ALERT

In observance of US Thanksgiving holiday, Agilent Cross Lab iLab Operations Software will be closed during US hours on Thursday November 23rd and Friday November 24th, 2017. EU and APAC support coverage will remain open during this time. We will resume US support hours on Monday November 27th, 2017. For urgent matters, please add "URGENT" to the ticket subject and these requests will be prioritized first.

qPCR CoRE

Overview of Services

The quantitative PCR (qPCR) CoRE provides access to fully automated instruments for Nanostring nCounter analysis, droplet digital PCR, real-time PCR, automated RNA/DNA isolation, 10X Genomics Chromium, 1CellBio inDrop system, and liquid handling. The facility offers services involving Nanostring nCounter analysis, PCR assay development, allelic discrimination assays, RNA/DNA extrac­tions, cDNA synthesis, setting-up PCR reactions, single-cell seq library preparation, and data analysis.

Instruments:

  • 2 ABI PRISM 7900HT sequence detection systems with robotic arms (Applied Biosystems)
  • QX100 Droplet Digital PCR System (Bio-rad)
  • NanoString nCounter platform (Nanostring Technologies)
  • BiomekNX Laboratory Automation Workstation (Beckman)
  • BiomekFX Laboratory Automation Workstation (Beckman)
  • 10X Genomics Chromium
  • 1CellBio inDrop system
  • Fragment Analyzer (Advanced Analytical)
  • Bioanalyzer (Agilent)
  • Qubit
  • Nanodrop2000
  • Omni International Bead Ruptor

Services:

  • Real-time PCR plate (384 and 96 well) run
  • Allelic discrimination run (plate read)
  • PCR assay set up using Beckman Biomek robot
  • Automated DNA/RNA extraction from any tissues
  • DNA/RNA extraction from tissues, whole blood, and FFPE samples
  • Reverse transcription
  • Primer design, synthesis, and validation
  • TaqMan assay acquisition
  • Real-time PCR assays (SYBR-green and TaqMan) and data analysis
  • SNP genotyping assays
  • Digital PCR: Droplet generation, amplification, and reading
  • NanoString assays and data analysis
  • Rodent pathogen (pinworm and helicobacter) detection assays
  • Single-Cell RNA-Seq library preparation using 10x Genomics Chromium and 1CellBio inDrop system

Supplies:

  • ABI 384 well PCR plates and covers
  • Validated human and mouse qPCR SYBR green assays (see below the links and resources for details)

Custom Services: 

We undertake small- to large-scale custom gene expression profiling services (sample to data) by qPCR, ddPCR, and NanoString assays on a fee-for-service basis. We also offer services to develop custom gene expression assays, SNP assays, single-cell RNA-seq library preparation using 10x Genomics Chromium and 1CellBio inDrop sytem, and diagnostic assays for the detection of pathogens in biological samples. For details, please contact venugopalan.nair@mssm.edu.

Leadership

Venugopalan Nair, PhD - Director
Associate Professor of Neurology
Phone: 212-241-5809, 212-241-1155
E-mail: venugopalan.nair@mssm.edu

Location and Hours of Operation

Hours Location

Monday - Friday 9:00am - 5:00pm 

Annenberg Building
14th Floor, Room 72         
1468 Madison Avenue
New York, NY 10029
Phone: 212-241-6413

Links and Resources

  1. Quantitative PCR CORE website
  2. iLab qPCR CoRE user instructions
  3. iLab customer help manual
  4. iLab user training video
  5. Standard real-time PCR conditions
  6. ddPCR protocol
  7. NanoString sample submission instructions
  8. 10X Genomics Chromium and 1CellBio inDrop system
  9. List of validated SYBR green qPCR assays available from the core

Contacts

Name Role Phone Email Location
Venugopalan Nair, PhD
Director
 
212-241-5809
 
venugopalan.nair@mssm.edu
 
Annenberg 14-72
 
Nada Marjanovic
CoRE Manager
 
212-241-6624
 
nada.marjanovic@mssm.edu
 
Annenberg 14-76