selection process generally favors probe sets measuring fewer transcripts. Probe sets with common probes among multiple transcripts (the "_s_at" probe sets), are frequent and are to be expected, due to alternative polyadenylation and alternative splicing. In most cases, "_s_at" probe sets represent transcripts from the same gene, but the same probe set can sometimes also represent transcripts from homologous genes. One transcript may be represented by both a unique and an "_s_at" probe set when the transcript variation is sufficient.

Answer Id: E14178

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Product FAQ

How should the thermal cycler settings be programmed for use with the CytoScan 750 array?

Answer

  Applied Biosystems Veriti 96-well Bio-Rad DNA Engine PTC-200 Eppendorf Mastercycler Pro S
Lid temperature 103 degrees C 103 degrees C 103 degrees C
Temperature mode N/A Calculated Safe
TSP heated lid N/A N/A Yes
Switch off lid at a low block temperature N/A N/A No

Answer Id: E14193

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Product FAQ

What is the array content for the CytoScan 750K Array?

Answer

The CytoScan 750K Array covers both constitutional and cancer genes with:

-Overall intragenic coverage at 1 marker / 1,737 bases
-ISCA constitutional coverage at 1 marker / 1,099 bases
-Complete cancer gene coverage at 1 marker / 1,269 bases
-12,000 OMIM genes at 1 marker / 2,204 bases
->36,000 RefSeq genes at 1 marker / 1,737 bases
-Backbone (non-gene) coverage at 1 marker / 6,145 bases across genome for breakpoints
-Overall (gene and non-gene backbone) coverage at 1 marker / 4,127 bases

Answer Id: E13927

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Product FAQ

Why does the alignment position detected by Probe Match tool differ from the probe interrogation position information associated with the probe sequence record?

Answer

The probe interrogation position, provided with the probe sequence information, indicates the base position on the consensus/exemplar sequence where the central base of the probe aligns (the 13th base of a 25mer probe). The position information generated by the Probe Match tool is strictly based on the alignment against the query (input) sequence. Because the consensus/exemplar may not be co-linear with your input sequence, the probe interrogation position in a probe sequence record may not match the output from the Probe Match tool.

Answer Id: E13638

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Product FAQ

How many and what species are not detected by the Axiom Microbiome Array?

Answer

81 species are not detectable on Axiom Microbiome Array. For a complete list of species not detected, please contact the Technical Support Team.

Answer Id: E14305

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Product FAQ

Will the Affymetrix Mouse Diversity Genoytping Array be available in plate format?

Answer

Content found on the Mouse Diversity Genotyping Array is so comprehensive that it will not fit on the format required for array plates.

Answer Id: E14152

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Product FAQ

I have noticed that the allele peaks calculation (ChAS 2.1 or below) is now called allele difference (ChAS 3.1 and above). Does this mean that the algorithm changed?

Answer

No, it is solely a name change for consistency.

Answer Id: E13887

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Product FAQ

Do I need to apply the high-resolution scanning patch for the HG-U133 2.0 Arrays?

Answer

Below is a list of circumstances and clarification regarding whether or not the high resolution scanning patch needs to be applied. Keep in mind that the high resolution scanning patch must only be applied on top of GCOS, not AGCC.

a. GeneChip Scanner 3000 (serial numbers 502xxxxx): The instrument service engineer has applied the high-resolution scanning patch to the computer that is controlling the GeneChip Scanner 3000 at installation, but not to the workstations or servers (see c and d below).

b. GeneChip Scanner 3000 (serial numbers 501xxxxx): The instrument service engineer will apply the high-resolution scanning patch to the computer that is controlling the GeneChip Scanner 3000 at the time of the upgrade, but not to the workstations or servers (see c and d below).

c. Analysis workstations and clients: You must apply the high-resolution scanning patch to GCOS analysis workstations.

d. GCOS Server upgrade: Your GCOS database administrator or an Affymetrix Software Support Engineer needs to apply the high-resolution scanning patch in coordination with the upgrade of server to GCOS.

e. Installation of library files post scanner installation or upgrade: The high-resolution scanning patch must be reapplied following the installation of library files for arrays that precede the HG-U133A 2.0 and HG-U133 Plus 2.0 Arrays. The HG-U133A 2.0 and HG-U133 Plus 2.0 library files are high-resolution-scanning ready. The error message "cannot read the parameters for probe array type from the database" appears when one tries to scan an array on a GeneChip Scanner 3000 high-resolution scanner when the high-resolution scanning patch has not been applied.

Answer Id: E13778

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Product FAQ

How were SNPs selected for the Axiom Genome-Wide BOS 1 Array?

Answer

SNPs were selected to represent polymorphisms from a comprehensive set of commercially important breeds of dairy and beef cattle from both Bos indicus and Bos taurus. Our primary goal was to obtain high levels of genetic coverage. SNP pairwise linkage disequilibrium (LD) values (r2) were calculated to identify SNPs in strong LD. Then we selected the fewest number of SNPs to cover the known genetic variation for each breed we prioritized (first five breeds in Table 1). After SNPs were selected for optimal genetic coverage, the distances between the selected SNPs were calculated, and inter-SNP gaps filled (starting with the largest) by selecting polymorphic SNPs from the five major breeds: Holstein, Angus, Nelore, Jersey, and Fleckvieh.

Answer Id: E14033

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Product FAQ

Do you have exon coverage in the high-resolution genes?

Answer

Yes, if using the Affymetrix defined workflow and depending on the size of the exon (our algorithm requires 20 contiguous markers to make a call). If using an “open” workflow, the user can define the number of probes they need to claim exon resolution.

Answer Id: E13856

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Product FAQ

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

Answer

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

Answer Id: E14135

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Product FAQ

How do I know if my first-cycle IVT reactions have worked well?

Answer

After the first cycle of amplification, it is often possible to quantitate the cRNA yield at this stage. Routinely, 400 ng - 1 µg of cRNA can be obtained from 50 to 100 ng of starting material. However, it is difficult to use the cRNA yield as the only metric to determine the success of the assay. Therefore, it may be most informative to combine the results from the first-cycle IVT yield with the second-cycle IVT yield, as well as array-quality metrics and data on various positive controls, to obtain a comprehensive view of how the assay has proceeded. [This answer refers to a product that has been discontinued.]

Answer Id: E14369

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Product FAQ

Why is my favorite array not listed in the sub-cluster databank in the NetAffx Analysis Center?

Answer

Some array designs, such as the GeneChip Mu19K array, are based on the sequences in The Institute for Genomic Research (TIGR) (http://www.jcvi.org/cms/home/) databanks. Sub-cluster information for these probe arrays is considered TIGR's proprietary information and therefore cannot be distributed by Affymetrix.

Answer Id: E13474

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Product FAQ

What is the purpose of the mPCR step in the DMET Plus assay?

Answer

The mPCR step allows for genes that have pseudogenes or other regions of high homology to be amplified for accurate genotyping. The mPCR is designed to preferentially amplify the real gene of interest.

Answer Id: E14300

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Product FAQ

Which assay do you recommend for use with Affymetrix miRNA Array Plates?

Answer

We only support use of the Affymetrix FlashTag Biotin HSR RNA Labeling Kit for preparing targets to be applied to GeneChip miRNA Array .

Answer Id: E14110

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Product FAQ

How do I limit an analysis in the TAC software to my genes of interest?

Answer

In the TAC software, you can filter the list of results by a list of gene symbols. This will also limit the hierarchical clustering of your expression data to the gene symbols found on your list. To do this, proceed with your analysis as you normally would. Once the results are returned, in the Table tab, you right click on the Gene Symbol column and choose the Filter option. A pop up will then appear allowing you to apply the filter logic. To filter on a list of Gene Symbols, select either the ‘In List' or ‘Not In List' option, as it pertains to your query. The Edit List window will appear, allowing you to type or paste in gene symbols. These must be separated by comma, semi-colon, or line breaks to be recognized properly by the software. Please also note that we use the official gene symbol determined by the NCBI Gene database. If your gene symbol of interest does not appear to function properly, please confirm that it is the official gene symbol by consulting the NCBI Gene database website.

Answer Id: E14332

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Product FAQ

In miRNA QC tool, how is the P-value calculated?

Answer

The p-value is calculated using the 4 probe replicates for each miRNA, and the corresponding variance for each set. Detection means: probe performance/detection using an algorithm and comparing to background.

Answer Id: E14085

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