Similar studies for GEO DataSets (Select 200042960) - GEO DataSets

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Items: 20

Select item 2000429601.

The effect of nicotinamide on dysregulated genes associated with frataxin deficiency in FRDA.

(Submitter supplied) To investigate the efficacy of nicotinamide treatment using our ex-vivo primary lymphocyte model, we performed high-throughput RNA sequencing on libraries generated from untreated and nicotinamide treated samples.

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL11154
4 Samples

Download data: TXT

Series

Accession:: GSE42960

ID:: 200042960

Select item 2000429612.

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

(Submitter supplied) 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.

Organism:: Homo sapiens

Type:: Other

Platform:: GPL11154
5 Samples

Download data: BED, PDF

Series

Accession:: GSE42961

ID:: 200042961

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Select item 2001451153.

Inhibition of the SUV4-20 H1 histone methyltransferase increases frataxin expression in Friedreich’s ataxia patient cells

(Submitter supplied) The molecular mechanisms of reduced frataxin (FXN) expression in Friedreich's ataxia (FRDA) are linked to epigenetic modification of the FXN locus caused by the disease-associated GAA expansion. Here, we identify that SUV4-20 histone methyltransferases, specifically SUV4-20 H1, play an important role in the regulation of FXN expression and represent a novel therapeutic target. Using a human FXN-GAA-Luciferase repeat expansion genomic DNA reporter model of FRDA, we screened the Structural Genomics Consortium epigenetic probe collection. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL20301
24 Samples

Download data: TXT

Series

Accession:: GSE145115

ID:: 200145115

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Select item 2001042884.

Comprehensive Analysis of Gene Expression Patterns in Friedreich’s Ataxia Fibroblasts by RNA Sequencing Reveals Altered Levels of Protein Synthesis Factors and Solute Carriers

(Submitter supplied) Friedreich’s ataxia (FRDA) is an autosomal recessive neurodegenerative disease usually caused by large homozygous expansions of GAA repeat sequences in intron 1 of the frataxin (FXN) gene. FRDA patients have low FXN mRNA and frataxin protein levels when compared with heterozygous carriers or healthy controls. Presently, there is no effective treatment for FRDA, and biomarkers to measure therapeutic trial outcomes and/or to gauge disease progression are lacking. Peripheral tissues, including blood cells, buccal cells, and skin fibroblasts, can readily be isolated from FRDA patients and used to define molecular hallmarks of disease pathogenesis. However, because these tissues are not directly involved in disease pathogenesis, their relevance as models of the molecular aspects of the disease is yet to be decided. Transcriptome profiling of FRDA skin fibroblasts revealed significantly upregulated expression of genes encoding plasma membrane solute carrier proteins. Conversely, the expression of genes encoding accessory factors and enzymes involved in cytoplasmic and mitochondrial protein synthesis was consistently decreased in the FRDA cells. Finally, comparison of genes differentially expressed in FRDA fibroblasts to 3 previously published gene expression signatures defined for FRDA blood cells showed substantial overlap between the independent datasets, including correspondingly deficient expression of antioxidant defense genes. Together, these results indicate that gene expression profiling of cells derived from peripheral tissues can, in fact, consistently reveal novel molecular pathways of the disease.

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL11154
35 Samples

Download data: TXT

Series

Accession:: GSE104288

ID:: 200104288

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Select item 2000107455.

HDAC Inhibitors Correct Frataxin Deficiency in a Friedreich Ataxia Mouse Model

(Submitter supplied) Background: Friedreich ataxia, an autosomal recessive neurodegenerative and cardiac disease, is caused by abnormally low levels of frataxin, an essential mitochondrial protein. All Friedreich ataxia patients carry a GAA/TTC repeat expansion in the first intron of the frataxin gene, either in the homozygous state or in compound heterozygosity with other loss-of-function mutations. The GAA expansion inhibits frataxin expression through a heterochromatin-mediated repression mechanism. more...

Organism:: Mus musculus

Type:: Expression profiling by array

Platform:: GPL6103
48 Samples

Download data: TXT

Series

Accession:: GSE10745

ID:: 200010745

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Select item 2000050406.

Polyamides alleviate transcription inhibition associated with long GAA•TTC repeats in Friedreich’s ataxia

(Submitter supplied) Lymphoblast cells from a patient with Freidriech's Ataxia were incubated with pyrrole-imidazole polyamides targeted to the GAA triplet repeat in the intron 1. The polyamides were shown in cell culture to increase levels of endogenous frataxin mRNA. A normal sibling derived lymphoblast cell line was used as a control. Keywords: human lymphoblast cells

Organism:: Homo sapiens

Type:: Expression profiling by array

Platform:: GPL570
24 Samples

Download data: CEL

Series

Accession:: GSE5040

ID:: 200005040

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Select item 2000226517.

Friedreich’s Ataxia Induced Pluripotent Stem Cells Recapitulate GAA•TTC Triplet-Repeat Instability

(Submitter supplied) The inherited neurodegenerative disease Friedreich’s ataxia (FRDA) is caused by hyperexpansion of GAA•TTC trinucleotide repeats within the first intron of the FXN gene, encoding the mitochondrial protein frataxin. Long GAA•TTC repeats causes heterochromatin-mediated silencing and loss of frataxin in affected individuals. We report the derivation of induced pluripotent stem cells (iPSCs) from FRDA patient fibroblasts through retroviral transduction of transcription factors. more...

Organism:: Homo sapiens

Type:: Expression profiling by array

Platform:: GPL6947
65 Samples

Download data: TXT

Series

Accession:: GSE22651

ID:: 200022651

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Select item 2000653998.

Epigenetic therapy for Friedreich ataxia.

(Submitter supplied) We set out to investigate whether a histone deacetylase inhibitor (HDACi) would be effective in an in vitro model for the neurodegenerative disease Friedreich ataxia (FRDA) and to evaluate safety and surrogate markers of efficacy in a phase I clinical trial in patients. In the neuronal cell model, HDACi 109/RG2833 increases FXN mRNA levels and frataxin protein, with concomitant changes in the epigenetic state of the gene. more...

Organism:: Homo sapiens

Type:: Expression profiling by array

Platform:: GPL10558
75 Samples

Download data: TXT

Series

Accession:: GSE65399

ID:: 200065399

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Select item 2002448869.

RNA-seq data for edited and unedited GAA repeats in FRDA patient iPSC-derived neurons

(Submitter supplied) Friedreich ataxia (FRDA) is a multisystemic, autosomal recessive disorder caused by a homozygous GAA expansion mutation in the first intron of frataxin (FXN) gene. FXN is a mitochondrial protein critical for iron-sulfur cluster biosynthesis and deficiency impairs mitochondrial electron transport chain functions and iron homeostasis within the organelle. Currently, there is no effective treatment for FRDA. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL24676
28 Samples

Download data: TXT

Series

Accession:: GSE244886

ID:: 200244886

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Select item 20020552610.

G-rich motifs within phosphorothioate-based antisense oligonucleotides (ASOs) drive activation of FXN expression through indirect effects

(Submitter supplied) Evaluation of the effect of 3 ASOs targeting FXN on mRNA levels

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL21697
21 Samples

Download data: TSV

Series

Accession:: GSE205526

ID:: 200205526

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Select item 20026165511.

Frataxin Deficiency Drives a Shift from Mitochondrial Metabolism to Glucose Catabolism, Triggering an Inflammatory Phenotype in Microglia

(Submitter supplied) Immunometabolism investigates the complex interplay between the immune system and cellular metabolism. This study highlights the effects of mitochondrial frataxin (FXN) depletion, which causes Friedreich's ataxia (FRDA), a neurodegenerative condition characterized by coordination and muscle control deficiencies. Using single-cell RNA sequencing, we identified specific cell groups in the cerebellum of a FRDA mouse model, emphasizing a notable inflammatory microglial response. more...

Organism:: Mus musculus

Type:: Expression profiling by high throughput sequencing

Platform:: GPL24247
8 Samples

Download data: MTX, TSV

Series

Accession:: GSE261655

ID:: 200261655

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Select item 20026165412.

Frataxin Deficiency Drives a Shift from Mitochondrial Metabolism to Glucose Catabolism, Triggering an Inflammatory Phenotype in Microglia (scRNA-Seq)

Organism:: Mus musculus

Type:: Expression profiling by high throughput sequencing

Platform:: GPL24247
2 Samples

Download data: MTX, TSV

Series

Accession:: GSE261654

ID:: 200261654

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Select item 20026165313.

Frataxin Deficiency Drives a Shift from Mitochondrial Metabolism to Glucose Catabolism, Triggering an Inflammatory Phenotype in Microglia (bulk RNA-Seq)

Organism:: Mus musculus

Type:: Expression profiling by high throughput sequencing

Platform:: GPL24247
6 Samples

Download data: TXT

Series

Accession:: GSE261653

ID:: 200261653

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Select item 20020090714.

A non-synonymous SNP in SIRT6 predicts neurological severity in Friedreich ataxia

(Submitter supplied) Friedreich ataxia (FRDA) is a recessive neurodegenerative disease characterized by progressive ataxia, dyscoordination, and loss of vision. The variable length of the pathogenic GAA triplet repeat expansion in the FXN gene in part explains Inter-individual variability in severity of disease. The GAA repeat expansion leads to epigenetic silencing of FXN; therefore, variability in properties of epigenetic effector proteins could also regulate the severity of FRDA. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL18573
20 Samples

Download data: CSV, TSV

Series

Accession:: GSE200907

ID:: 200200907

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Select item 20022664615.

Skeletal muscle transcriptomics dissects the pathogenesis of Friedreich's Ataxia

(Submitter supplied) RNA sequencing of skeletal muscle biopsies from healthy controls and Friedreich's Ataxia (FRDA) patients before and after treatment with recombinant human erythropoietin (rhuEPO) to dissect the mechanisms of disease.

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL17303
20 Samples

Download data: CSV

Series

Accession:: GSE226646

ID:: 200226646

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Select item 20009940316.

Synthetic transcription elongation factors

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:: GPL18573 GPL16791
58 Samples

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Series

Accession:: GSE99403

ID:: 200099403

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Select item 20009940217.

ChIP-RX of GM15850 cells treated with synthetic transcription elongation factors

(Submitter supplied) Switching a paused RNA polymerase II into productive elongation is tightly-regulated, especially at genes involved in human development and disease. To exert control on this rate-limiting step, we designed sequence-specific synthetic transcription elongation factors (Syn-TEFs). These molecules are composed of programmable DNA-binding ligands flexibly tethered to a small molecule that binds a component of the transcription elongation machinery. more...

Organism:: Homo sapiens

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL18573
18 Samples

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Series

Accession:: GSE99402

ID:: 200099402

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Select item 20009940018.

RNA-seq of GM15850 and GM15851 cells treated with synthetic transcription elongation factors.

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL16791
40 Samples

Download data: TXT

Series

Accession:: GSE99400

ID:: 200099400

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Select item 20023383019.

TNRC18 recognizes H3K9me3 to mediate transposable elements silencing at ERV regions [WGBS]

(Submitter supplied) Trimethylation of histone H3 lysine 9 (H3K9me3) is critical for regulation of gene repression and heterochromatin formation, cell-fate determination, and organismal development. In particular, H3K9me3 provides an essential mechanism for silencing various transposon elements (TEs). However, previous studies showed that the canonical H3K9me3 readers (e.g. HP1 and MPP8) play rather limited roles in silencing endogenous retroviruses (ERVs), one of major TE classes in the mammalian genome. more...