Microbiome and Genomics Lab

The following are the major equipment that is located in Dr. Khan’s research group.

• Applied Biosystems VeritiPro Thermal Cycler: It delivers proven reliability with advanced temperature control technology and connectivity. Take advantage of next-level PCR optimization with the precision offered by VeriFlex Block technology (96-well, 0.2 mL; 6-zone VeriFlex Block; 6.0°C/sec; 96 reactions; USB port and 16 GB onboard memory; onboard capacity >1,000 protocols). Connect to the cloud-enabled VeritiPro Thermal Cycler remotely. Conveniently design and securely upload your methods, monitor runs, and check instrument availability from any mobile device or desktop computer with Connect. 
• Applied Biosystems Flex Purification System: 
• BluePippin, DNA Size Selection for Next-Gen Sequencing, with Pulsed-Field (100bp – 50kb): The BluePippin has the DNA capabilities of the Pippin Prep, plus the extra benefit of pulsed-field electrophoresis for resolving and collecting high molecular weight DNA.  For long-range genomic applications, high-pass filtering allows users to collect all fragments above a size threshold set by the user. Target sizes or ranges of sizes are entered in software, and fractions are collected in buffer. Up to 5 samples/gel cassette may be run, with no possibility of cross contamination. Gel cassettes for DNA selections are available in four agarose concentrations to provide a full range of size selection options between 100bp up to 50kb.  For smaller fragment sizes, internal standards may be used for higher accuracy and increased sample capacity (from 4 to 5 samples/cassette).  Higher molecular weight fragments require a dedicated lane to run a calibration marker.  Run times are as little as 30 minutes. This can be used for mRNA isolation, DNA sequencing, RNA-seq, genotyping, ChIP-seq and Long-read sequencing (PacBio, Oxford Nanopore). 

• Thermo Scientific™ Savant™ SpeedVac™ SPD120 Vacuum Concentrator and Kits:
• Thermo Scientific Invitrogen Qubit 4 Fluorometer:
• gBrite™ LED Plant Growth Chambers:

• Nanopore Sequencing (MinION Mk1C): Up to 50 Gb per MinION Flow Cell / 2.8 Gb per Flongle Flow Cell. Theoretical max output when system is run for 72 hours (or 16 hours for Flongle) at 420 bases / second. Outputs may vary according to library type, run conditions, etc. Nanopores read the length of DNA or RNA presented to them — from short to ultra-long (longest >4 Mb); Nanopores read the length of DNA or RNA presented to them — from short to ultra-long (longest >4 Mb) 

• Portable Photosynthesis and Chlorophyll meter: Fastest & most accurate mobile system for simultaneous leaf gas exchange & chlorophyll fluorescence measurement. This is an ideal setup for plant-stress-interaction related experiments. It measures broader photosynthesis related parameters which can predict the effects of environmental changes. The CIRAS-3 offers fully-automatic, complete and independent control of CO₂, H₂O temperature and light for response curves (i.e. fast A/Ci curves, light response, etc.). Control of all environmental parameters can be dynamic or preprogrammed. The CIRAS-3’s temperature stability and control are the most reliable in the industry. We also offer one of the widest temperature control ranges available with an extensive variety of different controlling options. 
• Isotemp Digital Dry Baths: 
• Gel electrophoresis system: The lab is equipped with horizontal gel electrophoresis system that analyze 24 samples in one go in 30 min time. This can be used for both RNA and DNA analysis. This is an important basic system for any of the workflow of metagenomics, genomics, and transcriptomics. 
• Incubator shaker: This ideally suits for microbes subculturing and growing in an optimal condition. This can accommodate 10 liters of microbial medial. The changing stub is helpful to adjust the flask and volume required for growing microbes. 
• Eppendorf™ Centrifuge 5920 R: Centrifuge 5920 R has superior capacity of up to 4 × 1,000mL; thus, making it the ideal instrument for high-throughput applications. It features a powerful state-of-the-art refrigeration system with advanced temperature management to keep your samples safe. It has swing-bucket rotors and adapters accommodate tubes and bottles from 0.2mL to 1,000mL. Plate rotor options for centrifugation of all types of MTP, PCR or Deep well Plates. Fixed-angle rotors for high-speed molecular biology applications in tubes from 0.2 mL to 50 mL. High centrifugation speed of up to 25,062 × g (13,700 rpm).   

 Other Equipment’s available in Khan’s Lab:

• Shakers (open)
• Plate spinner Fisherbrand
• Vertex table top Fisherbrand
• portable soil moisture
• Potable pH/EC/Salinity meter Hanna
• Portable Balance (3 decimal places; higher capacity)
• Magnetic Sterir
• Heating plate Fisher
• Waring industrial blender (microbial isolations from soils)
• Climate controller
• Hirayama Autoclave, medical autoclave is a device that uses steam to sterilize equipment and other objects.
• Several refrigerators and freezers are available to store the samples at 4^oC, -20^oC.
• -80^oC deep freezer to store antibodies, purified enzymes for long period of time.

Instruments available in Department: Following instruments are located in College of Technology that will be available for used by the Khan research group at no operating cost. 

• Applied Biosystems ProFlex™ 3×32-Well PCR machine
• Applied Biosystems QuantStudio™ 7 Flex Real-Time PCR System
• Dionex™ ICS-5000+ with Electrochemical and UV Detector
• BioTek ELx405^™ Plate Washer
• Shimadzu LC-2010HT HPLC System
• GE AKTA Fast Performance Liquid Chromatography Protein Purification system
• Double Beam UV-VIS Spectrophotometer
• New Brunswick BioFlo 110 Fermentation System
• Shimadzu GC-FID system
• Opentrons OT-One S Automatic microplate based pipetting station
• Tecan microplate reader
• Confocal laser scanning microscope
• Fluorescence Imaging Microscope
• CD spectrophotometer
• Powder X-ray diffraction machine
• Multiple photobioreactors (1 gal to 25 gallons) to cultivate algae.
• A bench-scale and mobile continuous flow reactor connected with online sampling arrangement connected to a gas chromatograph (TCD & FID) for the gas analysis.
• A high temperature (500°C) and high pressure (5000 psi) 500 mL batch reactor (Parr Reactor)
• Multiple high pressure tubular reactors
• Two 9.5-liter complete mix batch reactors for anaerobic digestion
• Fluidized sand bath (Techne) for batch reactions
• A bench-scale automated bioreactor
• The Automatic Methane Potential Test System (AMPTS)
• Labconco freeze dryer.
• Rotary vacuum evaporator