Techniques

Next Generation Sequencing applications 

(Please contact Ana Dopazo for more detailed information)

  • RNA-Seq (from ≤ 100 ng total RNA)
  • Low input RNA Seq:
    • starting from as little as 500 pg total RNA (and lower)
    • starting from isolated cells
    • Single-cell RNA-seq
  • Small RNA-Seq (from 250 ng total RNA or less)
  • ChIP-Seq
  • PCR Seq
  • Exome Seq
  • Targeted Resequencing

Automation

The Genomics Unit offers two free informatics applications developed “in situ”. Automatic Genomics Next Generation Sequencing (AG-NGS), for the automation of library preparation for Next Generation Sequencing and Automatic Genomics for qPCR (AG-qPCR), for the automation of medium throuput qPCR experiments.

  • AG-NGS
    From this page you can download AG-NGS, an user friendly informatics application that allows any non professional programmer user, to automate library preparation process for Illumina Next Generation Sequencing experiments by using TruSeq protocols and a Tecan liquid handling robot.
  • AG-qPCR
    From this page you can download AG-qPCR, an informatics application that allows any non professional programmer user, to automate medium throughput qPCR experiments by using a Fredom Evo series (Tecan) liquid handling robots (Callejas S, Alvarez R, Dopazo A. Biotechniques 2011, 50(1):46-50). The user is able to optimize the plate design according to the characteristics of the experiment in terms of number of genes, number of samples and different controls that would like to include.

Other techniques

  • Real time cuantitative PCR (only for CNIC users)
    • maintenance and management of real-time PCR instruments
    • user advice and training on qPCR technology
    • training on qPCR data analysis
    • development of informatic tools to handle and analyse qPCR data
    • Taqman array processing service
  • DNA and RNA shearing by Covaris

 

IMPORTANT: Users from outside the CNIC should contact the Genomics Unit before ordering/planning any service.

Equipment

NGS sequencers:

  • Illumina HiSeq 2500
  • Illumina HiSeq 4000
  • Illumina MiSeq

Liquid Handling & Automation Systems:

  • Robotic Platform Freedom EVO 200, Tecan
  • Robotic Platform Fluent, Tecan

Single-Cell Analysis Systems:

  • Fluidigm C1 Single Cell Auto Prep System
  • Chromium Controller (10x Genomics) for single cell analysis

Real-Time PCR Systems:

  • ABI PRISM® 7900HT Sequence Detection System
  • ABI PRISM® 7900HT FAST Real-Time PCR System
  • ABI PRISM® 7000 Sequence Dectection System
  • BIORAD CFX 384 Touch Real Time PCR Detection System
  • BIORAD CFX 96 Touch Real Time PCR Detection System

Others:

  • DNA ultrasonicator Covaris E220
  • Agilent 2100 Bioanalyzer System
  • Agilent 4200 TapeStation system
  • Affymetrix Microarray Platform