• A260/A280 should be at least 1.8.
• The RNA needs to be re-suspended in RNase free/DEPC-treated water between 1 to 3 μg/μl concentrations.
• The samples need to be shipped on dry ice to VIMTA Life Sciences.
• Each RNA sample must be properly labeled as described in sample submission requirement form.
• The Affymetrix service request form must accompany all samples. The control or baseline sample must be clearly mentioned on the service form.

No. Chips cannot be reused.

Go to www.affymetrix.com to view the various genechips available. Go to "Additional Support" under each chip to download genelists.

Replication is important because it offers statistical power that enables you to find real differences between experimental groups. With adequate replication, "real" differences in levels of gene expression can be distinguished from differences caused by random variation. Without replication, it is difficult to know whether observed differences are real or random. Statistical precision enables you to accurately characterize gene expression for a particular experimental unit. With adequate replication, you get a more accurate overall picture of expression. Without replication, you have more random variation, leading to a less accurate picture and no way to fully characterize the uncertainty in the data.

There is no simple guidance on the number of replicates needed. A minimum of three or four replications for each experimental condition and/or time point is a good starting point; however, more may be needed to achieve the goals of many experiments.

All data generated using GeneChip Operating Software (GCOS) and Expression Console is provided to the user. Upon request, more in-depth data analysis using commercially available software such as ArrayAssist/Partek’s Genomics Suite and GenMapp will be provided at additional cost.

For each array experiment that is performed using the Affymetrix GeneChip arrays, six files are generated (*.DAT, *.CEL, *.CHP, *.EXP, *.RPT, *.txt).

The types of extensions are as follows:

Yes, we will help you understand the data in the preliminary analysis.  Similarly, if requested, training in usage of GeneChip Operating Software and Expression Console will also be provided.  In order to accommodate these requests, it is necessary to schedule an appointment in advance.

In-depth data analysis using commercially available software (ArrayAssist/Partek’s Genomics Suite, GenMapp and Affymetrix data mining tools) service is provided by VIMTA Life Sciences at an additional cost.

It is the responsibility of the investigators to collect unused/or left over products (total RNA, cDNA, cRNA, fragmented cRNA, hybridization mix). We will store them in the facility for a period of 30 days after the completion of the project.  After that period samples will be discarded without any notice.

For any particular SNP, the genomic DNA fragment containing the SNP must        have Nsp I (or Sty I) restriction sites intact so that ligation can occur on both      ends of the fragment and PCR can be successful. The approximate average size of genomic DNA may be assessed on a 1% or 2% agarose gel using an appropriate size standard control. High quality genomic DNA will run as a major band at      approximately 10-20 kb on the gel.

If a genomic DNA preparation is suspected to contain inhibitors, the following cleanup procedure can be used:
1. Add 0.5 volumes of 7.5 M NH4OAc, 2.5 volumes of absolute ethanol (stored at –
    20°C), and 0.5 μL of glycogen (5 mg/mL) to 250 ng genomic DNA.
2. Vortex and incubate at –20°C for 1 hour.
3. Centrifuge at 12,000 x g in a microcentrifuge at room temperature for 20 minutes.
4. Remove supernatant and wash pellet with 0.5 mL of 80% ethanol.
5. Centrifuge at 12,000 x g at room temperature for 5 minutes.
6. Remove the 80% ethanol and repeat the 80% ethanol wash one more time.
7. Re-suspend the pellet in reduced EDTA TE buffer (10 mM Tris, pH 8.0, 0.1 mM
     EDTA, pH 8.0).

All data generated using GeneChip Operating Software and Genotyping Console 2.1 is provided to the user. Upon request, more in-depth data analysis using commercially available software such as Partek’s Genomics Suite will be provided at additional cost.

For each array experiment that is performed using the Affymetrix GeneChip arrays, six files are generated (*.DAT, *.CEL, *.CHP, *.EXP, *.RPT, *.txt).

The types of extensions are as follows:

In-depth data analysis using commercially available software (Genotyping Console 2.1/Partek’s Genomics Suite and Affymetrix data mining tools) service is provided by VIMTA Life Sciences at an additional cost.

The first step of SNP data analysis is determination of SNP genotype calls from the .DAT or .CEL file. This can be done using: