Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Molecule template estimation using Validator Barcodes as an alternative to UMIs in multiplex PCR for adaptive immune repertoire profiling

ABSTRACT: Molecule template estimation using Validator Barcodes as an alternative to UMIs in multiplex PCR for adaptive immune repertoire profiling

PROVIDER: PRJNA1263821 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Molecule template estimation using Validator Barcodes as an alternative to UMIs in multiplex PCR for adaptive immune repertoire profiling

Project description:TCR- and BCR-sequencing (TCR/BCR-seq) are two important technologies in studying the immune repertoire of samples such as PBMCs or tumors. In their most common form, these assays combine multiplex PCR of the repertoire using primers targeting regions of the V(D)J and the constant region with next-generation sequencing (NGS). The data produced by this assay provide a slew of information regarding immune repertoire(s) including the presence critical clonotypes, repertoire diversity, variable (V) gene usage, analysis of public clonotypes, etc. One issue that can arise during generation of the TCR/BCR-seq data is sequence bias during the PCR or NGS steps. To combat this, unique molecular identifiers (UMIs) have been used to identify and eliminate sequence bias. However, UMI fragments can be long and very diverse, resulting in the UMI sequences interfering with any of the multitude of primers during multiplex PCR. Here, we introduce Validator Barcodes (VBCs), a set of eight short barcodes (6-9 nucleotides in length). This compact set of barcodes improves PCR efficiency and facilitates PCR primer designs. Also, like UMIs, the VBCs may be used to estimate the number of template molecules (RNA or DNA). Very similar analytic results and minimal template values have been generated when using VBC-labeled primers in TCR and BCR repertoire profiles from PBMCs to those generated by UMI-based assay counts. Overall, VBCs are a useful and simpler alternative to UMIs in assaying TCR and BCR repertoires.

2025-05-16 | GSE297422 | GEO

Digital counting of nucleic acid molecules using random base molecular barcodes

Project description:Several template DNA molecules with random base molecular barcodes were amplified and sequenced, and the efficacy of the random base barcode for digital counting was shown.

2017-10-19 | GSE94895 | GEO

BIGenomics HPV zipcode array multiplex PCR tests

Project description:Comparison of two different multiplex PCR primer pools in amplifying target HPV types from plasmid templates. Template concentrations are either 1 ng or 1 pg. Templates are detected by type-spcific LDR probes hybridized on microarray.

2011-05-01 | E-MEXP-3154 | biostudies-arrayexpress

BIGenomics HPV zipcode array multiplex PCR tests 2

Project description:Comparison of two different multiplex PCR primer pools in amplifying target HPV types from plasmid templates. Template concentrations are either 10 pg or 100 pg. Templates are detected by type-spcific LDR probes hybridized on microarray.

2011-08-20 | E-MEXP-3268 | biostudies-arrayexpress

Bambusa multiplex

Project description:Bambusa multiplex overview

| PRJNA399780 | ENA

Template-based assembly of proteomic short reads for de novo antibody sequencing and repertoire profiling

Project description:We developed a software package STITCH (https://github.com/snijderlab/stitch) to perform template-based assembly of de novo peptide reads from antibody samples. As a test case we generated de novo peptide reads from protein G purified whole IgG from COVID-19 patients.

2022-07-21 | PXD031941 | Pride

Anopheles funestus pooled-template sequencing.

Project description:Anopheles funestus pooled-template sequencing.

| PRJEB13485 | ENA

RNA-Seq of STAR-PROM Barcodes

Project description:We report the application of a massively parallel STAR-PROM assay based on the RNA-seq of 3000+ luciferase barcodes

2017-01-12 | GSE81271 | GEO

RNA Encoded Peptide Barcodes Enable Efficient in vivo Screening of RNA Delivery Systems

Project description:LNPs have been demonstrated to hold great promise for the clinical advancement of RNA therapeutics. Continued exploration of LNPs for application in new disease areas requires identification and optimisation of leads in a high throughput way. Currently available high throughput in vivo screening platforms are well suited to screen for cellular uptake but less so for functional cargo delivery. We report on a platform which measures functional delivery of LNPs using unique peptide ‘barcodes’. We describe the design and selection of the peptide barcodes and the evaluation of these for the screening of LNPs. We show that proteomic analysis of peptide barcodes correlates with quantification and efficacy of barcoded reporter proteins both in vitro and in vivo and, that the ranking of selected LNPs using peptide barcodes in a pool correlates with ranking using alternative methods in groups of animals treated with individual LNPs. We show that this system is sensitive, selective, and capable of reducing the size of an in vivo study by screening up to 10 unique formulations in a single pool, thus accelerating the discovery of new technologies for mRNA delivery.

2024-10-17 | PXD053797 | Pride

Projection-TAGs enable multiplex projection tracing and multi-modal profiling of projection neurons

Project description:Single-cell multiomic techniques have sparked immense interest in developing a comprehensive multi-modal map of diverse neuronal cell types and their brain-wide projections. However, investigating the complex wiring diagram, spatial organization, transcriptional, and epigenetic landscapes of brain-wide projection neurons is hampered by the lack of efficient and easily adoptable tools. Here we introduce Projection-TAGs, a retrograde AAV platform that allows multiplex tagging of projection neurons using RNA barcodes. By using Projection-TAGs, we performed multiplex projection tracing of the mouse cortex and high-throughput single-cell profiling of the transcriptional and epigenetic landscapes of the cortical projection neurons. Projection-TAGs can be leveraged to obtain a snapshot of activity-dependent recruitment of distinct projection neurons and their molecular features in the context of a specific stimulus. Given its flexibility, usability, and compatibility, we envision that Projection-TAGs can be readily applied to build a comprehensive multi-modal map of brain neuronal cell types and their projections.

2025-04-01 | GSE277718 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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