Techniques

    Next Generation Sequencing applications 

    (Please contact Ana Dopazo for more detailed information)

    • RNAseq (from ≤ 100 ng total RNA)
    • Low input RNAseq
    • Small RNAseq (from 250 ng total RNA or less)
    • ChIP-Seq
    • PCR Seq
    • Exome Seq
    • Targeted Resequencing
    • Single-cell RNAseq, single cell immune profiling
    • Single-nucleus RNAseq, single-nucleus multiome (RNA + ATAC)

    Other techniques

    • Real time cuantitative PCR (only for CNIC users)
    • DNA and RNA shearing by Covaris

    Automation

    The Genomics Unit has developed two free informatics applications to automate sample processing. Automatic Genomics Next Generation Sequencing (AG-NGS), for the automation of library preparation for NGS 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.
    • 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 NextSeq 2000
    • Illumina MiSeq
    • NovaSeq 6000
    • MinION (Oxford Nanopore Technologies), a portable sequencer.

    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
    • BD Rhapsody™ Single-Cell Analysis System

    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