Welcom to muti-species TR and IG Database !

Introduction

T cell receptor (TCR) is composed of two different protein chains. The vast majority of T cells express TCRs composed of α (alpha) and β (beta) chains while a small subset expresses TCR composed of γ (gamma) and δ (delta) chains. The sequence encoded by the V(D)J junction is called complementarity determining region 3 or CDR3. This sequence has the highest variability in both alpha and beta chains and determines the ability of a T cell to recognize an antigen peptide presented by the MHC molecule.

Each B cell expresses a single B cell receptor (BCR), and the diverse range of BCRs expressed by the total B cell population of an individual is termed the 'BCR repertoire'. Many B cells undergo 'isotype switching', in which stepwise DNA deletion and recombination from immunoglobulin M (IgM) generates downstream isotypes (IgG1, IgG2, IgG3 and IgG4, IgA1 and IgA2, IgD and IgE) that confer distinct functional characteristics and roles in disease.

News

2023.12.12: TRIgdb version v1.0 published.
2024.05.30: TRIgdb version v2.0 published. Added user data upload for analysis on the Clonal Analysis page.
2025.06.10: TRIgdb v3.0 published. Implemented a DeepSeek-powered search feature on the Chat page.
2026.05.23: TRIgdb v4.0 published. Added Macaca fascicularis data, FASTA sequences for all species on the download page, and TSV files for multiple species (available via the provided hyperlink) for users to download.

Overview

TRIgdb contains 380 samples from 13 species. For each sample, the database provides the immune repertoire information, including TRA, TRB, TRD, and TRG, as well as antibodies such as IgG, IgH, IgM, IgA, and others. The recovery of the immune repertoire is derived from bulk RNA-seq using the TRUST software. Additionally, the website also offers CDR3 sequence alignment functionality, as well as analysis of immune repertoire diversity and richness for each sample or species.

Function

1. Download TR and IG tables and meta information for 13 species.
2. Providing CDR3 sequence alignment functionality.
3. Analysis of immune repertoire for 13 species.
4. Upload your data for immune repertoire analysis.
5. Providing DeepSeek-powered search functionality across 4.31 × 105 TCR and 6.23 × 106 BCR sequences.

TR and IG tab

Contact: 1120210577@mail.nankai.edu.cn
Download
Contact: 1120210577@mail.nankai.edu.cn
Download

Data Upload for Analysis

File Upload Format Requirements:

Choose Files(.tsv):

File format: Files must have the .tsv extension.

File content: Files must contain at least the following columns: clone count (Count), amino acid sequence (CDR3Aa), nucleotide sequence (CDR3nt), V, J, C. If conducting group comparisons, it is recommended to have a minimum of 2 samples per group.


Choose Files(metadata.xlsx)

File format: Metadata table must have the .xlsx extension

File content: Metadata table must contain at least the following columns: file name (File_name), sample ID (ID). It can also include grouping information (Condition) and sample sequencing depth (Seq_depth).


Remove batch effects:

Raw_count: Use the count values from the .tsv file for further analysis.

Sequencing_Depth: Ensure that the Metadata table includes a column for sequencing depth (Seq_depth) for each sample.

TRIG_Count: Use the number of immune repertoire libraries to remove batch effects.


Group or not:

If you need to perform group comparisons, please ensure that the Metadata table includes a column for grouping information (Condition) to enable group comparisons.


Analysis content:

Clonotype Analysis

Gene Uasge Analysis

Diversity Analysis


Please prepare the files for upload according to the above requirements.

Uploaded files are temporarily cached on the server only for the duration of the analysis session and are automatically deleted within 24 hours.

All data transmissions are encrypted via HTTPS.

Here is an example: a .tsv file and a metadata file

.tsv file:


metadata.xlsx file:

Download

1. Immune repertoire summary data and metadata

Immune repertoire summary data(columns):

Species_ID, File_name, Sample_ID, Read_count, Recovered_count, TRA_sum, TRB_sum, TRD_sum, TRG_sum, IGH_sum, IGL_sum, IGK_sum

Download TR/IG Data


Metadata file (columns):

Species_ID, File_name, Sample_ID, Condition, Status, Tissue, Sex, Age, Sampling_Time

Download Metadata

2. Merged CDR3 sequences in FASTA format for 13 species are available for download:

Download CDR3 FASTA (ZIP)

3. Processed TSV files from publicly available datasets

We have included processed TSV files from the following public datasets: Dolphins (GSE138765), Dogs (GSE167201), Cattle (PRJEB27764, PRJEB44470, and GSE192537).

The corresponding metadata files for dolphins, cattle, and dogs are provided in our GitHub repository: https://github.com/Anikagir/TRIgdb

4. Sequencing data from tumor-bearing cats and dogs

We have generated sequencing data from tumor-bearing cats and dogs. These data have been deposited in the Genome Sequence Archive under accession number PRJCA064318.