microbiome block

Bacterial RNA Sequencing

Overview

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.

Technology

We use the following commercially available kits and platforms for sequencing library preparation and sequencing.

  • Zymo Research/KAPA Biosystem/Illumina, RNA Library prep Kits
  • NextSeq 550 SE75 sequencing
  • NextSeq 550 PE75 sequencing
  • NovaSeq 6K PE150 sequencing

Key Features

High resolution gene expression analysis

microbiome block

ITS (Internal transcribed spacer) Sequencing for Fungi Detection

Overview

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.

Technology

We use the following commercially available kits and platforms for sequencing library preparation and sequencing.

  • Zymo Research Library prep Kits
  • MiSeqDx 500 cycle sequencing
  • MiSeqDx 600 cycle sequencing

Key Features

Rapid and high resolution taxonomy of Fungi.

microbiome block

Full-length 16S rRNA Gene Sequencing

Overview

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.

Technology

We use the following commercially available kits and platforms for sequencing library preparation and sequencing.

  • Oxford Nanopore Library prep kit
  • MinION R9.4.1 flow cell
  • EPI2ME data analysis pipeline

Key Features

Rapid and high resolution taxonomy of bacteria.

microbiome block

16S V3-V4 Amplicon Sequencing

Overview

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.

Technology

We use the following commercially available kits and platforms for sequencing library preparation and sequencing.

  • Zymo Research Library prep Kits
  • MiSeqDx 500 cycle sequencing
  • MiSeqDx 600 cycle sequencing

Key Features

OTU clustering analysis for microbiome profiling

microbiome block

DNA/RNA Extraction MRL

Overview

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.

Technology

We use following commercially available kits/reagents and platforms for nucleic acid extraction

  • ZymoBIOMICS
  • Qiagen
  • PURELINK
  • Customer approved kits for extractions
  • Qiagen Homogenizer for bead-beating

Key Features

Microbial DNA enriched nucleic acid extraction

microbiome block

Sample Quality Control-MRL

Overview

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.

Technology

Samples quantity and quality checks are done using following platforms

  • TapeStation 4150 System
  • Bioanalyzer 2100 system
  • Qubit Flex
  • Picogreen Victor x3

Key Features

Precise estimate of nucleic acid concentration and molecular weight for NGS

Bo Zhang

Bo Zhang

Carlos Arana

Carlos Arana

Tulasi Relangi

Tulasi Relangi

Srisha Sridharan

Srisha Sridharan