Cogent ngs immune profiler software

Manufactured by Takara Bio

Sourced in United States

The Cogent NGS Immune Profiler Software is a bioinformatics tool designed for the analysis of high-throughput sequencing data generated from immune repertoire studies. The software provides a comprehensive workflow for the processing, annotation, and visualization of T-cell receptor (TCR) and B-cell receptor (BCR) sequencing data.

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Lab products found in correlation

Nucleospin rna plus xs, by Takara Bio (1 mentions) Smarter human tcr a b profiling kit v2, by Takara Bio (1 mentions) Miseq system, by Illumina (1 mentions) 2100 bioanalyzer, by Agilent Technologies (1 mentions) Nucleospin rna plus kit, by Macherey-Nagel (1 mentions) Dna 1000 kit, by Agilent Technologies (1 mentions)

2 protocols using cogent ngs immune profiler software

Bulk TCR Profiling via Illumina MiSeq

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Bulk sequencing of tetramer-positive cells (SMARTer Human TCR a/b Profiling Kit v2, Takara Bio USA) was performed after amplifying cDNA from mRNA (NucleoSpin RNA Plus XS, Takara Bio USA), using an Illumina MiSeq system (paired-end 300 bp). Raw reads were assembled using Cogent NGS Immune Profiler Software (Takara Bio USA).

Mayer-Blackwell K., Ryu H., Codd A.S., Parks K.R., MacMillan H.R., Cohen K.W., Stewart T.L., Seese A., Lemos M.P., De Rosa S.C., Czartoski J.L., Moodie Z., Nguyen L.T., McGuire D.J., Ahmed R., Fiore-Gartland A., McElrath M.J, & Newell E.W. (2023). mRNA vaccination boosts S-specific T cell memory and promotes expansion of CD45RAint TEMRA-like CD8+ T cells in COVID-19 recovered individuals. Cell Reports Medicine, 4(8), 101149.

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Profiling of Immune Cell Receptors

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RNA was isolated from PBMCs using NucleoSpin RNA Plus Kit (Macherey-Nagel). T cell and B cell receptor (TRA, TRB, and BCRH) libraries were prepared using 100 ng RNA by using SMARTer Human TCR a/b and BCR IgG H/K/L Profiling Kit (Takara) according to the manufacturer’s instructions. The library validation was performed by amplicon size measurement on 2100 Bioanalyzer using the DNA 1000 kit (Agilent). The repertoire library was sequenced on NextSeq 550 platform. The immune profiling data was generated by using Cogent NGS Immune Profiler Software (Takara). Data analyses were performed on R Studio using Immunarch Package (https://immunarch.com/, https://github.com/immunomind/immunarch) and IMGT (the international ImMunoGeneTics information system) HighV-QUEST and StatClonotype [9 (link)].

Aba Ü., Maslak İ.C., İpşir C., Pehlivan D., Warnock N.I., Tumes D.J., Cildir G, & Erman B. (2024). A Novel Homozygous Germline Mutation in Transferrin Receptor 1 (TfR1) Leads to Combined Immunodeficiency and Provides New Insights into Iron-Immunity Axis. Journal of Clinical Immunology, 44(2), 55.

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