Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

FusionTranscriptsHCB

ABSTRACT: Fusion transcripts

PROVIDER: PRJEB76865 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR13624600_1.fastq.gz	Fastqsanger.gz
	ERR13624600_2.fastq.gz	Fastqsanger.gz
	ERR13624601_1.fastq.gz	Fastqsanger.gz
	ERR13624601_2.fastq.gz	Fastqsanger.gz
	ERR13624602_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 218

Similar Datasets

Project description:Fusion Transcripts in BI-ALCL and cALCL

| PRJNA786444 | ENA

Identification of novel fusion transcripts in neuroblastoma

Project description:Identification of novel fusion transcripts in neuroblastoma

| PRJNA605944 | ENA

RNA sequencing of follicular T cell lymphoma

Project description:RNA sequencing of follicular T cell lymphoma to identify novel fusion transcripts.

| EGAS00001004646 | EGA

5b5aa7a4-3dff-4a5b-98c1-c6477bf986af - samples

Project description:Paired-end RNA-seq of follicular T cell lymphoma for the discovery of fusion transcripts

| EGAD00001006379 | EGA

ena-DATASET-SCI-19-05-2017-14:11:25:029-170 - samples

Project description:Identification of fusion transcripts by RNA-sequencing and Whole genome sequencing of a breast cancer patient sample (METABRIC ID MB-0152)

| EGAD00001003342 | EGA

mRNA capture sequencing and RT-qPCR for the detection of pathognomonic, novel and secondary fusion transcripts in formalin-fixed paraffin-embedded tissue: a sarcoma showcase

Project description:RNA sequencing is widely used to study gene abundance patterns, but less frequently to assess structural alterations such as fusion transcripts. In this study, we assess the performance of messenger RNA (mRNA) capture sequencing to identify fusion transcripts in formalin-fixed paraffin-embedded (FFPE) tissue of different types of sarcoma, followed by orthogonal confirmation using RT-qPCR. To validate our workflow, we used the TruSight RNA Pan-Cancer Panel to analyze a first cohort of 6 positive control tumors for which the diagnostic workup demonstrated the presence of a specific chromosomal rearrangement. Fusion transcript calling by FusionCatcher confirmed all known aberrations and enabled the identification of both fusion gene partners and breakpoints. Next, whole transcriptome TruSeq RNA Exome sequencing was applied to a second cohort of 17 patients, diagnosed with fusion gene-negative alveolar rhabdomyosarcoma (ARMS) or undifferentiated round cell sarcoma (URCS), for whom fluorescence in situ hybridization (FISH) did not identify the classical pathognomonic rearrangements. Remarkably, for 6 out of 17 patients, mRNA capture sequencing readily detected a pathognomonic fusion transcript, i.e. PAX3-FOXO1 in 2 ARMS patients, and EWSR1-FLI1, EWSR1-ERG or EWSR1-NFATC2 in 4 URCS patients. These data show that RNA capture sequencing may enhance the detection rate of pathognomonic fusion genes in sarcoma. For the 11 patients with no known pathognomonic fusion transcript, 11 newly identified fusion transcripts were confirmed by RT-qPCR, including COPS3-TOM1L2, NCOA1-DTNB, WWTR1-LINC01986, PLAA-MOB3B, AP1B1-CHEK2 and BRD4-LEUTX fusion transcripts in ARMS patients. Additionally, recurrently detected secondary fusion transcripts in two patients diagnosed with EWSR1-NFATC2-positive sarcoma were confirmed (COPS4-TBC1D9, PICALM-SYTL2, SMG6-VPS53 and UBE2F-ALS2). Our results provide new insights into the underlying genetic causes of these malignancies.

| EGAS00001005202 | EGA

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

Copy number analysis of Hodgkin lymphoma cell lines KM-H2 and L-428

Project description:We identified copy number changes associated with fusion transcripts and breakpoints on chromosomes 15 and 16.

2010-12-11 | GSE25989 | GEO

Whole transcriptome sequencing in 274 glioma patients reveals gene fusion profiling and novel candidate fusion genes

Project description:We detected fusion genes in 274 fresh surgical samples of gliomas using whole transcriptome sequencing. Using this approach we screened a panel of glioma samples and identified a number of activating novel fusion transcripts. Fusion detection in 274 glioma patients

2014-07-20 | E-GEOD-48865 | 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