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Benchmarking V(D)J Repertoire Reconstruction: Bulk RNA-Seq vs PCR-Based RepSeq Validated by SMRT Sequencing [RACE_RepSeq]

ABSTRACT: The aim of this study is to benchmark methods for immunoglobulin repertoire profiling using human B-cell samples. We compare targeted VDJ mRNA sequencing and repertoire reconstruction from bulk RNA-seq data to PCR-independent full-length transcript sequencing using Single-Molecule Real-Time technology. The objective is to assess methodological biases and establish a robust reference framework for immunoglobulin repertoire analysis.

ORGANISM(S): Homo sapiens

PROVIDER: GSE326977 | GEO | 2026/04/10

REPOSITORIES: GEO

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Benchmarking V(D)J Repertoire Reconstruction: Bulk RNA-Seq vs PCR-Based RepSeq Validated by SMRT Sequencing [SMRT]

Project description:The aim of this study is to benchmark methods for immunoglobulin repertoire profiling using human B-cell samples. We compare targeted VDJ mRNA sequencing and repertoire reconstruction from bulk RNA-seq data to PCR-independent full-length transcript sequencing using Single-Molecule Real-Time technology. The objective is to assess methodological biases and establish a robust reference framework for immunoglobulin repertoire analysis.

2026-04-10 | GSE326988 | GEO

Benchmarking V(D)J Repertoire Reconstruction: Bulk RNA-Seq vs PCR-Based RepSeq Validated by SMRT Sequencing [RNA-Seq]

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Benchmarking V(D)J Repertoire Reconstruction: Bulk RNA-Seq vs PCR-Based RepSeq Validated by SMRT Sequencing [SMRT]

Project description:Benchmarking V(D)J Repertoire Reconstruction: Bulk RNA-Seq vs PCR-Based RepSeq Validated by SMRT Sequencing [SMRT]

| PRJNA1448050 | ENA

Benchmarking V(D)J Repertoire Reconstruction: Bulk RNA-Seq vs PCR-Based RepSeq Validated by SMRT Sequencing [RACE_RepSeq]

Project description:Benchmarking V(D)J Repertoire Reconstruction: Bulk RNA-Seq vs PCR-Based RepSeq Validated by SMRT Sequencing [RACE_RepSeq]

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Benchmarking V(D)J Repertoire Reconstruction: Bulk RNA-Seq vs PCR-Based RepSeq Validated by SMRT Sequencing [RNA-Seq]

Project description:Benchmarking V(D)J Repertoire Reconstruction: Bulk RNA-Seq vs PCR-Based RepSeq Validated by SMRT Sequencing [RNA-Seq]

| PRJNA1448034 | ENA

Antibody repertoire sequencing of human tonsillar B cell subsets

Project description:In response to antigen challenge, human B cells clonally expand, undergo selection and differentiate within secondary lymphoid tissues to produce mature B cell subsets and high affinity antibodies necessary for an effective immune response. However, the interplay between affinity, antibody class and different B cell fates has proved challenging to decipher in primary human tissue. We have applied an integrated analysis of bulk and single-cell antibody repertoires paired with single-cell transcriptomics of human B cells from a model secondary lymphoid tissue. Specifically, here we have performed bulk B cell repertoire sequencing of the immunoglobulin heavy chain (IgH) for sorted B cell subsets from paediatric tonsil tissue. Matched single-cell gene expression and single-cell VDJ data are also available for the same patient donors.

2020-05-01 | E-MTAB-8999 | biostudies-arrayexpress

Igh repertoire analysis in primary pro-B cells from WT, NE1-/- , Site1.3 -/- mice (VDJ-seq)

Project description:Analysis of the antibody repertoire composition is now possible using VDJ-seq. We used this recently developed method for unbiased amplification from genomic DNA (gDNA) to directly compare the Igh repertoire of C57Bl/6 (WT), NE1-/- and Site1.3 -/- pro-B cells. We find that a group of contiguous proximal and intermediate VH genes are under-utilized in V->DJ rearrangement in the absence of NE1 revealing a NE1 zone of influence. We report the VH gene usage profile from WT, NE1-/- and Site1.3 -/- primary pro-B cells from the VDJ-seq data.

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Revisiting proliferative glomerulonephritis with monoclonal immunoglobulin deposits through immunoglobulin repertoire sequencing

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Local Chromatin Features Including PU.1 and IKAROS Binding and H3K4 Methylation Shape the Repertoire of Immunoglobulin Kappa Genes Chosen for V(D)J Recombination

Project description:Background: V(D)J recombination is an essential process for the generation of diverse antigen receptor (AgR) repertoires. In B cells, immunoglobulin kappa (Igk) light chain locus recombination follows recombination of the immunoglobulin heavy chain (Igh) locus. We recently developed the DNA-based VDJ-seq assay for the unbiased quantitation of Igh VH and DH repertoires. In conjunction with genome-wide datasets for several epigenetic features, we showed that two active chromatin states, located at the recombination signal sequences (RSS) of VH genes, are highly predictive of recombination. The contribution of chromatin features to Vk gene choice in recombination remains poorly understood. Results: We adapted the VDJ-seq assay to profile the Igk VkJk repertoire, and obtained a comprehensive readout of highly variable Vk gene usage in mouse bone marrow pre-B cells. We identified PU.1 binding at the RSS as highly predictive of whether a gene will actively recombine or not. Prediction of the frequency of recombination was more dependent on H3K4 methylation and IKAROS binding. Conclusions: Epigenetic features within the Vk region are able to explain much of the variation in Vk gene usage. Whilst PU.1 binding at the RSS appears to play a binary, all-or-nothing role, priming Vk genes for recombination, the frequency with which these genes recombine is shaped by the presence and enrichment of a number of other epigenetic features. In contrast to the Igh locus, the epigenetic landscape of the promoter as well as the RSS is predictive of Vk gene recombination.

2017-11-03 | GSE101606 | GEO

Ablation of SetD2 impaired the lymphocyte development in mouse models.

Project description:The repertoire of diverse T-cell receptors (TCRs) and immunoglobulins is generated through restrictedly lineage and stage specific DNA rearrangements of variable (V), diversity (D) and Joining (J) gene segments at early T and B cell development. Histone modifications has been demonstrated to ensure proper VDJ recombination. However, the epigenetic mechanisms and the role of enzymes that catalyze epigenetic modifications in regulating VDJ recombination still remain largely unexplored. Herein we report that deletion of SetD2, the histone methyltransferase to catalyze the trimethylation of lysine 36 on histone 3, leads to severe lymphopenia due to development blockage of T lymphocyte at the double negative 3 (DN3) stage and differentiation arrest of B cell development at the pro-B stage in genetically engineered mouse models. SetD2 deficiency causes a loss of H3K36me3 and markedly impairs VDJ rearrangement of TCRβ and immunoglobulin heavy chain. Our study demonstrates that SetD2 and its mediated H3K36M3 modification are required for the VDJ recombination and normal lymphocyte development.

2019-02-01 | GSE116685 | GEO

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