scholarly journals clonotypeR--high throughput analysis of T cell antigen receptor sequences

2015 ◽  
Author(s):  
Charles Plessy ◽  
Encarnita Mariotti-Ferrandiz ◽  
Ri-Ichiroh Manabe ◽  
Shohei Hori
Keyword(s):  
T Cell ◽  
High Throughput ◽  
Complex Mixture ◽  
Data File ◽  
Third Party ◽  
Antigen Receptors ◽  
High Throughput Analysis ◽  
Reference Segment ◽  
Large Numbers ◽  
Pcr Products

Motivation The T cell receptors are expressed as millions of different rearrangements. Amplified as a complex mixture of PCR products, they can be sequenced directly on next-generation instruments without the need for cloning. This method is increasingly used to characterize, quantify and study these highly diverse receptors. Results We present here clonotypeR, a software package to identify and analyze antigen receptors from high-throughput sequence libraries. ClonotypeR is designed to process, organize and analyze very large numbers of sequences, in the order of millions, typically produced by Roche 454 or Illumina instruments, and is made of two parts. The first contains shell scripts and reference segment sequences to produce a data file where each line represents a the detection of a clonotype in a sequence read. The second part is a R module available from Bioconductor, to load and filter the data, and prepare clonotype abundance tables ready for analysis with third-party tools for differential representation analysis, sample clustering, etc. To analyze clonotype data at the nucleotide level, we introduce unique clonotype identifiers based on those developed by Yassai et al. (2009), that we corrected to avoid identifier collisions. Availability http://clonotyper.branchable.com (CC0 license).

scholarly journals High Throughput Sequencing of T Cell Antigen Receptors Reveals a Conserved TCR Repertoire

Medicine ◽  
2016 ◽  
Vol 95 (10) ◽  
pp. e2839 ◽  
Author(s):  
Xianliang Hou ◽  
Chong Lu ◽  
Sisi Chen ◽  
Qian Xie ◽  
Guangying Cui ◽  
...  
Keyword(s):  
T Cell ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Antigen Receptors ◽  
Cell Antigen ◽  
Tcr Repertoire ◽  
T Cell Antigen Receptors

scholarly journals High‐throughput analysis of T cell–monocyte interaction in human tuberculosis

2020 ◽  
Vol 201 (2) ◽  
pp. 187-199
Author(s):  
M. Habtamu ◽  
G. Abrahamsen ◽  
A. Aseffa ◽  
E. Andargie ◽  
S. Ayalew ◽  
...  
Keyword(s):  
T Cell ◽  
High Throughput ◽  
High Throughput Analysis ◽  
Throughput Analysis

scholarly journals High-throughput cell transplantation establishes that tumor-initiating cells are abundant in zebrafish T-cell acute lymphoblastic leukemia

Blood ◽  
2010 ◽  
Vol 115 (16) ◽  
pp. 3296-3303 ◽  
Author(s):  
Alexandra C. H. Smith ◽  
Aubrey R. Raimondi ◽  
Chris D. Salthouse ◽  
Myron S. Ignatius ◽  
Jessica S. Blackburn ◽  
...  
Keyword(s):  
T Cell ◽  
Single Cell ◽  
Cell Transplantation ◽  
High Throughput ◽  
Large Scale ◽  
Lymphoblastic Leukemia ◽  
Rapid Screening ◽  
Tumor Initiating Cells ◽  
Self Renewal ◽  
Large Numbers

Abstract Self-renewal is a feature of cancer and can be assessed by cell transplantation into immune-compromised or immune-matched animals. However, studies in zebrafish have been severely limited by lack of these reagents. Here, Myc-induced T-cell acute lymphoblastic leukemias (T-ALLs) have been made in syngeneic, clonal zebrafish and can be transplanted into sibling animals without the need for immune suppression. These studies show that self-renewing cells are abundant in T-ALL and comprise 0.1% to 15.9% of the T-ALL mass. Large-scale single-cell transplantation experiments established that T-ALLs can be initiated from a single cell and that leukemias exhibit wide differences in tumor-initiating potential. T-ALLs also can be introduced into clonal-outcrossed animals, and T-ALLs arising in mixed genetic backgrounds can be transplanted into clonal recipients without the need for major histocompatibility complex matching. Finally, high-throughput imaging methods are described that allow large numbers of fluorescent transgenic animals to be imaged simultaneously, facilitating the rapid screening of engrafted animals. Our experiments highlight the large numbers of zebrafish that can be experimentally assessed by cell transplantation and establish new high-throughput methods to functionally interrogate gene pathways involved in cancer self-renewal.

Sign in / Sign up

Export Citation Format

Share Document