Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Epigenetically-controlled tumor antigens derived from splice junctions between exons and transposable elements [ChIP-seq]

ABSTRACT: To analyze regulation of JET expression, we generated Setdb1-deficient MC38 and B16OVA cells, using lentivirus-based CRISPR/Cas9. Ctrl and KO cells lines were used to perform ChIP-seq against H3K9me3 and H3K9Ac, with 3 biological replicates.

ORGANISM(S): Mus musculus

PROVIDER: GSE208567 | GEO | 2022/11/22

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Epigenetically-controlled tumor antigens derived from splice junctions between exons and transposable elements [RNA-seq]

Project description:To study the expression of junctions between exons and transposable elements (TEs), we generated paired-end RNAseq from various mouse tumor cell lines, with several biological replicates (cultures from different days). To analyse regulation of JET expression, we generated Setdb1-deficient B16F10 and B16OVA cells, using lentivirus-based CRISPR/Cas9. Ctrl and KO cells lines were used to generate paired-end RNAseq, with several biological replicates (cultures on different days). We generated paired-end RNAseq from healthy female mouse tissues, to compare JET expression in healthy and tumor cells.

2022-11-22 | GSE208388 | GEO

Epigenetically-controlled tumor antigens derived from splice junctions between exons and transposable elements

Project description:This SuperSeries is composed of the SubSeries listed below.

2022-11-22 | GSE218085 | GEO

Epigenetically-controlled tumor antigens derived from splice junctions between exons and transposable elements

Project description:Epigenetically-controlled tumor antigens derived from splice junctions between exons and transposable elements

| PRJNA902299 | ENA

Epigenetically-controlled tumor antigens derived from splice junctions between exons and transposable elements [ChIP-seq]

Project description:Epigenetically-controlled tumor antigens derived from splice junctions between exons and transposable elements [ChIP-seq]

| PRJNA860111 | ENA

Epigenetically-controlled tumor antigens derived from splice junctions between exons and transposable elements [RNA-seq]

Project description:Epigenetically-controlled tumor antigens derived from splice junctions between exons and transposable elements [RNA-seq]

| PRJNA859788 | ENA

Non-canonical splicing junctions between exons and transposable elements represent a source of immunogenic recurrent neo-antigens in cancer patients

Project description:ost characterized tumor antigens are ‘genomic’, i.e. encoded by canonical, non-canonical or somatically mutated genomic sequences. We investigate here the presentation and immunogenicity of tumor antigens derived from non-canonical mRNA splicing events between coding exons and transposable elements (TEs). Comparing non-small cell lung cancer (NSCLC), an immunogenic tumor type, and diverse non-tumor tissues, we identify several thousand splicing junctions between exons and diverse TE classes. A subset of these junctions is both tumor-specific and shared across patients. HLA-I peptidomic identifies peptides encoded by tumor-specific junctions in primary NSCLC samples and lung tumor cell lines. Recurrent junction-encoded peptides are immunogenic in vitro and CD8+ T cells specific for junction-encoded epitopes are present in tumors and tumor-draining lymph nodes from NSCLC patients. We conclude that non-canonical splicing junctions between exons and TEs represent a source of recurrent, immunogenic tumor-specific antigens in NSCLC cancer patients.

2023-02-27 | PXD034820 | Pride

The emergence of alternative 3' and 5' splice site exons from constitutive exons.

Project description:Alternative 3' and 5' splice site (ss) events constitute a significant part of all alternative splicing events. These events were also found to be related to several aberrant splicing diseases. However, only few of the characteristics that distinguish these events from alternative cassette exons are known currently. In this study, we compared the characteristics of constitutive exons, alternative cassette exons, and alternative 3'ss and 5'ss exons. The results revealed that alternative 3'ss and 5'ss exons are an intermediate state between constitutive and alternative cassette exons, where the constitutive side resembles constitutive exons, and the alternative side resembles alternative cassette exons. The results also show that alternative 3'ss and 5'ss exons exhibit low levels of symmetry (frame-preserving), similar to constitutive exons, whereas the sequence between the two alternative splice sites shows high symmetry levels, similar to alternative cassette exons. In addition, flanking intronic conservation analysis revealed that exons whose alternative splice sites are at least nine nucleotides apart show a high conservation level, indicating intronic participation in the regulation of their splicing, whereas exons whose alternative splice sites are fewer than nine nucleotides apart show a low conservation level. Further examination of these exons, spanning seven vertebrate species, suggests an evolutionary model in which the alternative state is a derivative of an ancestral constitutive exon, where a mutation inside the exon or along the flanking intron resulted in the creation of a new splice site that competes with the original one, leading to alternative splice site selection. This model was validated experimentally on four exons, showing that they indeed originated from constitutive exons that acquired a new competing splice site during evolution.

| S-EPMC1876488 | biostudies-literature

Back-splice junctions of KSHV circular RNAs

Project description:Total RNA of KSHV-infected cells were extracted and RT-PCR was performed using viral circRNA specific divergent primers. Amplicons were sequenced with MiSeq.

2021-06-30 | GSE165527 | GEO

TopHat: discovering splice junctions with RNA-Seq.

Project description:MotivationA new protocol for sequencing the messenger RNA in a cell, known as RNA-Seq, generates millions of short sequence fragments in a single run. These fragments, or 'reads', can be used to measure levels of gene expression and to identify novel splice variants of genes. However, current software for aligning RNA-Seq data to a genome relies on known splice junctions and cannot identify novel ones. TopHat is an efficient read-mapping algorithm designed to align reads from an RNA-Seq experiment to a reference genome without relying on known splice sites.ResultsWe mapped the RNA-Seq reads from a recent mammalian RNA-Seq experiment and recovered more than 72% of the splice junctions reported by the annotation-based software from that study, along with nearly 20,000 previously unreported junctions. The TopHat pipeline is much faster than previous systems, mapping nearly 2.2 million reads per CPU hour, which is sufficient to process an entire RNA-Seq experiment in less than a day on a standard desktop computer. We describe several challenges unique to ab initio splice site discovery from RNA-Seq reads that will require further algorithm development.AvailabilityTopHat is free, open-source software available from http://tophat.cbcb.umd.edu.Supplementary informationSupplementary data are available at Bioinformatics online.

| S-EPMC2672628 | biostudies-literature

Splice junctions are constrained by protein disorder.

Project description:We have discovered that positions of splice junctions in genes are constrained by the tolerance for disorder-promoting amino acids in the translated protein region. It is known that efficient splicing requires nucleotide bias at the splice junction; the preferred usage produces a distribution of amino acids that is disorder-promoting. We observe that efficiency of splicing, as seen in the amino-acid distribution, is not compromised to accommodate globular structure. Thus we infer that it is the positions of splice junctions in the gene that must be under constraint by the local protein environment. Examining exonic splicing enhancers found near the splice junction in the gene, reveals that these (short DNA motifs) are more prevalent in exons that encode disordered protein regions than exons encoding structured regions. Thus we also conclude that local protein features constrain efficient splicing more in structure than in disorder.

| S-EPMC4446445 | biostudies-literature

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