Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genome-wide co-localization of RNA-DNA interactions and fusion RNA pairs (iMARGI)

ABSTRACT: Genome-wide co-localization of RNA-DNA interactions and fusion RNA pairs (iMARGI)

PROVIDER: PRJNA506020 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR8206680_1.fastq.gz	Fastqsanger.gz
	SRR8206680_2.fastq.gz	Fastqsanger.gz
	SRR8206679_1.fastq.gz	Fastqsanger.gz
	SRR8206679_2.fastq.gz	Fastqsanger.gz

Items per page:

1 - 4 of 4

Similar Datasets

Genome-wide co-localization of RNA-DNA interactions and fusion RNA pairs

Project description:Genome-wide co-localization of RNA-DNA interactions and fusion RNA pairs

| PRJNA506013 | ENA

Genome-wide co-localization of RNA-DNA interactions and fusion RNA pairs (RNAseq)

Project description:Genome-wide co-localization of RNA-DNA interactions and fusion RNA pairs (RNAseq)

| PRJNA506022 | ENA

Genome-wide co-localization of RNA-DNA interactions and fusion RNA pairs (RNAseq)

Project description:Despite the ever-increasing speed of detecting fusion transcripts in cancer, it remains formidable to predict what unreported RNA pairs can form new fusion transcripts. By systematic mapping of chromatin-associated RNAs (caRNAs) and their respective genomic interaction loci, we obtained genome-wide RNA-DNA interaction maps from two non-cancerous cell types. The gene pairs involved in RNA-DNA interactions in these normal cells exhibited strong overlap with those with cancer-derived fusion transcripts. These data suggest an RNA-poise model, where the spatial proximity of one gene’s transcripts and the other gene’s genomic sequence poises for the creation of fusion transcripts. We validated this model with 96 additional lung cancer samples. One of these additional samples exhibited fusion transcripts without a corresponding fusion gene, suggesting that genome-recombination is not a required step of the RNA-poise model.

2019-01-14 | GSE122688 | GEO

Genome-wide co-localization of RNA-DNA interactions and fusion RNA pairs (iMARGI)

2019-01-09 | GSE122689 | GEO

Genome-wide co-localization of RNA-DNA interactions and fusion RNA pairs

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

2019-01-09 | GSE122690 | GEO

Genome-wide colocalization of RNA-DNA interactions and fusion RNA pairs.

Project description:Fusion transcripts are used as biomarkers in companion diagnoses. Although more than 15,000 fusion RNAs have been identified from diverse cancer types, few common features have been reported. Here, we compared 16,410 fusion transcripts detected in cancer (from a published cohort of 9,966 tumor samples of 33 cancer types) with genome-wide RNA-DNA interactions mapped in two normal, noncancerous cell types [using iMARGI, an enhanced version of the mapping of RNA-genome interactions (MARGI) assay]. Among the top 10 most significant RNA-DNA interactions in normal cells, 5 colocalized with the gene pairs that formed fusion RNAs in cancer. Furthermore, throughout the genome, the frequency of a gene pair to exhibit RNA-DNA interactions is positively correlated with the probability of this gene pair to present documented fusion transcripts in cancer. To test whether RNA-DNA interactions in normal cells are predictive of fusion RNAs, we analyzed these in a validation cohort of 96 lung cancer samples using RNA sequencing (RNA-seq). Thirty-seven of 42 fusion transcripts in the validation cohort were found to exhibit RNA-DNA interactions in normal cells. Finally, by combining RNA-seq, single-molecule RNA FISH, and DNA FISH, we detected a cancer sample with EML4-ALK fusion RNA without forming the EML4-ALK fusion gene. Collectively, these data suggest an RNA-poise model, where spatial proximity of RNA and DNA could poise for the creation of fusion transcripts.

| S-EPMC6386723 | biostudies-literature

RNA localization to stress granules

Project description:RNA localization to stress granules

| PRJNA875210 | ENA

Identification of RNA-binding proteins interacting with axonal localization elements

Project description:Here, we used axonal RNA localization motifs as baits coupled with mass spectrometry (MS) to identify the RNA binding proteins that bind to Nrn1 (also called Cortical Plasticity Gene 15), Hmgb1 (also called Amphoterin), Actb, and Gap43 mRNA localization motifs.

2018-01-10 | MSV000081910 | MassIVE

Regulation of RNA localization by FMR1

Project description:Regulation of RNA localization by FMR1

| PRJNA573700 | ENA

Centrosomal Localization of DNAJ-PKAc Fusion Heightens PLK1 Inhibitor Sensitivity in Fibrolamellar Cancer

Project description:Centrosomal Localization of DNAJ-PKAc Fusion Heightens PLK1 Inhibitor Sensitivity in Fibrolamellar Cancer

| PRJNA1051952 | ENA