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Total RNA sequencing of FXN knockdown in pulmonary artery endothelial cells

ABSTRACT: Total RNA sequencing of FXN knockdown in pulmonary artery endothelial cells

PROVIDER: PRJNA720606 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR14182434_1.fastq.gz	Fastqsanger.gz
	SRR14182434_2.fastq.gz	Fastqsanger.gz
	SRR14182435_1.fastq.gz	Fastqsanger.gz
	SRR14182435_2.fastq.gz	Fastqsanger.gz
	SRR14182436_1.fastq.gz	Fastqsanger.gz

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Total RNA sequencing of FXN knockdown or RNA editing gene knockdown in pulmonary artery endothelial cells

Project description:This data set provides different RNA expression data for primary human pulmonary endothelial cells with and without FXN deficiency or with and without RNA editing genes achieved by RNAi transfection in an effort to understand the endothelial-specific effects of acquired frataxin (FXN) deficiency and acquired RNA editing deficiency on pulmonary vascular disease.

2021-04-09 | GSE171692 | GEO

Human Mitochondria NFS1-ISCU-FXN XL-MS

Project description:Frataxin (FXN) is involved in mitochondrial iron-sulfur (Fe-S) cluster biogenesis and serves to accelerate Fe-S cluster formation. FXN deficiency is associated with Friedreich ataxia, a neurodegenerative disease. Using chemical cross-linking (XL) accompanied with LC-MS/MS, we studied the the interaction between the core complexes Acp-ISD11-NFS1 (AIN) and AIN-ISCU (AINU) with FXN.

2018-07-11 | PXD006938 | Pride

Human Mitochondrial NFS1-FXN XL LS-MS/MS

2018-07-11 | PXD006928 | Pride

Correction of splicing defect in compound heterozygous FRDA patient carrying FXN 165+5G>C point mutation.

Project description:Friedreich’s ataxia is an autosomal recessive disease caused by mutations in the FXN gene. Approximately 95% of patients harbor homozygous GAA repeat expansion in the intron 1 of the FXN, while the remaining 5% are compound heterozygotes carrying GA expansion on 1 allele and point mutation on the other allele. Here, we characterized a G to C transversion in position 5 of the intron 1 of the FXN. Mutation results in profound downregulation of FXN mRNA and protein levels. Transcriptome and RT-PCR analyses demonstrated aberrant splicing of the FXN gene caused by this mutation that can be at least in part corrected with antisense oligonucleotides (ASOs) targeting intron 1.

2025-07-10 | GSE262763 | GEO

Transcriptional profiling of mouse embryonic fibroblasts harboring the Fxn G127V mutation

Project description:Friedreich's ataxia (FRDA) is a neurodegenerative disease caused by mutations in the frataxin (FXN) gene. In this study, we immortalized mouse embryonic fibroblasts (MEFs) derived from G127V Fxn mutant mice and compared them to the wild-type (WT) MEFs. Mutant G127V MEFs demonstrated decreased cell proliferation and ATP production, as well as an increase in reactive oxygen species (ROS) production when compared to WT cells. These phenotypes are partially corrected by exogenous expression of frataxin. Surprisingly, extended passaging of immortalized G127V Fxn MEFs improves their proliferation, and alleviates ATP deficiency as well as decreases ROS levels despite persistent frataxin deficiency. We defined gene expression changes associated with phenotypic adaptation of G127V mutant MEFs by comparing transcriptional profiles of early and late passage G127V MEFs with WT cells.

2025-01-22 | GSE255810 | GEO

Total RNA sequencing of RBMS1 knockdown cells

Project description:Total RNA sequencing of RBMS1 knockdown cells

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Total RNA sequencing of AKAP12 knockdown cells

Project description:Total RNA sequencing of AKAP12 knockdown cells

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Determination of the spatial organization of the FXN gene locus by using Chromosome Conformation Capture technique coupled with High-throughtput sequencing (3C-seq).

Project description:Accumulating data from different groups have demonstrated that alteration of post-translational histone modifications is an important underlying mechanism for FXN silencing in FRDA. The relationship between chromatin architecture and histone modification marks in the FXN gene locus is likely to be important for understanding the silencing mechanism. We therefore investigated the spatial organization of the FXN gene locus using the 3C-sequencing method. EBV transformed lymphoblastoid cell lines derived from patients (GM15850, GM16234 and GM16798) and Healthy control (GM14664 and GM15851) were used for generating 3C-seq libraries.

2013-12-16 | E-GEOD-42961 | biostudies-arrayexpress

Cas13d-mediated isoform-specific RNA knockdown with a unified computational and experimental toolbox

Project description:Pre- and post-transcriptional mechanisms, including alternative promoters, termination signals, and splicing, play essential roles in diversifying protein output by generating distinct RNA and protein isoforms. Two major challenges in characterizing the cellular function of alternative isoforms are the lack of experimental methods to specifically and efficiently modulate isoform expression and computational tools for complex experimental design and analysis. To address these gaps, we developed and methodically tested an isoform-specific knockdown strategy which pairs the RNA-targeting CRISPR/Cas13d system with guide RNAs that span exon-exon junctions in the mature RNA. We performed a high-throughput essentiality screen, quantitative RT-PCR assays, and PacBio long read sequencing to affirm our ability to specifically target and robustly knockdown individual RNA isoforms. Using the example gene RBFOX2, we validated protein-level changes and assessed the functional impact of isoform-specific knockdown. In parallel, we provide computational tools for experimental design and screen analysis. Considering all possible splice junctions annotated in GENCODE for multi-isoform genes and our gRNA efficacy predictions, we estimate that our junction-centric strategy can uniquely target up to 89% of human RNA isoforms, including 50,066 protein-coding and 11,415 lncRNA isoforms. Importantly, this specificity spans all transcriptional and splicing events, including exon skipping and inclusion, alternative 5’ and 3’ splice sites, and alternative starts and ends.

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Gene expression changes due to frataxin deficiency and restoration in frataxin knockdown mouse model.

Project description:Friedreich's ataxia (FRDA), the most common inherited ataxia in humans, is caused by recessive mutations that lead to a substantial reduction in the levels of frataxin (FXN), a mitochondrial iron binding protein. FRDA is a multi-system disease, involving multiple neurological, cardiac, and metabolic manifestations whose study is hindered by a paucity of animal models that faithfully recapitulate human disease features. We developed an inducible (doxycycline) mouse model of Fxn deficiency (FRDAkd) that enabled us to control the onset, progression and potential rescue of disease phenotypes by the modulation of Fxn levels using RNA interference. We found that systemic knockdown of Fxn in adult mice led to multiple features paralleling those observed in human patients, including electrophysiological, cellular, biochemical and structural phenotypes associated with cardiomyopathy, as well as dorsal root ganglion and retinal neuronal degeneration and reduced axonal size and myelin sheath thickness in the spinal cord. Fxn knockdown mice also exhibited other abnormalities similar to patients, including weight loss, reduced locomotor activity, ataxia, reduced muscular strength, and reduced survival, as well as genome-wide transcriptome changes. We performed microarray analysis of heart, cerebellum and dorsal root ganglia in FRDAkd mouse model of frataxin deficiency, and found several molecular pathway dysfunction via genome-wide transcriptome analyses. We also found that, upon restoration of near wild-type FXN levels, we observed significant recovery of function, pathology and associated transcriptomic changes, even after significant motor dysfunction was observed. The rapidity of Fxn expression due to doxycycline removal and its robust correction of various parameters, even when restored after the onset of motor dysfunction, makes this FRDAkd mouse model an appealing potential preclinical tool for testing various therapeutics for FRDA.

2017-12-19 | GSE98790 | GEO

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