Genotyping & Gene Expression Solutions

Under these services we focused on DNA typing or genotyping by PCR method  using common dominant and co-dominant markers as well as sanger based SNP detection.

In Gene expression service, we are providing one stop solution for any gene expression study by SYBR Green or TaqMan chemistry.

Under this services we have below Service

Fragment Analysis/Microsatellite Genotyping- ABI3730XL

Fragment analysis (Genotyping) can be performed on DNA fragments that have fluorescent labels. Using a labeled primer with PCR amplification is a common method used to incorporate these labels. The Molecular Biology Core lab is already set to run multiple fluorescent dye sets.

6-FAM, VIC, NED, PET, LIZ (for ABI Dye Set G5, DS-33)

6-FAM, HEX, NED, ROX (for ABI Dye Set D, DS-30)

Post PCR reaction products should be visible on a gel as a strong band. For capillary electrophoresis analysis, samples need to be diluted down to a working concentration. Our recommended starting point would be about 1 in 50 dilution of the PCR product. Add 1µl of this dilution to 10µl of Hi-Di Formamide (ABI# 4311320), along with 0.25µl of your selected size standard (we recommend ABI GS500 LIZ ABI# 4322682 or GS500 ROX ABI #401734 for the Dye set listed above) for a total reaction volume of 10.25µl for each sample.

The amount of the PCR product used for each reaction may need to be further optimized. With too much product the signals can be saturated preventing the software from reading some of the fragments or the size standard signals. Too little product and fragments may not be detected above the background. Adjustments will need to be made based on the amount PCR product generated. Multiple amplicons generated in a single reaction may need to be more dilute while a single amplicon may need to be less dilute.

The reactions need to be set up in an approved 96 well plate (ABI cat# N8010560 or similar plate) before you give them to the core. Samples are run by the sequencer by every other column on the plate, so set up samples by filling all the odd number wells first  (column 1A through H followed 3,5,7, 9 and 11 A through H. Then fill all the even numbered columns 2,4,6,8,10, 12, A through H. See Instructions for submitting samples in 96 well plates for more information.

Sample submission

• 20µl gDNA @ 100ng/µl
• Unpurified Tagged /labeled PCR product
• Purified Tagged /labeled PCR product
• Provide the entire samples name according to the plate format. If you need sizing information, please provide the details of labeling and product size.  Please find the order form here (link)

Deliverables:

• Compiled report FSA file

Genotyping by PCR

 We are using traditional PCR based markers like RAPD, ISSR, SSR for determining polymorphism among samples. This service provides simple, robust, low cost, and easy to perform solution for most of the genetic screening program which need to screen bulk samples.  We are synthesizing primers as per requirement in our in-house facility for more convenient and faster result delivery. 

We also provide additional analysis services to identify the degree of polymorphism and diversity in population/ origin of the species or the relatedness.

Sample submission

• 500 mg to 1g Tissue
• gDNA,  Vol. 50µl (should be provide according to number of markers),  Conc. 30ng/µl,
•  Primers (optional)

Deliverables:

• Compiled report with publishable quality Agarose gel profiling picture.

SNP Genotyping

• SNPs are our passion. With our services you can either take a deep look into the genome or search for unknown genotype-phenotype connections or genotype already known variations. No matter what, you always benefit from our fast turnaround times and high quality results.
• SNPs (single nucleotide polymorphisms) or point mutations are the most common types of genetic variation determining to a major part the phenotype diversity between individuals. Causal point mutations change the amino acid sequence of the encoded protein and hence such SNPs are involved in the characteristics of an individual.
• We are using two different approaches for SNP detection; provide maximum flexibility for researches, by using SNPShot Kit based or by using General Sanger sequencing method.

Sample submission

• 20µl gDNA @ 100ng/µl

Deliverables:

• Compiled report containing SNP list with minor allelic frequency