Genomics facility of RGCB provides service to meet the demand of
scientists in various research fields. This facility is greatly
helping their research work, catering to the needs of the Institute.
Services include DNA sequencing, Genotyping using DNA analyzers, Real
time PCR, Droplet digital PCR and Microarray analysis.
DNA sequencing by Sanger method
Automated DNA Sequencing Facility is equipped with 3730 DNA Analyzer
(48 capillary high throughput DNA Sequencer) and 3730xL DNA Analyzer
(96 capillary high throughput DNA Sequencer). The fluorescence-based
DNA sequencing systems, with capillary electrophoresis is operating in
parallel for Sanger sequencing. The system automatically performs
sample injection, gel matrix replacement, DNA separation, detection,
and data analysis. This system sequence 48-96 samples in 2 hours' time
and perform up to 12 runs per day. Average read length with big dye
terminator (BDT) chemistry is 800bp. This system can also be used for
fragment analysis, AFLP, genotyping and SNP analysis.
The Core accepts DNA samples (pure plasmids, mini-prep plasmids, M13
clones, cosmids, lambda clones, PCR products, gel isolated fragments,
bacterial genomic), sequenced PCR products, and processes them
according to protocols for Applied Biosystems DNA Sequencers (BDT
Chemistry). One sequencing run (one template, one primer) typically
produces 700-800 nucleotides of high-quality sequence data or more for
good quality template and a well-designed primer. The results are
returned in three forms: a raw sequence file, sequence with blue score
and a chromatogram file. The sequence file (a flat ASCII text file) is
returned to the researcher by electronic mail. Each sequencing plate
includes at least one lane of standard DNA known to generate good
sequence. The sample handling and data analysis are extremely reliable
and have a very low rate of error. If any problems are indicated in
our sample processing, we repeat the affected samples on request. We
typically process samples within two days after receipt. Samples are
processed Monday through Friday for overnight instrument runs. The
data are processed and returned by email to the users.
3730 & 3730xL Genetic Analyzers- Electrophoresis only
Users can opt for sequencing PCR, electrophoresis and analysis or
only electrophoresis and sequence analysis of DNA products after clean
up procedure. Samples can be provided in tubes or plates in dried form
after sequencing PCR and subsequent cleanup.
Genotyping (Gene scan) using 3730 & 3730xL Genetic Analyzers
In polymorphism screening, microsatellite analysis and phylogenetic
studies, genomic DNA can be amplified by using fluorescent labeled
primers (eg., FAM, ROX etc) which can be given to the facility for
electrophoresis along with size standard and subsequent analysis.
Real Time PCR (7500, 7500 HT, Quant Studio5 & Droplet Digital PCR
The facility equipped with RealTime PCRs (7900HT Real-Time, 96-384
well format and 7500 Real time PCR-96 well and Quantstudio 5, 94
well-0.2ml) and droplet digital PCR (QX 100-Biorad). The systems can
be used for methods such as
Taqman Low density (TLDA) array
digital PCR applications
Microarray (Genechip scanner 30007G system - Affymetrix )
The microarray facility comprises Genechip 3000 7G, with Genechip
Scanner, Genechip Fluidics station and Genechip Hybridization oven.
The microarray can measure changes in gene expression levels, copy
number analysis, drug metabolism analysis, genome wide genotyping,
molecular cytogenetics, gene regulation analysis, miRNA analysis,
whole transcript analysis, SNP detection, genotyping and resequencing
of mutant genomes. System can be used with HD arrays, 750k arrays,
human gene expression arrays, mouse arrays and custom arrays.
Rajiv Gandhi Centre for Biotechnology (RGCB), Thycaud Post,
Poojappura, Thiruvananthapuram - 695 014, Kerala, India +91-471-2529400
| 2347975 | 2348753 +91-471-2348096