You searched for: 

genechip products

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

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

Why are the probes on the DMET Plus Array different lengths?

Answer

Different probe lengths can help differentiate alleles when the GC content varies. Since we are using a single condition for hyb and wash, it is difficult to optimize across a wide range of GC content. So for example if a SNP is in a sequence that is high GC, a shorter probe (23 or 21 mer) might improve allelic discrimination. If the SNP is in an AT rich sequence and has an overall lower Tm, then a slightly longer probe could improve discrimination.

Answer Id: E14291

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

What sample populations and criteria were used to select the markers for DMET Plus Array?

Answer

We used multiple populations (HapMap and Extended HapMap) when building the large internal reference set. The actual SNPs that are on the array come largely from the literature and we are unaware of any population bias that is in this collection. Much of the content did in fact come from the Pharma ADME web site. This consortia assembled a list of markers in genes that were prioritized into different classes. The most important of these is referred to as Core markers which mean that they have been validated in the scientific literature as having clinical relevance in drug responses. Markers were reviewed with several Pharmaceutical companies as well for input on important ADME markers.

Answer Id: E14292

Was this answer helpful?

Yes
No
Thank you for your response

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

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

What is the correct fluidics script for CytoScan HD Array?

Answer

The correct fluidics script is CytoScanHD_Array_450.

Answer Id: E13992

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

On average, how many probes are used to represent a corresponding GeneChip Human Genome U133 (HG-U133) Array probe set where there are 11 probe pairs?

Answer

The majority of the HG-U133 Plus 2.0 Array consensus sequences are well covered in the new design with approximately 75% of them containing over 8 probes on the Exon Array. The remaining 25% have less overlap with the new exon probes, and are mostly attributed to EST-based HG-U133 Array probe sets that do not contain an annotated coding region. As a result, in many such cases, the entire HG-U133 Array EST-based consensus sequence is designated as one PSR, with around 4 probes selected for that entire region.

Answer Id: E13664

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

How is gender determined/called in DMET Console?

Answer

In DMET console, gender calls can be found by looking at the CHP summary table, “Show All Columns”. Column “cn-probe-chrXY-ratio_gender_ratio”, shows how clearly a sample was called male or female. If this ratio is at least 0.68, it's called “male”. If this ratio is no more than 0.17, it's called “female”. This is basically a ratio of average raw signal of selected X and Y chromosome probesets and is performed on raw signal data, independent of genotyping method.

Answer Id: E14293

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

Which fluidics protocol should I use when processing a Gene 1.0 ST Array?

Answer

FS450_00007 should be used when processing Gene 1.0 ST Array. Up-to-date fluidics scripts can be obtained from the website.

Answer Id: E14097

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

Can array results from different laboratories and different times be compared with each other directly and how do you control the variables in this type of experiment?

Answer

Array results can potentially be compared directly. However, it is important to check the following important elements before doing so:

-Experimental design strategy should be the same at various sites.
-Identical target labeling protocols should be followed, and yields from cDNA and IVT reactions should be within the same range as specified for that study.
-Same algorithm parameters should be used.
-Similar results from 3'/5' ratios, background, noise, and scaling factors. Check arrays for scratches and even hybridization/staining.
-Comparability of results obtained from different operators should be evaluated before including their results in the same study.

Answer Id: E13598

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

What file sizes are associated with CytoScan HD Array?

Answer

The CEL file is ~66 MB, and the CYCHP file is ~119 MB.

Answer Id: E13993

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

Will SST-RMA be available in APT?

Answer

Yes, the SST-RMA analysis algorithm will be available in APT.

Answer Id: E14023

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

How do I correlate the SNPs on the mapping GeneChip array with this design?

Answer

Associations between SNPs and exon probe sets can be obtained by using genome assembly position information which is provided for both the mapping array and the exon array. One useful tool for doing this is the UCSC Table Browser at http://genome.ucsc.edu/cgi-bin/hgTables.

Answer Id: E13536

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

How often do I need to do maintenance on the fluidics station?

Answer

With normal use (e.g., 20 arrays/module/week), we recommend the following schedule: Every week, the needle bleaching protocol (i.e., "Bleach" fluidics protocol) should be performed; on a monthly basis, the full-fluidics bleaching protocol (i.e., "Monthly Decontamination" protocol) should be performed and the peristaltic-pump tubing replaced. Please refer to Section 4, Fluidics Station Maintenance Procedures, for more detail.

Answer Id: E13665

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

Can the input material be polyA RNA or mRNA instead of total RNA for microarray studies?

Answer

While mRNA should yield good results, we have not validated the product for use outside of total RNA. If you wanted to use mRNA, you will have to do some optimization to determine the correct amount of input material.

Answer Id: E14310

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

How many times can the DMET Reagents be used/how many freeze/thaws?

Answer

The DMET Plus Reagents are for single-use only. Do not thaw and refreeze reagents. This information is also available on the package insert of the reagents.

Answer Id: E14294

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

Which fluidics protocol should I use when processing a Gene 2.0 ST Array?

Answer

FS450_00002 should be used when processing Gene 2.0 ST Array. Up-to-date fluidics scripts can be obtained from the website.

Answer Id: E14098

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

Is the PM only plate array content exactly the same as the cartridge?

Answer

No, the PM only arrays have probes that are perfect match only. The mismatch probes have been removed. For the HT HGU133 plus PM product roughly 3/4 of the probesets have 9 probes, a small portion has 10; the remaining probesets have 11. The Mouse and Rat PM only plate arrays utilize all 11 probes for each probeset.

Answer Id: E13599

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

What software is available for analysis for genoytping and copy number analysis?

Answer

All genotyping and copy number analysis is done with ChAS. CytoScan Cytogenetics Suite is not intended for genome-wide association studies.

Answer Id: E13995

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

Can I hybridize the DNA target to the HG-U133 arrays?

Answer

The WT Plus Assay is optimized to produce targets specifically for hybridization to the Whole Transcriptome(WT) type of design. The target is in the sense orientation and the GeneChip Human Genome U133 Plus 2.0 Array is designed to be compatible with anti-sense targets. Therefore, it is not recommended to mix and match the assays and the array types.

Answer Id: E13654

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

Does the ChAS database require an internet connection?

Answer

The ChAS server home page requires an active internet connection, which requires a web browser. (Chrome and Internet Explorer v11 are recommended.) If you are using the local ChAS DB, an active internet connection is not required.

Answer Id: E13885

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

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

Answer

GeneChip miRNA Array 130 µL of hybridization cocktail
Thermo Fisher Scientific miRNA Array Plates 120 µL of hybridization cocktail
Thermo Fisher Scientific miRNA Array Strips 120 µL of hybridization cocktail

Answer Id: E14137

Was this answer helpful?

Yes
No
Thank you for your response

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

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

When I loaded the GeneChip Exon Array design information and array data into IGB, it seems that the probes were selected from outside of the RefSeq exons. Why?

Answer

The most likely explanation is that a different version of the genome assembly has been used to display the array design information and the array results. At launch, two versions of the library files are provided for array analysis corresponding to the Human Genome Build 34 and 35. Take care to use a consistent version number to match the array design with the actual array data for visualization in IGB.

Answer Id: E13537

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

Is there a possibility of contaminating the fluidics station with RNase when gene expression, genotyping, and health management applications are being performed on a shared station?

Answer

It is extremely important to change the vials each time a sample is removed or loaded onto a probe array. This prevents cross-contamination as well as sample loss. RNase contamination is not an issue with gene expression applications due to the fact that the cRNA sample is fragmented prior to hybridization and is removed prior to array processing on the fluidics station.

Answer Id: E13666

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

For the GeneChip Mouse Expression Set 430, what is a probe set? What do the different suffixes attached to a probe set name mean?

Answer

A probe set is a collection of probes designed to interrogate a given sequence. A probe set name is used to refer to a probe set, which looks like the following:
12345_at or 12345_a_at or 12345_s_at or 12345_x_at
The last three characters (_at, in RED) identify the probe set strand. Probe sets that are designed to detect the anti-sense strand of the gene of interest are annotated with "_at".

There are different types of probe sets that can result from the probe selection process. Most probe sets have an extension of an underscore and a letter to designate the probe set type, except for unique probe sets. These different probe set types are shown in the example above in BLUE. Probes in a gene family probe set (_a set) all cross-hybridize to the same set of sequences that belong to the same gene family (i.e., having same name in the "geneCluster" column). This probe set type is only created if the "geneCluster" column is included in the Instruction File and contains information. Probes in a unique probe set do not cross-hybridize to any other sequences in the design (including any additional pruning sequences provided). Probes in an identical probe set (_s set) all cross-hybridize to the same set of sequences that are used for the design (including any additional pruning sequences if provided). These sequences are not defined as from the same gene family for one the following reasons: the values in the "geneCluster" column are different, or the gene family information is not provided. Probes in a mixed probe set (_x set) contain at least one probe that cross-hybridizes with other sequence(s) used for the design. Cross-hybridizing probes have a cross-hybridization penalty applied to their raw probe scores, and thus, favoring unique probes of the same quality over cross-hybridizing probes.

Answer Id: E14184

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

Can I start using the new 3' IVT Express Kit right away, even in the middle of my experiment?

Answer

We would recommend completing any current project with the same labeling method that you have been using. Although concordance is quite high between the kits, it is best to continue with one labeling method in any experiment. [This answer refers to a product that has been discontinued.]

Answer Id: E14348

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

How can I determine the limit of detection?

Answer

In Partek, the limit of detection = 2 Standard Deviations over background. In miRNA QC Tool, click 2X to subtract the background. At this point, anything above background (as defined by the project description table) is significant, if the p-value is also significant (as determined by the researcher).

Answer Id: E14090

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

What is the correct fluidics script for the Clariom S (human, mouse and rat) array?

Answer

The Clariom S array is a 400 format, the correct script is FS450_0007.

Answer Id: E14311

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

Which fluidics protocol should I use when processing human, mouse, or rat transcriptome assays?

Answer

FS450_0001 should be used when processing human, mouse, or rat transcriptome assays. Up-to-date fluidics scripts can be obtained from the website.

Answer Id: E14105

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

What are the system requirements to run the Midas software?

Answer

A minimum of 16 GB RAM and 30 GB available disk space is required to perform analysis of Axiom Microbiome cel files.

Answer Id: E14318

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

Where can I download the HapMap CEL files for SNP 6.0 array?

Answer

The SNP 6.0 HapMap CEL files have been archived by NCBI. The files are available for download through the NCBI ftp server. To get the full set of CEL files, all the files with the extension .tgz should be downloaded. Any .tgz files will need to be extracted (or unzipped) twice. There is freeware called 7-Zip File Manager that can be used to extract the files. For additional information, please contact support.

Answer Id: E14295

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

What is the hybridization temperature and rotation speed for CytoScan arrays?

Answer

The hybridization temperature is 50 degrees C. The rotation speed is 60 rpm.

Answer Id: E16629

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

What format is the GeneChip Gene 1.0 ST Array?

Answer

The GeneChip Gene 1.0 ST Array is an 81/4 format. Please note that 81/4 format is to be treated equivalent to 100 format arrays.

Answer Id: E14099

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

What algorithm(s) can be used to make copy number calls?

Answer

We recommend the TuScan algorithm. This algorithm has fixed settings based on 19 probes/call to ensure high sensitivity and specificity at the stated resolution claims. Nexus Express Software for OncoScan FFPE Assay Kit has an additional algorithm for copy number calls from OncoScan FFPE Assay Kit: SNPFASST2 algorithm, developed and supported by BioDiscovery. This allows the user to adjust settings and make custom calls (e.g., with fewer probes). Use cases are:
When breakpoints are clear with fewer probes
When probe re-centering is needed

Answer Id: E13857

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

What are the definitions of the array QC metrics terms "MAPD" and "SNPQC"; what does each metric measure and how are they used in assessing array performance?

Answer

MAPD: Median of the Absolute values of all Pairwise Differences is a per-microarray estimate of variability, like standard deviation (SD) or interquartile range (IQR). It measures the variability in log2 ratios by looking at the pair difference of all probes and taking a median value. The effect of an occasional big difference in log2 ratios between probes is removed by taking a median value and not a mean. This variability can come from different sources: Intrinsic variability in the starting material, hybridization cocktail preparation, microarray, or scanner.

Apparent variability induced by the fact that the reference may have systematic differences from the sample on this microarray. Regardless of the source of variability, increased variability decreases the quality of the CN calls. A high MAPD can be attributed to any of the above factors and indicates that CN calls may be inaccurate, leading to a higher false positive/negative rate.

SNPQC: This is a measure of how well genotype alleles are resolved in the microarray data. In other words, it estimates the distributions of homozygous AA, heterozygous AB, and homozygous BB alleles and calculates the distance between them. The better the separation of these distributions, the better the ability to identify a genotype based on its cluster position. The larger the difference between the peaks and the troughs, the better the resolution of homozygotes and heterozygotes and the higher the SNPQC metric is. If the three peaks are not well resolved, the difference between peaks and troughs will be low, resulting in a lower SNPQC value. A low SNPQC value indicates that quality of the SNP allele data is compromised, due to higher noise within the array, which compromises the overall quality and clarity of results.

Answer Id: E13996

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

Can I use the WT Sense Target Labeling Assay protocol for prokaryotic arrays?

Answer

This has not been tested at the moment; therefore, it is not recommended to use the protocol for any application other than on the Exon Arrays.

Answer Id: E13655

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

I cannot see gene descriptions when I analyze the .dat file in Microarray Suite 4.x. How do I fix this?

Answer

First, verify that you are running the correct version of the Library Files (starting with November 2000), and that you are running Microarray Suite version 4.0.1 (required). If these versions are correct and you still encounter the problem, then there is, most likely, something wrong with the Microsoft Data Engine (SQL Manager). Contact us by e-mail at techsupport@thermofisher.com.

Answer Id: E13617

Was this answer helpful?

Yes
No
Thank you for your response

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

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

How do I see the Gene Names for the probe set IDs?

Answer

To see the NetAffx information associated with a particular probe set, view the probe level summaries under the REPORT menu item and double click on the probe ID of interest.

Answer Id: E14012

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

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

Answer

GeneChip miRNA Array 17 +/- 1 hr
Thermo Fisher Scientific miRNA Array Plates 17 +/- 1 hr
Thermo Fisher Scientific miRNA Array Strips 20 +/- 1 hr

Answer Id: E14138

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

Once I have deleted a file from the ChAS database, is there a way to recover the file?

Answer

No, once a file has been deleted, the only way to replace that file in the database is to publish the original xxchp file again.

Answer Id: E13895

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

How were the normalization controls determined in the GeneChip Mouse Expression Set 430?

Answer

A candidate list of probe sets was obtained in collaboration with an external site based on a large number of tissue samples run on MG-U74v2 arrays. Criteria for selection included evidence of constitutive expression (detection in at least 95% of replicates) and minimal variation in signal across the tissues tested. The 11 probe pair probe sets for these transcripts were evaluated by hybridizing 11 tissues and 4 cell lines on Mouse 430A and B arrays. One hundred probe sets were selected that had detection in at least 95% of replicates and had minimal signal variation. Preference was given to RefSeq sequences where possible, probe sets were selected to give a range of signal values and to represent 100 unique UniGene clusters.

Answer Id: E13730

Was this answer helpful?

Yes
No
Thank you for your response

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

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

How do you move the .cel files out of GCOS to be imported into Expression Console?

Answer

GCOS users must use DTT v1.1, using the Flat File option, to transfer files to be analyzed by the Expression Console software from the GCOS database to an independent folder.

Answer Id: E13538

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

What are the general genomic DNA requirements for the CytoScan assay?

Answer

DNA must be double-stranded genomic DNA.
DNA must be free of PCR inhibitors.
DNA must not be contaminated with other human genomic DNA sources or with genomic DNA from other organisms.
DNA must not be degraded.
DNA should have an A260/A280 between 1.7-2.1 (numeric rounding allowed).

Answer Id: E13949

Was this answer helpful?

Yes
No
Thank you for your response

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

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

What is the probe interrogation position?

Answer

The probe interrogation position indicates the base position on the consensus/exemplar sequence where the central base of the probe aligns, which is the 13th base of a 25mer probe.

Answer Id: E14283

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

On which operating systems is Genotyping Console (GTC) 4.2 supported?

Answer

Genotyping Console has been verified on the following operating systems:
-Windows 7 Professional SP1 (64-bit)
-Windows 8.1 Pro (64-bit)
-Microsoft Windows 2003 Server
-32-bit operating systems only

Answer Id: E13668

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

How many SNPs and Copy Number Probes are on the SNP 5.0 array?

Answer

500,568 SNPs on the SNP 5.0 array can be accessed utilizing Genotyping Console 2.1. In addition, the SNP 5.0 array contains 420,000 non-polymorphic copy number probes.

Answer Id: E13746

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

What is on the Mouse 430A and what is on the Mouse 430B Arrays?

Answer

The Mouse 430A chip contains primarily probe sets against well annotated full-length genes. The Mouse 430B chip contains probe sets against gene clusters containing only EST sequences and some gene clusters with non-EST sequences.

Classification: Mouse 430A: Mouse 430B
Full Lengths: 14,484: 0
Full Length End and Strong Evidence for Polyadenlation: 6839: 0
Strong Evidence for Polyadenylation: 2408: 0
Full Length End: 4452: 0
Consensus End: 785: 0
Non-ESTs (excluding Full Lengths): 3771: 5679
Strong Evidence for Polyadenylation: 1880: 1510
Consensus End: 1891: 4169
ESTs: 4371: 16732
Strong Evidence for Polyadenylation: 3362: 4979

Library Coverage >1
Evidence for Polyadenylation > 1: 260: 11509
Single Evidence for Polyadenylation: 50: 51
No Direct Evidence for Polyadenylation: 108: 37

Single Library Coverage
Evidence for Polyadenylation > 1: 28: 7
Single Evidence for Polyadenylation: 297: 85
No Direct Evidence for Polyadenylation: 266: 64

Answer Id: E14185

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

Can I use less than 50ng of Total RNA as input with the 3' IVT Express Kit?

Answer

Yes, for some RNAs it may be possible to generate sufficient labeled aRNA with less than 50ng input (particularly for smaller array formats with lower aRNA requirements). However, lower input amounts have not been rigorously tested during development and therefore, we cannot guarantee array performance. [This answer refers to a product that has been discontinued.]

Answer Id: E14349

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

How is fold change calculated in TAC?

Answer

Fold change is a number describing how much the signal changes from an initial condition group to a final condition group. These changes are represented in linear space. There are a couple of ways to describe fold change. One way a user might calculate this is to simply divide Sample A by Sample B and asses the result.

For example:
Array 1: Gene X - 1000 Gene Y - 5000 Gene Z - 500
Array 2: Gene X - 10000 Gene Y - 1000 Gene Z - 500
If comparing Array 1 vs Array 2: Gene X: 1000 / 10000 = 0.1 Gene Y: 5000 / 1000 = 5 Gene Z: 500 / 500 = 1
The way TAC displays fold change is to use the straight fold-change value if it is greater than or equal to 1.0 or display (-(1/fold change)) for values between 0 and 1. Let's look at the example above in TAC format:
Again, comparing Array 1 vs Array 2: Gene X: 1000 / 10000 = 0.1, so (-(1/0.1)) = -10 Gene Y: 5000 / 1000 = 5 Gene Z: 500 / 500 = 1
If doing the comparison the other way (Array 2 vs Array 1): Gene X: 10000 / 1000 = 10 Gene Y: 1000 / 5000 = 0.2 (or in TAC, (-(1/0.5)) = -5 Gene Z: 500 / 500 = 1

Answer Id: E14325

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

How do I perform genotype trait association studies once I obtain genotype calls?

Answer

The output of the GTC is a text file that is compatible with multiple third-party software tools. Affymetrix works closely a number of GeneChip-compatible software providers that offer genome-wide linkage or association analysis solutions for Affymetrix genotyping arrays. GeneChip-compatible software providers that have been shown to support the genotype format for the Mouse Diversity Genotyping Array include:

- Golden Helix SNP & Variation Suite (SVS) - Golden Helix has tested data from the Mouse Diversity Genotyping Array and demonstrated compatibility. SVS can import SNP calls from the output text files through an automated import wizard. Once imported, data can be easily manipulated, augmented, and prepared with a full complement of QC tools, and then analyzed with powerful association methods, in-depth statistical analyses, and robust visualization tools. SVS can also import intensity data directly from the array's CEL files, detecting changes in copy number and enabling CNV association studies. For more information, please visit www.goldenhelix.com or email info@goldenhelix.com.

- JMP Genomics from SAS - JMP Genomics can import text genotypes and annotation for the new array using the import individual text files process. Imported genotype text files should be transposed into standard JMP Genomics SNP format for downstream analysis (individuals in rows, SNPs in columns) using the transpose rectangular process. For more information, please visit www.jmp.com/software/genomics/ or email genomics@jmp.com.

- Partek Genomics Suite - Partek has tested sample data from the Mouse Diversity Genotyping Array and can import SNP calls from the output text files. Partek Genomics Suite supports single-marker association workflows as well as inheritance tests. For more information, please visit www.partek.com or email support@partek.com. Additional information about these and other GeneChip-compatible software providers can be found on our website.

Answer Id: E14160

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

Can custom annotation files be used for SNP genotyping in GTC 4.2?

Answer

Yes, custom annotation files can be used for SNP genotyping and copy number analysis in GTC 4.2.

Answer Id: E13684

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

Can GTC 4.2 coexist with older GTC versions on the same computer?

Answer

No, prior GTC versions cannot run on the same computer with GTC 4.2.

Answer Id: E13671

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

Are there any articles that describe miRNA Array data analysis?

Answer

F Sato. Intra-Platform Repeatability and Inter-Platform Comparibility of microRNA microarray technology. PLoS ONE May 2009, volume 4, issue 5, e5540.
D Sarkar. Quality Assessment and data analysis for microRNA expression arrays. Nucleic Acids Research 2009, vol. 37, no. 2, e17 (doi: 10.1093/ner/gkn932).

Answer Id: E14091

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

What are the available assay options for running the Clariom S array?

Answer

Depending on input, sample type, and platform, you have several options:
Cartridge: Assays for 100 pg-50 ng of total RNA isolated from whole blood, cultured cells, and fresh/fresh frozen or FFPE tissues.
Pico Assay Assays for 50-500 ng of total RNA isolated from whole blood, cultured cells, and fresh/fresh frozen tissues.
WT Plus Assay Plates: Assays for 100 pg-50 ng of total RNA isolated from whole blood, cultured cells, and fresh/fresh frozen or FFPE tissues for analysis on GeneTitan Instrument.
Pico Assay HT Assays for 50-500 ng of total RNA isolated from whole blood, cultured cells, and fresh/fresh frozen tissues for analysis on GeneTitan Instrument.

Answer Id: E14312

Was this answer helpful?

Yes
No
Thank you for your response

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

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

Which Affymetrix platforms support CNP analysis?

Answer

CNP analysis is supported in GTC 4.2 for the SNP Array 6.0.

Answer Id: E13696

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

How are the new Command Console file formats better than those for GCOS?

Answer

1) Sample information is now stored in the sample file (ARR) that uses an industry-standard XML formatted file, enabling software packages outside of Command Console Software to easily access sample information.
2) File relationships (ARR/DAT/CEL/CHP) are now independent of file name, enabling users to rename and move files yet still retain parental lineage between the files. Contact the Affymetrix Developers' Network for more on technical aspects of Affymetrix files.

Answer Id: E14224

Was this answer helpful?

Yes
No
Thank you for your response