Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Multiplexed functional assessment of dominant genetic variants in CARD11

ABSTRACT: Multiplexed functional assessment of dominant genetic variants in CARD11

PROVIDER: PRJNA638386 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Multiplexed functional assessment of dominant genetic variants in CARD11

Project description:We describe the use of saturation genome editing to measure the effects of CARD11 variants on protein function, splicing and lymphoma cell survival. We find the results to predict the clinical effects of the variants.

2020-07-01 | GSE152129 | GEO

Multiplexed Functional Assessment of Genetic Variants in CARD11.

Project description: Not available

| S-EPMC7820631 | biostudies-literature

Multiplexed assessment of human glucokinase variant activity

Project description:Multiplexed assessment of human glucokinase variant activity

| PRJNA817232 | ENA

The functional impact of BRCA1 BRCT domain variants using multiplexed DNA double-strand break repair assays

Project description:In this study, we used multiplexed DNA repair assays of variants in the BRCA1 carboxy-terminus to functionally characterize 2271 variants for homology-directed repair function (HDR) and 1427 variants for cisplatin resistance (CR). We found a high level of consistent results in the two multiplexed functional assays with non-functional variants located within regions of the BRCA1 protein necessary for its tumor suppression activity.

2022-01-31 | GSE188426 | GEO

OCI-Ly3 CARD11 shRNA

Project description:Activation of NFkB pathway by CARD11 Keywords: time series design

2006-03-30 | GSE3896 | GEO

OCI-Ly3 CARD11 shRNA

Project description:Activation of NFkB pathway by CARD11 Cy3-labelled untreated sample and Cy5-labelled treated sample were hybridized to a Lymphochip microarray.

2010-07-01 | E-GEOD-3896 | biostudies-arrayexpress

A multiplexed assay for exon recognition reveals that an unappreciated fraction of rare genetic variants cause large-effect disruptions to splicing

Project description:Mutations that cause exon skipping can have severe consequences on gene function and cause disease. Here we explore how human genetic variation affects exon recognition by developing a Multiplexed Functional Assay of Splicing using Sort-seq (MFASS). We assayed 27,733 variants in the Exome Aggregation Consortium (ExAC) within or adjacent to 2,198 human exons in the MFASS minigene reporter, and found that 3.8% (1,050) of variants, most of which are extremely rare, led to large-effect splice-disrupting variants (SDVs). Importantly, we find that 83% of SDVs are located outside of canonical splice sites, are distributed evenly across distinct exonic and intronic regions, and are difficult to predict a priori. Our results indicate extant, rare genetic variants, even outside the context of disease, can have large functional effects at appreciable rates, and that MFASS enables their empirical assessment for large-effect splicing defects at scale.

2018-10-02 | GSE120695 | GEO

RNA-seq analysis of WT and CARD11 point mutation mouse spleen B cells

Project description:In order to investigate the molecular mechanism of CARD11 in immune cell system, we applied the RNA-seq analysis using RNA isolated from WT and CARD11 mutant (E134G and K215M) mouse spleen B cells. By comparing the transcriptome files, we found some different expressed gene involved in due to the CARD11 point mutation and in vitro RT-PCR had confirmed this result.

2020-01-27 | GSE136588 | GEO

Multiplexed Assays of Variant Effects (MAVE) of PALB2 single nucleotide variants in exon 10.

Project description:To validate a high-throughput screening data in human cells using Multiplexed Assays for Variant Effects (MAVE), we performed a high-throughput deep mutational scanning of single nucleotide changes in exon 10 encoding p.G1000 to p.I1037 of the WD40 domain of PALB2 using a cell survival assay in haploid human HAP1 cells. We obtained MAVE scores for 276 single-nucleotide variants, leading to 9 nonsense and 68 synonymous changes, as well as 199 amino acid substitutions. Both variant groups showed an asymmetric distribution that is skewed towards low MAVE scores of nonsense and damaging variants, respectively. These MAVE data included scores for 218 unique single-nucleotide variants, leading to 9 nonsense changes and 209 amino acid substitutions. We observed a good and significant correlation between the outcomes from the MAVE and high-throughput screens (n=179, r=-0,6439, p<0.0001), indicating concordance between the outcomes of high-throughput analysis of PALB2 variants in human and mouse cells.

2024-02-08 | GSE255117 | GEO

Integrated multiplexed assays of variant effect reveal determinants of catechol-O-methyltransferase gene expression

Project description:Multiplexed assays of variant effect are powerful methods to profile the consequences of rare variants on gene expression and organismal fitness. Yet, few studies have integrated several multiplexed assays to map variant effects on gene expression in coding sequences. Here, we pioneered a multiplexed assay based on polysome profiling to measure variant effects on translation at scale, uncovering single-nucleotide variants that increase and decrease ribosome load. By combining high-throughput ribosome load data with multiplexed mRNA and protein abundance readouts, we mapped the cis-regulatory landscape of thousands of catechol-O-methyltransferase (COMT) variants from RNA to protein and found numerous coding variants that alter COMT expression. Finally, we trained machine learning models to map signatures of variant effects on COMT gene expression and uncovered both directional and divergent impacts across expression layers. Our analyses reveal expression phenotypes for thousands of variants in COMT and highlight variant effects on both single and multiple layers of expression. Our findings prompt future studies that integrate several multiplexed assays for the readout of gene expression

2023-11-06 | GSE246139 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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