The TCR Sequencing Unit has developed a number of pipelines and protocols for the unbiased, high-throughput amplification, sequencing and analysis of TCR repertoires.

These approaches include using unique molecular barcoding error-correction procedures to produce robust quantitative repertoire data, which is analysed using our in-house Decombinator suite of analysis scripts that we have developed for the rapid identification and description of rearranged TCR sequences.

We are interested in using our TCR sequencing pipeline to explore T-cell biology in many different settings. This includes investigating the perturbance of repertoire features in response to infectious challenge, assessing the impact of primary immunodeficiencies, and exploring the clonal distribution between different T-cell subsets and tissues.

Some of the projects, we have been involved in are:

TracerX
ACED
COSMOS
BIOAID

TCR Sequencing Unit has two RNA based protocols to prepare libraries.

Ligate TCR Seq Protocol

Works for tissue, blood, sorted cells and PBMC RNA samples.
Results in Alpha and Beta Chain.
Unique Dual index.
For Mouse and Human samples.
Sequence on Novoseq X plus with paired end reads.

FUME TCR Seq Protocol

Works on FFPE and poor Quality RNA samples.
Results in only Beta chain.
Unique Dual index.
For Human samples only.
Sequenced with paired end reads.

Frequently Asked Questions

The TCR Sequencing Unit accepts extracted RNA samples.
TCR Sequencing Facility can extract RNA from Tempus and PAXGene tubes at an additional cost. Please contact the team to discuss individual requirements.
Ligate TCR requires 500ng total RNA for Blood or PBMC and 1000ng for tumor or low quality samples.
FUME TCR requires 50-100ng depending on the type of sample being submitted.
Samples do not need to be DNase treated as this is included in both protocols. However please ensure this is noted on the submission form.
Yes the TCR Sequencing Facility can QC RNA samples on Tapestation at an additional charge.
If QC is not being requested from the TCR Sequencing Unit , all RNA Samples should be checked on Tapestation, BioAnalyser or Qubit to see concentration and quality before submission. The resulting concentration and/or RIN should be noted on submission form.
The FUME TCR protocol was created to allow for FFPE samples to be processed, it is also useful on samples which have poor RIN or are degraded. FUME protocol currently only works on beta chain of samples.
Ligate TCR protocol works on blood, tissue, PBMC and cells but has shown to be more effective on RINs higher than 2.5.
The Sequencing Unit will recommend the protocol once the submission form has been viewed.
Samples should be shipped on Dry Ice, the sample tubes should be labelled with corresponding IDs to Submission form and stored in a Freezer box.
Please contact the Sequencing Unit before sending samples.
Once samples are submitted, the sequencing unit will inform the current turnaround time.
Sample quality can impact the turnaround time.
However the Unit will keep you informed of the current status of your samples.
You will have access to the Collapsed data which is the Unique TCR transcripts, the Translated data which is all data referring to the TCR present in the sample, and all of the Log data along with the Summary sheet.
The cost per sample depends on funding.
FEC: £386.84
Charity: £300.02
Industry: £464.21
(As of 2024)
For RNA tapestation QC, it is £6.00 per sample. (As of 2024).
For further analysis on TCR Sequencing data, please refer to the ARRP page on this website.