Director
Professor Dr. Md. Abdul Mazid
Vice Chancellor
Jashore University of Science and Technology
Jashore, Bangladesh.
Genome Center
Jashore University of Science and Technology
Genomic information is very important to unveil new opportunities for diagnostics and treatment of incurable diseases. For this purpose, the Genome Center of Jashore University of Science and Technology will serve as an important resource on the use of genomic data and will provide a specialized facility for advanced and high-throughput biomedical research. This center will herald a new age of cutting-edge research in Bangladesh. Its main task is to improve the responsible use of genomic information in the advancement of human wellbeing and to direct the national genome database. Genomic data have already restructured the diagnostics and treatment of several types of cancer and hereditary disease.
Background
The Faculty of Biological Sciences and Technology, Jashore
University of Science and Technology (JUST) has established a
world-class genome center. DNA detection at this center will unveil
new doors for health, forensics, agriculture and innovation. This
state-of-the-art center will be able to play a vital role in the
discovery of various types of genetic disorder as well as
identification of cancer genes.
Prior to the establishment of the laboratory, a committee of this
university visited the genome centers of North South University,
ICDDR,B, BARI, BSMMU, BCSIR and several other sophisticated
institutes and places to observe the laboratory structure and
facilities. The team found that Genome Library Preparation, PCR,
Real Time PCR are mandatory for a genome center and these priorities
have been ensured in this center.
Room no. 113 of the Bangabandhu Sheikh Mujib Academic Building of
JUST was selected for the center. The Next Generation Sequencing
(NGS) room of this laboratory is free from dust, magnetic resonance,
vibration and is always under controlled room temperature. After the
construction of the laboratory, a company named OVERSEAS MARKETING
CORPORATION (PVT) LTD (OMC) got the responsibility of supplying all
the equipment through proper tender process.
The laboratory has already been equipped with QuantStudio™ 3
Real-Time PCR Systems for Real Time PCR, Ion GeneStudio S5
Semiconductor Sequencer for Next Generation Sequencing (NGS),
SeqStudio™ Genetic Analyzer for 16S rRNA sequencing. In addition,
Field Emission Scanning Electron Microscope is going to be added to
this center very soon. Now the Genome Center can do Whole Genome
Sequencing and 16S Ribosomal RNA (rRNA) sequencing. This center is
trying to contact with various organizations for commercialization.
Along with the business, another goal of the genome center is to
spread the knowledge of bioinformatics in Bangladesh. For this,
training on Basic Bioinformatics will be provided.
Targets
Some institutes in Bangladesh have Next Generation Sequencing (NGS) facilities such as ICDDR,b; BARI, BSMMU and NSU but their services are hardly commercially available. Along with the16S ribosomal RNA (rRNA) sequencing, Next Generation Sequencing (NGS) and NGS data analysis facilities, this center is concerned with regard to examining the quality of imported and exported products through Benapole Land Port, Jashore. In addition, this Genome Center will play an important role in detecting cancer and genetic disorder as well as preparing the personalized medicine by using NGS data.
Facilities
16S ribosomal RNA (rRNA) sequencing facility
DNA Sequencing facility
Next Generation Sequencing (NGS) facility
NGS data analysis facility
Specific Gene Detection facility.
Instrumentation
#Next Generation Sequencing
Ion GeneStudio S5 Semiconductor Sequencer
The Ion GeneStudio S5 System is a semiconductor-based Next Generation Sequencing (NGS) system that enables simple targeted sequencing workflows. The Ion GeneStudio S5 System is optimized to provide affordability for labs focusing on smaller panels and lower sequencing throughput requirements. With cartridge-based reagents, the system is simple to use and offers scalability and flexibility. It uses Ion 5 Series chips to support a broad range of high-throughput sequencing for clinical research and research applications from microbial genomes and gene panels to exomes and transcriptomes.
Key features
Select the chip (Ion 510–540 chip) that fits your application
and throughput needs to achieve from 2–80 million reads per
run
Reduce setup time and complexity with cartridge-based
plug-and-play reagents
Complete run and analysis in hours and move forward with your
experiments
#Next Generation Sequencing
Ion OneTouch™ 2 System
The Ion OneTouch 2 System performs template amplification and enrichment as part of the manual workflow for the Ion PGM, Ion Proton, and Ion S5 and Ion S5 XL systems. It provides scalable template preparation for all Ion semiconductor chips. With its small footprint, the system fits easily on any bench top.
Specifications:
Name | Description |
|---|---|
| Chip Compatibility | Ion 314™ Chip, Ion 316™ Chip, Ion 318™ Chip, Ion PI™ Chip |
| For Use With (Equipment) | Ion OneTouch™ 2 System, Ion PGM™ System, Ion Proton™ System |
| High Throughput Compatibility | Automated Protocols, High Throughput-Compatible, Multiplexing |
| Library Type | Fragment Library, Mate-Paired Library, Targeted Sequencing Library, cDNA Library |
| Multiplex Capability | Up to 384 barcoded libraries |
| Operating Environment | Humidity: 20%-80% (non-condensing), Temperature: 15°C-25°C |
| Run Time | Hands-on time: Minutes, Ion PGM™ System: 5 hours total for template preparation, Ion Proton™ System: 8 hours total for template preparation |
#16S ribosomal RNA (rRNA) sequencing
SeqStudio™ Genetic Analyzer
The new Applied Biosystems SeqStudio Genetic Analyzer is a low-throughput, easy-to-use, and convenient benchtop system that delivers gold-standard Sanger sequencing technology and fragment analysis with just a simple click.
Specifications:
Name | Description |
|---|---|
| Number of capillaries | 4 |
| Number of dyes | Ion OneTouch™ 2 System, Ion PGM™ System, Ion Proton™ System |
| Sample format | Automated Protocols, High Throughput-Compatible, Multiplexing |
| Applications | ✔ Sanger sequencing (resequencing NGS confirmation, indels, heterozygote detection, minor variant detection) ✔ Fragment analysis (microsatellite analysis, compatible with MLPA™, Applied Biosystems SNaPshot applications, cell line authentication) |
| Secondary analysis software included | ✔ Sequence Analysis Software ✔ SeqScape Software ✔ Variant Reporter Software ✔ GeneMapper Software ✔ Minor Variant Finder Software ✔ Applied Biosystems Analysis Modules (Quality Check, Variant Analysis, and Next-Generation Confirmation) on Thermo Fisher Connect |
| Capillary array length | 28 cm (works with POP-1 polymer to resolve short and long reads) |
| Polymer type | Universal polymer POP-1 (for performing sequencing and fragment analysis) |
| On-instrument shelf life | 4 months after opening |
#Real Time PCR
QuantStudio™ 3 Real-Time PCR Systems
These instruments provide the latest advancements in touch-screen
usability, allowing to stay connected to the data easily.
Access, analyze, and share data anytime,
anywhere—Remotely monitor your runs, analyze sophisticated data sets
in minutes, store data in a secure space, and share results online
with colleagues across institutions and around the world, with Web
browser–based software. Monitor your runs in real time from mobile
devices through the Instrument Connect mobile app.
Obtain results you can trust—Detect differences in
target quantity as small as 1.5-fold in singleplex reactions, and
obtain 10 logs of linear dynamic range.
SimpliAmp™ Thermal Cycler
The SimpliAmp™ Thermal Cycler is a small, easy-to-use, and accurate thermal cycler that suits any lab's needs for everyday PCR. It is crafted with the reliable engineering and performance you’ve come to expect from Applied Biosystem® instruments. It is elegantly designed to deliver quiet cycling, and features an innovative, safe heated lid and a large LCD color touch screen.
Key Features and Benefits
VeriFlex™ blocks to optimize PCR temperature with
precision—the VeriFlex™ blocks provide 3 independent
temperature zones, for precise temperature control over your
PCR optimization
8-inch color touch screen to help save time—the large and
responsive color touch screen simplifies instrument operations
with an easy to read interface.
WiFi-enabled for remote monitoring—conveniently monitor your
instrument from anywhere with our free PCR Essentials mobile
app.
Simple lid design to protect your sample—the innovative
heated lid is easy to use and designed to help protect your
samples. When open, it is in an upright position for easy
handle access. Pull the handle forward to close the lid with
ease. The heated lid will open automatically if not closed
properly, to help safeguard your precious
sample.
SimpliAmp Thermal Cycler
#NanoDrop
Qubit 4 Fluorometer
The Invitrogen Qubit 4 Fluorometer is the next generation of the popular benchtop fluorometer designed to accurately measure DNA, RNA, and protein quantity. The new Qubit 4 also easily measures RNA integrity and quality.
Key features of the Qubit 4 Fluorometer include
More sensitive than UV absorbance–based quantification, making
it ideal for precious samples Accurately quantifies DNA, RNA, and protein in greater than 3
seconds per sample Fast, reliable detection of degraded RNA with the new RNA IQ
assay New integrated reagent calculator reports amount of dye and
buffer needed Uses as little as 1 μL of sample
Qubit 4 Fluorometer
Gel Documentation System
Quantum - Gel Documentation Imaging | VILBER
Optional epi or trans-illumination options Interchangeable application pad for UV, blue, green or red
fluorescence 10 positions filter wheel 10 narrow band filters available from 440 to
850nm Reproducible and comparable quantification
data ImageMaster™ technology to obtain the optimum image for
quantification Scientific TIFF file or proprietary file
format Clarity™ technology for razor sharp band revelation without
affecting data integrity
KingFisher Duo Prime System
The compact Thermo Scientific KingFisher Duo Prime purification system provides a flexible and user-friendly solution for automating nucleic acid and protein purification in labs with low- to medium-throughput
Features of the KingFisher Duo Prime include
Easy installation (ready to run in 10 minutes or
less)
Flexible configuration includes both 6-pin and 12-pin
magnetic heads to process different sample numbers and
volumes
Preloaded programs to perform protocols with MagMAX nucleic
acid isolation kits
Thermo Scientific BindIt Software, which allows programmable
instrument control and protocol modification, creation, and
upload (Windows 7 and 8 compatible)
New or edited protocols can be uploaded with a USB
stick
UV lamp for decontamination and optional barcode reader
provide enhanced usability
Services
Identification of bacteria by using 16S rRNA
sequencing
Sequencing of the DNA of various
microorganisms
Sequencing of the genomic DNA of bacteria through
next-generation sequencing (NGS)
Analysis of the NGS data
Training on basic bioinformatics
KingFisher Duo Prime System
QIAcuity Digital PCR System (dPCR)
Digital PCR (dPCR) is a technique use for absolute quantification of
nucleic acid that works by partitioning of a bulk reaction mixture
into thousands of small individual reaction chamber and then
measuring the endpoint fluorescence of each partition to determine
the presence or absence of the target. The QIAcuity Digital PCR
System is designed to deliver precise and multiplexed (up to 5 plex)
quantification results for mutation detection, copy number variation
(CNV), gene expression studies, gene-editing analysis, miRNA
research, Pathogen or Cancer detection, NGS library quantification
and many more. The microfluidic nanoplate technology puts every run
ahead of the curve with its precision and sensitivity. The system
integrates a standard dPCR workflow of partitioning, thermocycling
and imaging into a walk-away automated platform with minimal
hands-on time. It is also easy to adapt your current qPCR assays to
the Digital PCR System because of three simple steps like Pipette
and load, Run the experiment, Analyze results. The most advance
QIAcuity Digital PCR System provide fast, scalable, reliable and
absolute quantification that rise your research work at next level.
About MINICAP FLEX-PIERCING
The MINICAP FLEX-PIERCING instrument offers flexibility for small size laboratories. The fully automated instrument meets the needs of the laboratory while providing clear-cut and precise separations utilizing capillary electrophoresis technology. This multi-parameter, compact, automated capillary electrophoresis instrument offers a comprehensive menu on serum and whole blood for Protein, Immunotyping, HbA1c, Hemoglobin and CDT (Carbohydrate Deficient Transferrin) testing. For whole blood testing, the capped tubes are gently inverted to ensure adequate mixing of the samples providing accurate results. The instrument provides complete walk-away automation reducing overall labor requirements.
Key benefits Compact automated capillary electrophoresis
Sebia condensed its experience in a compact and fully featured instrument, with the same resolution as its CAPILLARYS instruments.
Compact but generous
7 capillary electrophoresis techniques available on this compact platform.
TEST MENU
Serum Protein Electrophoresis (SPE)
Serum Immunotyping
Hb A1c
Hemoglobin Electrophoresis
CDT & CDT
Sample types: whole blood, serum
Field Emission Scanning Electron Microscopy (FESEM)
for High-Quality Imaging & Advanced Analytical Microscopy for
Material and Life Sciences.
With the Sigma family you are entering the world of high-end nano-analysis.
Sigma 360 is the core imaging facility’s choice — an intuitive
FE-SEM for imaging and analytics.
Sigma 560 uses best-in-class EDS geometry to deliver high
throughput analytics and enable automated in situ
experiments.
Key Features:
Electron Source
Schottky Thermal Field Emitter
Resolution at 30 kV (STEM)
1.0 nm
Resolution at 15 kV
0.9 nm
Resolution at 1 kV
1.3 nm
Accelerating Voltage
0.02 – 30 kV
Magnification
10× – 1,000,000×
Probe Current
3 pA - 20 nA (100 nA optional)
Image Framestore
32 k × 24 k pixels
Ports
10
Brand: Carl Zeiss Microscopy GmbH, Germany.
People and Contacts
Deputy Director
Dr. Md. Alauddin
Chairman of the Department of Biochemistry and Molecular Biology and Assistant Professor Department of Nutrition and Food Technology.
Currently working as the associate director of this genome center.
Mobile: 01717061127
Email: chairman.bmb@just.edu.bd
Trainer
Dr. Md. Nazmul Hasan
Associate Professor
Department of Genetic Engineering and Biotechnology, JUST
Md. A. S. M. Rubayet-Ul-Alam
Lecturer
Department of Microbiology, JUST
Email: rubayetalam.mb@just.edu.bd
Md. Shazid Hasan
Lecturer
Department of Microbiology, JUST
Assistant Technical officer
PA of Director
Lab Technician
Information
| Contact Type | Details |
|---|---|
| Mobile | 01710686968 |
| Tel | +88 02 42142056 |
| PABX No. | 331 |
| genome.centre@just.edu.bd |
Future Plan
To add a more advanced NGS machine to this center to
accelerate the NGS work
To establish the Genome Center as a Bioinformatics Training
Institute
To examine the quality of imported and exported products
through Benapole Land Port, Jashore.
To use NGS data to detect cancer genes and genetic disorders
as well as help to prepare the personalized
medicine.