TCRb Sequencing

Featured Sequencing: T-Cell Receptor Profiling
Preferred Academic Partner of ThermoFisher
Full Data and Reports included!

Full data sets provided, custom reports generated and access to interactive data analysis tools to work with your data in ThermoFisher’s powerful Ion Reporter Cloud. Standard and Deep Sequencing options are available. Assistance with experiment design, sample preparation, study design and custom analysis from our data science group is available.

Key Features

  • Clonal Expansion Profiling of TCR’s
  • T-Cell Repertoire Comparison
  • T-Cell Convergence
  • TCRb targeted primer kits
  • CDR3 and CDR1+CDR2+CDR3 sequencing options with DNA and RNA
  • Competitive Pricing
  • 5-10 days turnaround time based on sample drop off days
  • Re-run guarantee* (we re-run samples one extra time for no additional cost if we see poor results)
  • Expert analysis available
  • Study Design available from PhD Biostatisticians
  • Partnerships on larger projects
  • Interactive Data Report AND sequencing files for further analysis

 

ThermoFisher Product Resources

TCR Beta-SR Assay
TCR Beta-SR Assay - DNA
TCR Beta-LR Assay

 

Sample Prep

Please refer to instructions in the extraction kit. If you have further questions, reach out to the core for clarification. For DNA, we can help match your samples to a workflow and kit that has previously performed well for us.
 

Sample Prep Guidance

1) TCRb
We have had success with the Qiagen kits for RNA and DNA. Please contact us for more information to match your sample sources and amounts

  • FFPE - Both RNA and DNA from the same sample- Recover Total Nucleic Acid Isolation kit for FFPE. Please contact the core to confirm your extraction method matches your sequencing needs.

  • MagMax FFPE DNA/RNA Ultra kit works well for low genomic amounts

 
2) DNA
There are many kits and applications for different cell sources. Please contact the core to confirm that your extraction method matches the sequencing technique being requested.

  • FFPE and low abundance samples will need a consult prior to submission.

 
3) RNA
For RNA extraction and sample prep, we have had success using RNeasy Mini or RNeasy Micro kit (Qiagen). We highly recommend performing all of the optional steps including the DNAse treatment in RNA extraction.

  • RNeasy Mini kit- elution at 30uL. Client must provide 5uL of QC aliquot, and the RNA stock. It is ok to do an internal QC.

  • RNeasy Micro kit- elution at 13uL. Send the the RNA stock. We prefer you NOT to perform internal QC when using this kit to preserve RNA amounts.

  • We highly recommend performing all of the optional steps including the DNAse treatment.

  • For the RNeasy mini kit, please provide concentration

  • Store and submit samples using DNA LoBind tubes (1.5 uL)

– Eppendorf Tubes Cat# 022431021

 

Labeling

  • Black permanent marker for labeling
  • Top tube label – 1A+Pi initials, 2A+Pi initials (i.e. 1AKW). Initials will be determined by us
  • Side of the tube = Sample name

 

Shipping

  • Parafilm tubes
  • Biohazard Ziploc filled with Kimwipes or napkins/tissues
  • Sandwiched between dry ice
  • Include sample sheet in the box in Ziploc back
  • Put QC tubes and Stock RNA in two separate Ziploc bags

 
Attn: Fatjon Leti, A642
National Jewish Health
1400 Jackson St
Genomics Facility CGEH
Denver, CO 80206

 

Supporting Papers

Comparative analysis of murine T-cell receptor repertoires, M Izraelson et al, Immunology. 2018 Feb;153(2):133-144

Quantifiable predictive features define epitope specific T cell receptor repertoires, P Dash et al., Nature. 2017 Jul 6;547(7661):89-93

Identifying specificity groups in the T cell receptor repertoire, J Glanville et al., Nature. 2017 Jul 6;547(7661):94-98

IMGT, the international ImMunoGeneTics database, M-P Lefranc et al., Nucleic Acids Res. 1999 Jan 1;27(1):209-12

VDJdb: a curated database of T-cell receptor sequences with known antigen specificity, M Shugay et al., Nucleic Acids Res. 2018 Jan 4;46(D1):D419-D427