Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: Translation of bi-directional transcripts enhances MHC-I peptide diversity

PROVIDER: PRJNA1235990 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR32731600_1.fastq.gz	Fastqsanger.gz
	SRR32731600_2.fastq.gz	Fastqsanger.gz
	SRR32731601_1.fastq.gz	Fastqsanger.gz
	SRR32731601_2.fastq.gz	Fastqsanger.gz
	SRR32731602_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 36

Similar Datasets

Translation of bi-directional transcripts generates peptides for the MHC-I pathway.

Project description:Antisense transcripts play an important role in generating regulatory non-coding RNAs but if these transcripts are also translated and for what purpose is yet poorly understood. Isolation of polysome fractions followed by RNA sequencing and mass spectrometry analysis of a six frame data-base revealed nascent peptides originating from different reading frames of bi-directional transcripts. Two peptides originating from the antisense strand stimulated the proliferation of CD8+ T cells when presented to peripheral blood mononuclear cells (PBMCs) from nine healthy donors. An antigenic peptide derived from the reverse strand of two cDNA constructs was presented on MHC-I molecules and induced CD8+ T cell activation. These results demonstrate that three frame translation of bi-directional transcripts generate antigenic peptide substrates for the immune system. This discovery holds significance for better understanding the origin of self-discriminating peptide substrates for the MHC-I pathway and for enhancing immune-based therapies against infected or transformed cells.

2025-05-07 | PXD057573 | Pride

TCR repertoire profiling of CMV specific and SARS-CoV2 Spike specific CD8+ T cells using single cell sequencing

Project description:We introduced single-chain trimer (SCT) technologies into a high throughput platform for pMHC library generation that can be used for screening antigen specific CD8+ T cells. We compared the diversity of T cell receptor repertoire captured by SCT and folded peptide-MHC multimer presenting HLA-A02:01 restricted CMV peptide. We then constructed SCT libraries designed to capture SARS-CoV-2 spike specific CD8+ T cells from COVID-19 participants and healthy donors. TCR sequencing with antigen specificity was analyzed. The immunogenicity of these epitopes was validated by functional assays of T cells with cloned TCRs captured using SCT libraries.

2022-01-01 | E-MTAB-11229 | biostudies-arrayexpress

Lever2014 - Phenotypic models of T cell activation.

Project description:This is a phenotypic model of a kinetic proofreading mechanism used to describe dynamics governing interactions between T cell receptors and peptide-MHC complexes.

2019-11-13 | MODEL1907260003 | BioModels

The differences in local translatome across distinct neuron types is mediated by both baseline cellular differences and post-transcriptional mechanisms

Project description:Local translation in neurites is a phenomenon that enhances spatial segregation of proteins and their functions away from the cell body, yet it is unclear how local translation varies across neuronal cell types. Further, it is unclear if differences in local translation across cell types simply reflect differences in transcription or if there is also a cell type specific posttranscriptional regulation of the location and translation of specific mRNAs. Most of the mRNAs discovered as locally translated have been identified from hippocampal neurons because their laminar organization facilitates neurite specific dissection and microscopy methods. Given the diversity of neurons across the brain, studies have not yet analyzed how locally translated mRNAs differ across cell types, particularly those with neurites intertwined into other cell types. Here, we used the SynapTRAP method to harvest two broad cell types in the forebrain: GABAergic neurons and pyramidal neurons. While some transcripts overlap, the majority of the local translatome is not shared across these cell types. While most differences are driven by baseline expression levels in the respective cells, some transcripts also evidence cell type specific post transcriptional regulation of localization. Finally, we provide evidence that GABAergic neurons specifically localize mRNAs for peptide neurotransmitters, including somatostatin and cortistatin, suggesting localized production of these key signaling molecules in the neurites of GABAergic neurons. Overall, this work suggests that differences in local translation in neurites across neuronal cell types are poised to contribute substantially to the variability between cells.

2018-10-12 | GSE121162 | GEO

Brief treatment in-vitro with Dasatinib does not appreciably alter gene expression by CD8+ T cells

Project description:Pre-incubation of T cells with the protein kinase inhibitor dasatinib prevents internalisation of T cell receptors upon binding by peptide-MHC multimers and enhances multimer staining. If used with downstream sc-RNAseq of sorted T cells, there is a possibility that this treatment could influence gene expression. No significant changes in gene expression were detected between dasatinib-treated and untreated cells.

2022-11-05 | GSE217149 | GEO

Bi-directional interactions of omental adipocytes and SKOV3ip1 cells

Project description:Bi-directional interactions of omental adipocytes and SKOV3ip1 cells

| PRJNA986819 | ENA

Project description:Bi-directional crosstalk between gut microbiota and NKT cells

| PRJNA916466 | ENA

DNA sequencing for multiple rounds of the pMHC-yeast display selection for 2W, Yae and Fat TCR

Project description:A peptide library was displayed on Ab MHC class II allele expressed on yeast. TCRs of interest were used to select and enrich for cognate peptide-MHC.

2020-06-15 | GSE151070 | GEO

DNA sequencing for multiple rounds of the pMHC-yeast display selection for TCR6, TCR7 and FluTCR [other]

Project description:A peptide library was displayed on Db MHC class I allele expressed on yeast. TCRs of interest were used to select and enrich for cognate peptide-MHC.

2020-01-01 | GSE133363 | GEO

Clinical drug resistance linked to inter-convertible phenotypic and functional states of tumor-propagating cells in multiple myeloma

Project description:To gain insights into the molecular mechanisms underpinning the reversible, bi-directional CD138- Pre-PC and CD138+ PC transition we subjected highly purified (>99%) Pre-PC - PC pairs from 9 patients to global mRNA expression profiling

2012-11-21 | E-MEXP-3772 | biostudies-arrayexpress

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