Genome Center

Jashore University of Science and Technology

Genome Center, JUST

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.

Professor Dr. M. Anwar Hossain, the honorable Vice Chancellor of this university felt the need to set up such a center as this to ensure the advantages to conduct genetic research, and took the timely initiative to set up a sophisticated genome center in the university in June 2017. 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.

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.

  1. 16S ribosomal RNA (rRNA) sequencing facility
  2. DNA Sequencing facility
  3. Next Generation Sequencing (NGS) facility
  4. NGS data analysis facility
  5. Specific Gene Detection facility.
  1. 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

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

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
  1. 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:

Number of capillaries 4
Number of dyes 6
Sample format 96-well standard plate and standard 8-tube strips
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
  1. 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.

  1. 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.
  1. NanoDrop

IMPLEN NanoPhotometer

  • Microvolume measurement with on-the-go analysis
  • Flexible control and data collection via computer, Mac, smartphone, or tablet
  • Choose a Touch model for a built-in touch screen tablet
  • Slot for a Kensington™ lock provides antitheft security

6. 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 <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

  1. 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
  1. 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

  1. Identification of bacteria by using 16S rRNA sequencing
  2. Sequencing of the DNA of various microorganisms
  3. Sequencing of the genomic DNA of bacteria through next-generation sequencing (NGS)
  4. Analysis of the NGS data
  5. Training on basic bioinformatics
  1. Identification of bacteria by using 16S rRNA sequencing
  2. Sequencing of the DNA of various microorganisms
  3. Sequencing of the genomic DNA of bacteria through next-generation sequencing (NGS)
  4. Analysis of the NGS data
  5. Training on basic bioinformatics
  1. To add a more advanced NGS machine to this center to accelerate the NGS work
  2. To establish the Genome Center as a Bioinformatics Training Institute
  3. To examine the quality of imported and exported products through Benapole Land Port, Jashore.
  4. To use NGS data to detect cancer genes and genetic disorders as well as help to prepare the personalized medicine.
1. Director
Professor Dr. M. Anwar Hossain, Honorable Vice-Chancellor of JUST.

Currently working as the director of this genome center.

2. Associate Director
Dr. Iqbal Kabir Jahid, Chairman of the Department of Microbiology.

Currently working as the associate director of this genome center.

3. Trainer
1.       Dr. Md. Nazmul Hasan

Associate Professor

Department of Genetic Engineering and Biotechnology, JUST

Email: mnhasan1978@gmail.com, mn.hasan@just.edu.bd

2.       Md. A. S. M. Rubayet-Ul-Alam

Lecturer

Department of Microbiology, JUST

Email: rubayetalam.mb@just.edu.bd

3.       Md. Shazid Hasan

Lecturer

Department of Microbiology, JUST

Email: shazidmb@gmail.com, shazid_mb@just.edu.bd

4. PA, Director Genome Center
Masudur Rahman

Mobile: 01724583453

Email: masudsagor@gmail.com

5. Lab Technician
Dipankar Chakrobortty

Mobile: 01747107977

Email: dipu.fmrt@gmail.com