Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Differential gene expression analyses after noncanonical peptide overexpression

ABSTRACT: Differential gene expression analyses after noncanonical peptide overexpression

PROVIDER: PRJNA892076 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR21972688.fastq.gz	Fastqsanger.gz
	SRR21972689.fastq.gz	Fastqsanger.gz
	SRR21972690.fastq.gz	Fastqsanger.gz
	SRR21972691.fastq.gz	Fastqsanger.gz
	SRR21972692.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 10

Similar Datasets

Differential gene expression analyses after noncanonical peptide overexpression

Project description:Ribosome profiling analyses showed thousands of translated open reading frames in a cell encoding noncanonical peptides. To examine their functional roles, we stably overexpressed two noncanonical peptides (uSLC35A4 and iPGRMC1) in MCF-7 cells. And then we performed RNA-seq to examine differential gene expression upon gene overexpression.

2024-02-01 | GSE216093 | GEO

Translatome analyses of HEK293T upon NSP12 overexpression

Project description:Translatome analyses of HEK293T upon NSP12 overexpression

| PRJNA757696 | ENA

pXg: Comprehensive identification of noncanonical MHC-I-associated peptides from de novo peptide sequencing using RNA-Seq reads

Project description:Discovering noncanonical peptides has been a common application of proteogenomics. Recent studies suggest that certain noncanonical peptides, known as ncMAPs (noncanonical MHC-I-associated peptides), that bind to major histocompatibility complex I may make good immunotherapeutic targets. De novo peptide sequencing is a great way to find ncMAPs since it can detect peptide sequences from their tandem mass spectra without using any sequence databases. However, this strategy hasn’t been widely applied for ncMAP identification because there is not a good way to estimate its false-positive rates. In order to completely and accurately identify immunopeptides using de novo peptide sequencing, we describe a unique pipeline called pXg. In contrast to current pipelines, it makes use of genomic data, RNA-Seq abundance and sequencing quality, in addition to proteomic features to increase the sensitivity and specificity of peptide identification. We show that the peptide-spectrum match quality and genetic traits have a clear relationship, showing that they can be utilized to evaluate peptide-spectrum matches. From ten samples, we found 24,449 cMAPs (canonical MHC-I-associated peptides) and 956 ncMAPs by using a target-decoy competition. 387 ncMAPs and 1,611 cMAPs were novel identifications that had not yet been published. We discovered 11 ncMAPs produced from a squirrel monkey retrovirus in human cell lines in addition to the 2 ncMAPs originating from a complementarity determining region 3 in an antibody thanks to the unrestricted search space assumed by de novo sequencing. These entirely new identifications show that pXg can make the most of de novo peptide sequencing's advantages and its potential use in the search for new immunotherapeutic targets.

2024-02-28 | PXD048006 | Pride

Transcriptome analyses of HEK293T and VERO upon overexpression

Project description:Transcriptome analyses of HEK293T and VERO upon overexpression

| PRJNA757693 | ENA

Engineered Peptide Barcodes for In-Depth Analyses of Binding Protein Ensembles

Project description:Engineered Peptide Barcodes for In-Depth Analyses of Binding Protein Ensembles

| PRJEB25673 | ENA

Differential Peptide Subtraction (DPS): mass spectrometry for human cancer virus discovery

Project description:Differential Peptide Subtraction (DPS): mass spectrometry for human cancer virus discovery

| PRJNA662225 | ENA

Next Generation Sequencing identifies differential genes regulated by FTSJ1 overexpression

Project description:Next Generation Sequencing identifies differential genes regulated by FTSJ1 overexpression

| PRJNA611060 | ENA

Ebola virus delta peptide is an enterotoxin

Project description:Transcriptomic analyses showed that Ebola virus delta peptide triggers damage response and cell survival pathways. Delta peptide also downregulates the expression of transporters and exchangers that mediate absorption of ions, sugars, and small chain fatty acids.

2021-12-01 | GSE189787 | GEO

Identifying interaction partners of noncanonical peptides.

Project description:Studies have revealed dozens of functional peptides in putative ‘noncoding’ regions and raised the question of how many proteins are encoded by noncanonical open reading frames (ORFs). We comprehensively annotated genome-wide translated ORFs across five eukaryotic by analyzing ribosome profiling reads. We revealed pervasive translation in annotated untranslated regions of mRNAs or off-frame regions (i.e., uORFs, dORFs, and iORFs). We developed a logistic regression model based on ORF features to calculate the peptide functional probability in humans. Systematic ectopic expression experiments showed that peptides encoded by ncORFs follow the basic principles governing conventional protein subcellular localization and carry out diverse biological functions.

2024-05-23 | PXD037658 | Pride

Differential mRNA expression upon microRNA-125a overexpression in murine hematopoietic cells

Project description:We report differential gene expression in hematopoietic cells (lineage-Sca+) upon overexpression and transplantation of murine hematopoietic stem cells.

2021-02-11 | GSE158126 | 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