Accessing Different Facilities Through SAHAJ

• SOP for Access
• Charges

DNA Sequencing & Real Time PCR

• Massively parallel sequencing platforms of GS-FLX (Roche-454), HiSeq-2000 & 2500 (Illumina), Ion Proton & Ion Torrent PGM (Life Technologies) for whole genome sequencing, exome sequencing, targeted resequencing, metagenomics, amplicon sequencing, RNA-Seq & small RNA-Seq, ChIP-Seq
• ABI3500XL Genetic Analyzer (Life Technologies) for Sanger/CE sequencing and fragment analysis
• ABI7900 HT (Life Technologies) and Lightcycler LC480 (Roche) for high throughput real time PCR
• 2100 Bioanalyzer (Agilent) for sequencing library QA/QC

Microarray

• Complete laboratory set up for processing Illumina bead arrays
• Bead arrays scanned in iScan (Illumina) and the data analyzed in Genome Studio
• Genome wide genotyping, gene expression and methylation array analyses

Cell Biology

• Tissue culture facility covering approximately 300sqft area with separate module of 100sqft "restricted-entry" sterile cell culture area: with all necessary equipment and gadgets needed for the primary culture of human tissues and maintenance of human and animal cell lines, which includes bio-safety cabinets, CO2 incubators, digital water baths, cell counters, fluorescence microscopes (both inverted and regular) with documentation system, liquid nitrogen bio-repositories, freezers, chromatography refrigerators, sonicator-tissue homogenizer with sound abatement chamber and high-speed refrigerated centrifuges.
• Bacterial culture facility for cloning and expression of recombinant genes: equipped with culture hood, shaker incubator, water bath and high speed centrifuges.
• Facilities for protein analysis: expression, Western blotting along with both an imaging system and dark room facility.
• Microscopy/Imaging facilities: for conducting Immunofluorescence assays, Immunocytochemical/Immunohistochemical assays.
• Cancer Stem Cell Culture and characterization Facility: clean room with biosafety cabinets, CO2 incubators, centrifuge, microscope, refrigerators and deep-freezers; equipped with instrumentations to perform cell based assays as well as cell sorting - MACS based cell sorting as well as fluorescence based cell analysis using microscopy and flow-cytometry; infrastructure for fluorescence-activated cell sorting (FACS) will be available shortly.

Data Analysis and Storage Infrastructure

The high performance computing and centralized data storage services of NIBMG are operated on 24x7 mode from a Data Centre located inside the institute. The facility consists of the following components:

• 300 TB Grid Scalar Central Data Storage platform (DDN)
• iCompute high performance system
• High performance parallel computing Clusters (PSSC Lab)
• High end servers and Workstations
• High performance computing cluster
• 10 GBPS Ethernet network

The zebrafish is a fresh-water vertebrate that has now become well established as a model for studying vertebrate development, evolution, genetics, and cell biology, due to its small size, high fecundity and transparent embryos. Its amenability for large scale forward genetic screens, morpholino mediated knock-down of gene activity, targeted mutations and knock-in with the CRISPR/Cas9 technology and ease of transgenesis makes it an ideal vertebrate system for experimental investigations. In addition, the zebrafish is significantly more economical to house and breed compared to the mouse and most importantly, its genome is fully sequenced and highly like mammalian and human genomes. This makes the zebrafish a versatile vertebrate for the systematic modeling human diseases that range from metabolic and infectious diseases to cancer and rare Mendelian disorders.

In NIBMG, we have established a zebrafish facility that primarily intends to utilize existing expertise within our institution in disease modelling, bioinformatics, zebrafish assay development and mechanistic studies. These studies will set the stage for investigating gene networks elemental in prevailing human disease phenotypes at a functional level, and create high-throughput biology in the zebrafish as a platform to complement genome-wide association studies (GWAS) across a wide spectrum of traits. Most importantly, this approach can instantly be implemented to drug response phenotypes and novel traits as they originate. Human genomic research has already detected a substantial number of loci associated with numerous common complex human diseases and have surpassed conventional experimental methodologies for understanding intrinsic disease mechanisms. Nowadays, multiple studies worldwide have established the benefit of the zebrafish model system in investigating functionally relevant genes at GWAS loci, and in comprehending the molecular mechanisms by which these genes influence human traits. The NIBMG zebrafish facility, therefore, provides support to researchers with broader classes of genomic variations. The major function of this resource includes confirming the functionality of genes and regulatory elements underlying human disease biology with high efficiency and generation of relevant animal models that uphold in-depth studies of disease mechanisms or potential drug discovery.