Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Quantifying RNA-Protein Interactions Characterizes Recurrent Mutations in RNA Binding Proteins in Cancer

ABSTRACT: Quantifying RNA-Protein Interactions Characterizes Recurrent Mutations in RNA Binding Proteins in Cancer

PROVIDER: PRJNA681609 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR13169561_1.fastq.gz	Fastqsanger.gz
	SRR13169561_2.fastq.gz	Fastqsanger.gz
	SRR13169562_1.fastq.gz	Fastqsanger.gz
	SRR13169562_2.fastq.gz	Fastqsanger.gz
	SRR13169563_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 64

Similar Datasets

Quantifying RNA-Protein Interactions Characterizes Recurrent Mutationsin RNA Binding Proteins in Cancer

Project description:Quantifying RNA-Protein Interactions Characterizes Recurrent Mutationsin RNA Binding Proteins in Cancer

| PRJNA645309 | ENA

Quantifying RNA-Protein Interactions Characterizes Recurrent Mutations in RNA Binding Proteins in Cancer

Project description:Quantitative criteria to identify proteins as RNA-binding proteins (RBPs) are presently lacking, as are criteria to define RBP “target” RNAs. To address this, an ultraviolet (UV) cross-linking immunoprecipitation (CLIP)-sequencing method, easyCLIP, was developed. easyCLIP, provides absolute cross-link rates, as well as increased simplicity, efficiency, and capacity to visualize unamplified libraries. 213 cross-link measurements were performed and found that RBPs could be distinguished from non-RBPs by RNA cross-link rates and that target RNAs could be defined as those with a complex frequency unlikely for a random protein. easyCLIP was used to study the 33 most recurrent cancer mutations across 28 RBPs. This demonstrated increased RNA binding per RBP molecule for KHDRBS2 and A1CF cancer mutants, and showed that the PCBP1L100P/Q cancer mutation also dramatically increased RNA binding. Quantitating RBP-RNA interactions can thus categorize proteins as RBPs or not and define the impact of specific disease-associated RBP mutations on RNA binding.

2020-12-01 | GSE162366 | GEO

Quantifying RNA-Protein Interactions Characterizes Recurrent Mutationsin RNA Binding Proteins in Cancer

Project description:Quantitative criteria to identify proteins as RNA-binding proteins (RBPs) are presently lacking, as are criteria to define RBP target RNAs. Here, we develop an ultraviolet (UV) cross-linking immunoprecipitation (CLIP)-sequencing method, easyCLIP. easyCLIP provides absolute cross-link rates, as well as increased simplicity, efficiency, and capacity to visualize RNA libraries. Measurement of >200 independent cross-link experiments across >35 proteins identifies an RNA cross-link rate threshold that distinguishes RBPs from non-RBPs and defines target RNAs as those with a complex frequency unlikely for a random protein. We apply easyCLIP to the 33 most recurrent cancer mutations across 28 RBPs, finding increased RNA binding per RBP molecule for PCBP1 L100P/Q cancer mutations. Quantitating RBP-RNA interactions can thus nominate proteins as RBPs and define the impact of specific disease-associated RBP mutations on RNA association.

2021-01-11 | GSE154168 | GEO

easyCLIP Quantifies RNA-Protein Interactions and Characterizes Recurrent PCBP1 Mutations in Cancer

Project description:easyCLIP Quantifies RNA-Protein Interactions and Characterizes Recurrent PCBP1 Mutations in Cancer

| PRJNA542907 | ENA

easyCLIP Quantifies RNA-Protein Interactions and Characterizes Recurrent PCBP1 Mutations in Cancer

Project description:RNA-protein interactions mediate a host of cellular processes, underscoring the need for methods to quantify their occurrence in living cells. RNA interaction frequencies for the average cellular protein are undefined, however, and there is no quantitative threshold to define a protein as an RNA-binding protein (RBP). Ultraviolet (UV) cross-linking immunoprecipitation (CLIP)-sequencing, an effective widely used means of characterizing RNA-protein interactions, would particularly benefit from the capacity to quantitate the number of RNA cross-links per protein per cell. In addition, CLIP-seq methods are difficult, have high experimental failure rates and many ambiguous analytical decisions. To address these issues, the easyCLIP method was developed and used to quantify RNA-protein interactions for a panel of known RBPs as well as a spectrum of random non-RBP proteins. easyCLIP provides the advantages of good efficiency compared to current standards, a simple protocol with a very low failure rate, troubleshooting information that includes direct visualization of prepared libraries without amplification, and a new form of analysis. easyCLIP, which uses sequential on-bead ligation of 5’ and 3’ adaptors tagged with different infrared dyes, classified non-RBPs as those with a per protein RNA cross-link rate of <0.1%, with most RBPs substantially above this threshold, including Rbfox1 (18%), hnRNPC (22%), CELF1 (11%), FBL (2%), and STAU1 (1%). easyCLIP with the PCBP1L100 RBP mutant recurrently seen in cancer quantified increased RNA binding compared to wild-type PCBP1 and suggested a potential mechanism for this RBP mutant in cancer. easyCLIP provides a simple, efficient and robust method to both obtain both traditional CLIP-seq information and to define actual RNA interaction frequencies for a given protein, enabling quantitative cross-RBP comparisons as well as insight into RBP mechanisms.

2019-05-17 | GSE131210 | GEO

Quantifying RNA Synthesis at Rate-Limiting Steps of Transcription Using Nascent RNA-sequencing Data

Project description:Quantifying RNA Synthesis at Rate-Limiting Steps of Transcription Using Nascent RNA-sequencing Data

| PRJNA750851 | ENA

RNA-Seq of Primary and Recurrent DSRCT Tumors

Project description:RNA-Seq of Primary and Recurrent DSRCT Tumors

| PRJNA961835 | ENA

Recurrent somatic mutations in POLR2A define a distinct subset of meningiomas [RNA-seq]

Project description:RNA polymerase II mediates the transcription of all protein-coding genes in eukaryotic cells, a process that is fundamental to life. Genomic mutations in this enzyme have not been previously linked to any pathology in humans, a testament to its indispensable role in cell biology. Based on a combination of next-generation genomic analyses of 775 meningiomas, we report that recurrent somatic p.Gln403Lys or p.Leu438_His439del mutations in POLR2A, which encodes the catalytic subunit of RNA polymerase II, are sufficient to hijack this essential enzyme and drive neoplasia. POLR2A mutant tumors reveal dysregulation of key meningeal identity genes, including WNT6 and ZIC1/ZIC4. In addition to POLR2A, NF2, SMARCB1, TRAF7, KLF4, AKT1, PIK3CA and SMO, we also report somatic mutations in AKT3, PIK3R1, PRKAR1A, and SUFU in meningiomas. Our results identify a role for essential transcriptional machinery in driving tumorigenesis and define mutually exclusive meningioma subgroups with distinct clinical and pathological features. RNAseq data from 19 meningioma tumors representing major mutation groups (NF2/chr22 loss, POLR2A, KLF4/TRAF7, PI3K mutant)

2016-08-21 | E-GEOD-85133 | biostudies-arrayexpress

Recurrent activating STAT5B N642H mutations in myeloid neoplasms with eosinophilia

Project description:Whole transcriptome sequencing (RNAseq) of 14 cases with suspected primary eosinophilia was performed to identify recurrent mutations which could be used as new diagnostic and prognostic markers as well as potential targets for therapy.

2019-01-12 | E-MTAB-7492 | biostudies-arrayexpress

Quantifying Micro RNA Levels of Colon

Project description:Colorectal cancer (CRC) is the third most common cancer and the fourth leading cause of cancer-related death in the world. Despite potentially curative surgery and the use of modern adjuvant chemotherapy, up to 40% of CRC patients subsequently develop local tumor relapse or metastatic disease. Currently, aside from post-operative pathological staging, early follow up of the patients does not include a specific test or any other evaluation that could predict disease recurrence. Therefore, exploring and identifying novel biomarkers of CRC’s following diagnosis of the primary tumor may help us in identifying patients at high risk for recurrence. Modifications in signaling pathways and their regulation by microRNAs (miRNAs) are being evaluated as biomarkers and therapeutic targets for cancer in general and CRC in particular. It has been established, although not completely, that miRNAs have a role in initiation and progression of CRC. Modifications of miRNAs have been recorded in CRC tumors, and the expression patterns of these miRNAs could in principle biomark this cancer’s phenotype. As miRNAs are well documented to regulate critical molecules in signaling pathways, their regulation of tumor relevant pathways may also serve to further sub-classify patients into drug responsive groups. Moreover, miRNAs may be sampled from peripheral blood and are available as a non-invasive diagnostic method, their application as biomarkers is of special interest. In this study the investigators aim to quantify miRNA levels in human colon and rectal tumors, tumor adjacent and normal tissues. By comparing this data from a large cohort of patients, the investigators aim to identify specific, relevant miRNAs that may serve as biomarkers to stratify CRC patients according to their clinical characteristics such as disease stage, specific treatment, prognosis and disease recurrence.

| 2134048 | ecrin-mdr-crc

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