Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Highly multiplexed and quantitative cell surface protein profiling using genetically barcoded antibodies

ABSTRACT: Next generation sequencing (NGS) allows for sensitive quantification of DNA and RNA. It would be highly desirable to have a systematic equivalent for assaying cellular protein levels on living cells. We present a highly multiplexed, quantitative, and inexpensive sequencing-based proteomic method using genetically barcoded antibodies called Phage-antibody Next Generation Sequencing (PhaNGS). We demonstrate the utility of PhaNGS by showing how a set of 144 targeted Fab-phage can reliably detect changes in 44 targeted cell surface proteins in drug sensitive and resistant B-cells, or upon induction of the Myc oncogene.

ORGANISM(S): Homo sapiens

PROVIDER: GSE102712 | GEO | 2018/02/12

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Shared Molecules

Only show the datasets with similarity scores above: 0.5

Threshold

0.5

Similar Datasets

Comparative analysis of gut bacteriophage between older and young people

Project description:Given the gut microbiota involve aging processing, we performed comparative analysis of gut bacteriophage between older and young subjects using next-generation sequencing (NGS). In our previous study, we found that the Ruminococcaceae is higher in aged subjects comparing to young one. To identify the bacteriophage targeting to the Ruminococcaceae, we also access the composition of phage in the Ruminococcaceae (ATCC, TSD-27) after incubated with human stool samples. The Lactobacillus (ATCC, LGG) targeting phage was used as the control. The virome sequencing analysis using NGS indicated that Myoviridae are high enrich in young subjects and predominate in TSD-27 targeting phage.

2022-07-20 | GSE196622 | GEO

NGS of phage antibody outputs from whole-cell panning

Project description:We present a target-unbiased approach for antibody discovery that relies on generating mAbs against native target cell surfaces via phage display. This method combines a previously reported method for improved whole-cell phage display selections with next-generation sequencing analysis to efficiently identify mAbs with the desired target cell reactivity. This approach enabled the identification of three multiple myeloma cell surface antigens, and cognate monoclonal antibody probes.

2023-01-18 | GSE222897 | GEO

BART-Seq: cost-effective massively parallelized targeted sequencing for genomics, transcriptomics, and single cell analysis [Genotyping]

Project description:We describe a novel workflow named Barcode Assembly foR Targeted Sequencing, which is a highly sensitive, quantitative, and inexpensive technique for targeted sequencing of transcript cohorts (rBART-Seq) or genomic regions (gBART-Seq) from thousands of bulk samples or single cells in parallel. Multiplexing is based on a simple method that produces extensive matrices of diverse DNA barcodes attached to invariant primer sets, for generating amplicons with dual indices. Here, we used the gBART-Seq for genetic screening of breast cancer patients and identified BRCA mutations with very high precision.

2019-07-07 | GSE130421 | GEO

Integrated omics reveal time-resolved insights into T4 phage infection of E. coli on proteome and transcriptome level

Project description:Bacteriophages are highly abundant viruses of bacteria. The major role of phages in microbial ecology to shape bacterial communities and their emerging medical potential as antibacterial agents have triggered a rebirth of phage research. It is of particular interest to understand the molecular mechanisms by which phages gain control over their host. Omics technologies such as next-generation sequencing and protein-profiling technologies can provide novel insights into transcriptional and translational events occurring during the infection process. Thereby, the temporal organization of the transcriptome and proteome of the phage and their bacterial hosts can be monitored. In this study, we performed next-generation sequencing and proteomics to study the transcriptome and proteome of the T4 phage and its host during the infection in a time-resolved manner. Our data shows the temporally resolved appearance of bacteriophage T4 transcripts and proteins, confirming previously described subgrouping of T4 gene products into early, middle and late infection phases. We observe specific early transcripts giving rise to middle or late proteins indicating the existence of previously not reported post-transcriptional regulatory mechanisms controlling the translation of T4 mRNAs. Moreover, we investigated the stability of E. coli-originated transcripts and proteins in the course of infection, identifying degradation of E. coli transcripts and preservation of the host proteome. This study provides the first comprehensive insights into the transcriptomic and proteomic takeover by the bacteriophage T4, exemplifying the power and value of high-throughput technologies to simultaneously characterize multiple gene expression events. Moreover, we created a user-friendly application available to the entire scientific community to access gene expression patterns for their host and phage genes of interest.

2022-09-19 | PXD035873 | Pride

Molecular Profiling to Improve Outcome of Patients in Cancer. A Pilot Study

Project description:Next Generation Sequencing in cancer: a feasibility study in France to assess sample circuit and to perform analyzes within a limited time.

| 2274538 | ecrin-mdr-crc

Role of Humoral Immunity against Hepatitis B Virus Core Antigen in the Pathogenesis of Acute Liver Failure

Project description:To investigate the role of viral and host factors in acute liver failure, we analyzed serum and multiple liver specimens obtained at the time of liver transplantation from four well-characterized patients. We carried out an integrated clinicopathological analysis, gene and microRNA expression profiling, next-generation sequencing, antibody-displaying phage libraries, and in vitro functional analysis of HBV variants.

2018-10-29 | GSE96851 | GEO

BART-Seq: cost-effective massively parallelized targeted sequencing for genomics, transcriptomics, and single cell analysis [Pluripotency]

Project description:We describe a novel workflow named Barcode Assembly foR Targeted Sequencing, which is a highly sensitive, quantitative, and inexpensive technique for targeted sequencing of transcript cohorts (rBART-Seq) or genomic regions (gBART-Seq) from thousands of bulk samples or single cells in parallel. Multiplexing is based on a simple method that produces extensive matrices of diverse DNA barcodes attached to invariant primer sets, for generating amplicons with dual indices. Here, we used the rBART-Seq for RNA quantification, and for the analysis of developmental states of thousands of single human pluripotent stem cells maintained in different media (mTeSR™1, KSR-bFGF, and E8).

2019-07-07 | GSE130422 | GEO

YerA41, a Yersinia ruckeri bacteriophage: determination of non-sequencable bacteriophage genome and investigation of bacterial response to infection.

Project description:YerA41 is a myoviridae bacteriophage that was originally isolated due its ability to infect Yersinia ruckeri bacteria, the causative agent of enteric redmouth disease of salmonid fish. Several attempts to determine its genomic DNA sequence using traditional and next generation sequencing technologies failed, indicating that the phage genome is modified such way that it is an unsuitable template for PCR amplification and sequencing. To determine the YerA41 genome sequence we isolated RNA from phage-infected Y. ruckeri cells at different time points post-infection, and sequenced it. The host-genome specific reads were substracted and de novo assembly was performed on the unaligned reads.

2020-03-04 | GSE146319 | GEO

BART-Seq: cost-effective massively parallelized targeted sequencing for genomics, transcriptomics, and single cell analysis [Differentiation]

Project description:We describe a novel workflow named Barcode Assembly foR Targeted Sequencing, which is a highly sensitive, quantitative, and inexpensive technique for targeted sequencing of transcript cohorts (rBART-Seq) or genomic regions (gBART-Seq) from thousands of bulk samples or single cells in parallel. Multiplexing is based on a simple method that produces extensive matrices of diverse DNA barcodes attached to invariant primer sets, for generating amplicons with dual indices. Here, we used the rBART-Seq to analyze cell subpopulations that emerge during 72 hours of Wnt/β-catenin pathway activation of H9 hESCs using recombinant Wnt protein (rWnt3a), a small molecule inhibitor of GSK-3 (CHIR99021), or Dox-inducible constitutively active β-catenin (ΔN90).

2019-07-07 | GSE130420 | GEO

POLYseq: A poly(ß-amino ester)-based vector for multifunctional cellular barcoding

Project description:Despite evolving stem cell and organoid application of next-generation sequencing (NGS) at single cell level, current techniques in NGS library preparation are restrictive as individual samples within a single library are indistinguishable, necessitating the laborious and costly preparation of distinct libraries for each sample. To combat this challenge, we report the development of a novel poly(ß-amino) ester labeling system synthesized with inexpensive, common reagents, termed POLYseq, capable of efficiently delivering fluorescent molecules or sample-distinguishing DNA barcodes through non-covalent binding enabling rapid creation of custom libraries.

2021-06-22 | GSE163971 | 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