Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Repeat Detector: accurate, efficient, and flexible sizing of expanded CAG/CTG repeats from targeted DNA sequencing

ABSTRACT: Repeat Detector: accurate, efficient, and flexible sizing of expanded CAG/CTG repeats from targeted DNA sequencing

PROVIDER: PRJNA817815 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR18364022_subreads.fastq.gz	Fastqsanger.gz
	SRR18364023_subreads.fastq.gz	Fastqsanger.gz
	SRR18364024_subreads.fastq.gz	Fastqsanger.gz
	SRR18364025_subreads.fastq.gz	Fastqsanger.gz
	SRR18364026_subreads.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 26

Similar Datasets

Repeat Detector: accurate, efficient, and flexible sizing of expanded CAG/CTG repeats from targeted DNA sequencing

Project description:Targeted DNA sequencing approaches will improve how the size of short tandem repeats is measured for diagnostic tests and pre-clinical studies. The expansion of these sequences causes dozens of disorders, with longer tracts generally leading to a more severe disease. In addition, interruptions are sometimes present within repeats and can alter disease manifestation. Despite advances in methodologies, determining repeat size and identifying interruptions in targeted sequencing datasets remains a major challenge. This is because standard alignment tools are ill-suited for the repetitive nature of these sequences. To address this, we have developed Repeat Detector (RD), a deterministic profile weighting algorithm for counting repeats in targeted sequencing data. We tested RD using blood-derived DNA samples from Huntington’s disease (HD) and Fuchs endothelial corneal dystrophy patients sequenced using either Illumina MiSeq or Pacific Biosciences single-molecule, real-time sequencing platforms. RD was highly accurate in determining repeat sizes of 609 HD blood-derived samples and did not require prior knowledge of the flanking sequences or their polymorphisms within the patient population. We demonstrate that RD can be used to identify individuals with repeat interruptions and may provide a measure of repeat instability within an individual. RD is therefore highly versatile and may find applications in the diagnosis of expanded repeat disorders and the development of novel therapies.

2022-03-22 | GSE199005 | GEO

Three-dimensional chromatin interactions remain stable upon CAG/CTG repeat expansion

Project description:Expanded CAG/CTG repeats underlie thirteen neurological disorders, including myotonic dystrophy type 1 (DM1) and Huntington’s disease (HD). Upon expansion, CAG/CTG repeat loci acquire heterochromatic characteristics. This observation raises the hypothesis that repeat expansion provokes changes to higher-order chromatin conformation and thereby affects both gene expression in cis and the genetic instability of the repeat tract. Here we tested this hypothesis directly by performing 4C sequencing at the DMPK and HTT loci from DM1 and HD patient-derived cells. Surprisingly, chromatin contacts remain unchanged upon repeat expansion at both loci. This was true for expanded alleles with different DNA methylation levels and CTCF binding. Repeat tract sizes ranging from 15 to 1,700 repeats displayed strikingly similar chromatin interaction profiles. Moreover, the ectopic insertion of an expanded CAG repeat tract did not change the three-dimensional chromatin conformation of the surrounding genomic region. Our findings argue that extensive changes in heterochromatic properties are not enough to alter chromatin conformation at expanded CAG/CTG repeat loci. We conclude that 3D chromatin conformation is unlikely to drive repeat expansions or changes in gene expression in expanded CAG/CTG repeat disorders. This SuperSeries is composed of the SubSeries listed below.

2020-04-07 | GSE148185 | GEO

Effect of CWG-cPIP on CAG/CTG triplet repeat mouse brain

Project description:Effect of CWG-cPIP on CAG/CTG triplet repeat mouse brain

| PRJNA867693 | ENA

Three-dimensional chromatin interactions remain stable upon CAG/CTG repeat expansion

Project description:Three-dimensional chromatin interactions remain stable upon CAG/CTG repeat expansion

| PRJNA623390 | ENA

Contracting CAG/CTG repeats using the CRISPR-Cas9 nickase.

Project description: Not available

| S-EPMC5105158 | biostudies-literature

Stabilization of expanded (CTG)•(CAG) repeats by antisense oligonucleotides.

Project description: Not available

| S-EPMC3242663 | biostudies-literature

APOBEC3A deaminates CTG hairpin loops to promote fragility and instability of expanded CAG/CTG repeats.

Project description: Not available

| S-EPMC11745325 | biostudies-literature

Gene expression profiles in the striatum of the R6/2 mouse model of Huntington's disease injected with LNA-oligonucleotides complementary to the CAG repeats (LNA-CTG)

Project description:We investigated gene expression signatures in the striatum of wild-type mice injected with a control/scrambeled LNA-oligonucleotide (LNA-SCB) and R6/2 mice injected with LNA-SCB or LNA-CTG. Five mice were used per condition. Each group of mice received two consecutive intrastriatal injections of LNA-CTG or LNA-SCB (0.05 nmols per injection, separated by 3 days) at 11 weeks of age , when motor symptoms appeared in the R6/2 mice. Injection of LNA-CTG resulted in a signifficant attenuation of the R6/2 mice motor defficits, as early as one week after administration (12 weeks of age) and persisted for at least 4 additional weeks (15 weeks of age). Overal gene expression in each group was evaluated short before motor improvement was observed (5 days post-injection), to detect gene expression changes and signalling pathway alterations underlying the benefficial effects. Gene expression was assessed with Agilent SurePrint G3 Mouse GE 8 × 60K Microarray. Target genes were validated using real-time quantitative PCR.

2017-01-01 | GSE85126 | GEO

Author Correction: Contracting CAG/CTG repeats using the CRISPR-Cas9 nickase.

Project description: Not available

| S-EPMC11487176 | biostudies-literature

Bidirectional transcription stimulates expansion and contraction of expanded (CTG)*(CAG) repeats.

Project description: Not available

| S-EPMC3016912 | biostudies-literature