Check the RNA/DNA quality to get RIN/DIN and concentration
Agilent 2100 Bioanalyzer system and Agilent 4150 TapeStation Systems are used to get the RIN/DIN, Nanodrop and Picogreen to measure the concentration
RIN/DIN > 7 is considered good quality
Whole-genome sequencing (WGS) is a comprehensive assay for analyzing the entire genome. This assay generates deep sequencing data on genomic DNA extracted from bacterial culture or clinical isolates. About 500-1000 ng of high complexity genomic DNA is required for sequencing library preparation using kits from KAPA biosystem, Illumina, etc. Genomic fragments of 300-500bp size are ligated with Illumina recommended adapters containing unique barcodes or Unique Molecular Identifiers (UMIs). These libraries can be sequenced on MiSeqDx, HiSeq or NextSeq platforms to achieve 70-100 fold sequencing coverage across the entire genome.
We use the following commercially available kits and platforms for sequencing library preparation and sequencing.
This assay allows complete quantification and characterization of native RNA or cDNA molecules present in a sample. A sequencing library is constructed on poly-A enriched RNA followed by sequencing on MinION/Mk1c platform from Oxford Nanopore.
We use the following commercially available kits and platforms for sequencing library preparation and sequencing.
RNA sequencing or RNA-seq is a next-generation sequencing (NGS) based assay to quantify the gene expression. It is a method of choice for the study of differential gene expression. In this assay, we construct a sequencing library on total RNA and perform high depth sequencing to capture the number of transcripts per gene. This assay requires high integrity RNA (RNA integrity number >7) as input for sequencing library construction followed by deep sequencing on Illumina platform.
We use the following commercially available kits and platforms for sequencing library preparation and sequencing.
High resolution gene expression analysis
This assay sequence internally transcribed spacer (ITS) region that lies between highly conserved nuclear ribosomal DNA (rDNA) genes (18S, 5.8S, 28S). Fungal ITS sequencing can recognize sample diversity from samples to investigate the biological significance.
We use the following commercially available kits and platforms for sequencing library preparation and sequencing.
Rapid and high resolution taxonomy of Fungi.
This assay sequences full-length 16S rRNA gene sequence (V1-V9) which allows high resolution taxonomic classification of microbes in a given specimen. We provide this service using Oxford Nanopore long-read sequencing technology. Full length 16S rRNA gene is amplified and sequenced on MinION /Mk1c R9.4.1. Flow cell. We input about 50-100 nanogram DNA for this assay.
We use the following commercially available kits and platforms for sequencing library preparation and sequencing.
Rapid and high resolution taxonomy of bacteria.
This assay sequences targeted hypervariable regions i.e. v3-v4 of Bacterial 16S rRNA gene for identification and taxonomic classification of bacterial communities in a given specimen. We provide services to sequence various hypervariable regions (V1-V9) of 16S rRNA gene for bacterial taxonomy and phylogeny. Customers can select the hypervariable region/s based on their sample source and study aims. We input about 10-100 nanogram DNA for this assay.
We use the following commercially available kits and platforms for sequencing library preparation and sequencing.
OTU clustering analysis for microbiome profiling
Microbiome core provides nucleic acids (DNA / RNA) extraction service for various kinds of samples including, but not limited to Saliva, Sputum, Stool, Urine, Blood, Solid tissue, Oral swab, Skin swab, Bacterial culture, Biofilm, Environmental specimens.
We use following commercially available kits/reagents and platforms for nucleic acid extraction
Microbial DNA enriched nucleic acid extraction
This service determines nucleic acid concentration and quality of sample for microbiome sequencing analysis. Sample quality checks are done using TapeStation Systems or Bioanalyzer Agilent TapeStation or the 2100 Bioanalyzer system is an established high-sensitivity automated electrophoresis tool for the sample quality control of biomolecules. The Bioanalyzer or Tapestation can be used to assess the size and quality of DNA /RNA over a range of sizes and concentrations.
Samples quantity and quality checks are done using following platforms
Precise estimate of nucleic acid concentration and molecular weight for NGS
The Illumina iScan system is an array scanner that supports sensitive and accurate imaging of Illumina’s array based genetic analysis products.
Illumina bead-based microarray technology uses silica microbeads. As DNA fragments pass over the BeadChip, each probe binds to a complementary sequence in the sample DNA, stopping one base before the locus of interest. Allele specificity is conferred by a single base extension that incorporates one of four labeled nucleotides. When excited by a laser, the nucleotide label emits a signal. The intensity of that signal conveys information about the allelic ratio at that locus.
Wide range of arrays available: