Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Unbiased quantification of immunoglobulin diversity at the DNA level with VDJ-seq

ABSTRACT: Unbiased quantification of immunoglobulin diversity at the DNA level with VDJ-seq

PROVIDER: PRJNA416923 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Unbiased quantification of immunoglobulin diversity at the DNA level with VDJ-seq

Project description:For high-throughput sequencing and quantification of immunoglobulin repertoires, most methodologies utilise RNA. However, output varies enormously between recombined genes due to different promoter strengths and differential activation of lymphocyte subsets, precluding quantitation of recombinants on a per cell basis. To date, DNA-based approaches have used V gene primer cocktails, with substantial inherent biases. Here we describe VDJ-seq, which accurately quantitates immunoglobulin diversity at the DNA level in an unbiased manner. This is accomplished with a single primer extension step using biotinylated J gene primers. By addition of unique molecular identifiers (UMI) before primer extension, we reliably remove duplicate sequences and correct for sequencing and PCR errors. Furthermore, VDJ-seq captures productive and non-productive VDJ and DJ recombination events on a per cell basis. Library preparation takes 3 days, with 2 days of sequencing, and 1 day of data processing and analysis.

2017-12-16 | GSE106458 | GEO

Exon Level Expression Profiling: a Novel Unbiased Transcriptome

Project description:Exon Level Expression Profiling: a Novel Unbiased Transcriptome

| PRJNA503118 | ENA

Exon Level Expression Profiling: a Novel Unbiased Transcriptome

Project description:Exon Level Expression Profiling: a Novel Unbiased Transcriptome

| PRJNA725491 | ENA

Exon Level Expression Profiling: a Novel Unbiased Transcriptome

Project description:Exon Level Expression Profiling: a Novel Unbiased Transcriptome

| PRJNA607048 | ENA

Exon Level Expression Profiling: a Novel Unbiased Transcriptome (Mouse)

Project description:Exon Level Expression Profiling: a Novel Unbiased Transcriptome (Mouse)

| PRJNA704058 | ENA

Exon Level Expression Profiling: a Novel Unbiased Transcriptome (Human)

Project description:Exon Level Expression Profiling: a Novel Unbiased Transcriptome (Human)

| PRJNA704059 | ENA

Igh repertoire analysis in primary pro-B cells from WT and NE1-/- 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) and NE1-/- 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 and NE1-/- primary pro-B cells from the VDJ-seq data.

2022-12-22 | GSE203484 | GEO

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

VDJ N-addition study

Project description:Nucleotide composition of human immunoglobulin N segments depends on trimming of the flanking gene segments and Terminal Deoxynucleotidyl Transferase favors cytosine, not guanosine, in most VDJ rearrangements

| PRJEB25944 | ENA

Gene expression and VDJ profiling at single cell level of CD4 T cells isolated from the female reproductive tract (FRT) of Chlamydia muridarum infected WT (B6) and Bhlhe40-/- mice

Project description:CD4 T cells are recruited to the FRT following Chlamydia intravaginal infection. We use single-cell RNA sequencing and VDJ profiling to compare CD4 T cells sorted from WT (B6) and Bhlhe40-/- mice at 14 days post Chlamydia muridarum intravaginal infection.

2024-01-21 | GSE253394 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data