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Affymetrix CytoScan 750K array data for a parthenogenetic SMA human embryonic stem cell line

ABSTRACT: A diploid 46(XX) human embryonic stem cell (HESC) line affected by Spinal muscular atrophy type 1 (SMA) due to homozygosity for a common deletion in the SMN1 gene was derived. By characterizing the methylation status of three different imprinted loci (MEST, SNRPN and H19) and carrying out genome-wide SNP analysis, we provide evidence that this cell line was established from the activation of a mutant haploid oocyte through parthenogenesis, resulting in homozygote diploidization of the entire genome.

ORGANISM(S): Homo sapiens

PROVIDER: GSE72284 | GEO | 2015/09/01

SECONDARY ACCESSION(S): PRJNA293668

REPOSITORIES: GEO

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Affymetrix CytoScan 750K array data for a parthenogenetic SMA human embryonic stem cell line

Project description:A diploid 46(XX) human embryonic stem cell (HESC) line affected by Spinal muscular atrophy type 1 (SMA) due to homozygosity for a common deletion in the SMN1 gene was derived. By characterizing the methylation status of three different imprinted loci (MEST, SNRPN and H19) and carrying out genome-wide SNP analysis, we provide evidence that this cell line was established from the activation of a mutant haploid oocyte through parthenogenesis, resulting in homozygote diploidization of the entire genome. Affymetrix CytoScan 750K array analysis was performed according to the manufacturer's directions on DNA extracted from tissue culture. Copy number and LOH analysis of the Affymetrix CytoScan 750K array was performed for the SMA HESC line.

2015-09-01 | E-GEOD-72284 | biostudies-arrayexpress

affy2sv: an R package to pre-process Affymetrix CytoScan HD and 750K arrays for SNP, CNV, inversion and mosaicism calling.

Project description:BackgroundThe well-known Genome-Wide Association Studies (GWAS) had led to many scientific discoveries using SNP data. Even so, they were not able to explain the full heritability of complex diseases. Now, other structural variants like copy number variants or DNA inversions, either germ-line or in mosaicism events, are being studies. We present the R package affy2sv to pre-process Affymetrix CytoScan HD/750k array (also for Genome-Wide SNP 5.0/6.0 and Axiom) in structural variant studies.ResultsWe illustrate the capabilities of affy2sv using two different complete pipelines on real data. The first one performing a GWAS and a mosaic alterations detection study, and the other detecting CNVs and performing an inversion calling.ConclusionBoth examples presented in the article show up how affy2sv can be used as part of more complex pipelines aimed to analyze Affymetrix SNP arrays data in genetic association studies, where different types of structural variants are considered.

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CytoScan 750K array data for the ataxia patient's sample

Project description:CytoScan 750K array was performed for the detection of CNV associated with the patient's phenotype CytoScan 750K array was performed according to the manufacturer's directions on DNA extracted from peripheral blood sample.

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Affymetrix CytoScan 750K data for validation of the BoBs/CNV-seq comparison study

Project description:BACs-on-Beads (BoBs) assay and Copy Number Variation Sequencing (CNV-Seq) are two frequently used methods in today’s prenatal diagnosis. Several researches studies were conducted to investigate the performance of each approach, but they were never compared side by side. This dataset is intended to be used as the 'gold standard dataset' for the validation of BoBs/CNV-seq test reasults on 10 amniotic fluid samples with pathogenic fetal CNVs.

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Expression data from SMA fibroblasts treated with amiloride or EIPA

Project description:Spinal muscular atrophy (SMA) is an autosomal recessive, pediatric-onset disorder caused by the loss of spinal motor neurons thereby leading to generalized muscle atrophy. SMA is caused by the loss of or mutations in the survival motor neuron 1 (SMN1) gene. SMN1 is duplicated only in human to give rise to the paralogous SMN2 gene. These paralogs are nearly identical except for a cytosine to thymine (C-to-T) transition within an exonic splicing enhancer (ESE) element within exon 7. As a result, the majority of SMN2 transcripts lack exon 7 (SMNΔ7) which produces a truncated and unstable SMN protein. Since SMN2 copy number is inversely related to disease severity, it is a well-established target for SMA therapeutics development. 5-(N-ethyl-N-isopropyl)amiloride (EIPA), an inhibitor of sodium/proton exchangers (NHEs), has previously been shown to increase exon 7 inclusion and SMN protein levels in SMA cells. In this study several different types of NHE inhibitors were evaluated for their ability to modulate SMN2 expression. EIPA as well as 5-(N,N-hexamethylene)amiloride (HMA) increase exon 7 inclusion in SMN2 splicing reporter lines as well as in SMA fibroblasts. The EIPA-induced exon 7 inclusion occurs via a mechanism unique from that used by RG7800, another SMN2 splicing modulator, and does not involve previously identified splicing factors. Transcriptome analysis identified novel targets, including TIA1 and FABP3, for further characterization. EIPA and HMA are more selective at inhibiting the NHE5 isoform, which is expressed in fibroblasts as well as in neuronal cells. These results show that NHE5 inhibition increases SMN2 expression and may be a novel target for therapeutics development.

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Mitochondrial defects contribute to impaired translational in SMA motor neurons

Project description:Spinal muscular atrophy (SMA) is a neuromuscular disease, characterized by loss of lower alpha motoneurons, which leads to proximal muscle weakness. SMA is caused by reduced levels of Survival of Motor Neuron protein due to biallelic deletions or mutations in the SMN1 gene. Dysfunctional mitochondria can harm cells by decreased ATP production, but also by increased oxidative stress due to elevated production of reactive oxygen species (ROS). In this study, whole proteome analysis was performed using the Taiwanese SMA mouse model on an FVB/N background to identify changes in the proteome related to oxidative stress. Therefore, primary WT and SMA motoneurons were treated with a known anti-oxidant N-Acetylcysteine, the ROS inducer menadione and the cell culture supplement sodium pyruvate. Furthermore, this study aims to investigate changes in mRNA translation initiation affected by oxidative stress in SMA.

2020-12-23 | PXD020403 | Pride

Affymetrix CytoScan 750K and HD data for developmental delay and/or physical disability phenotypes samples

Project description:Chromosomal copy number variations (CNV) have been associated with various neurological and developmental disorders and chromosomal microarray (CMA) is a method of choice to diagnose Copy Number Gain/Loss syndromes. Recently, next-generation sequencing (NGS)-based low-coverage whole genome sequencing (LC-WGS) has been applied to detect Copy Number Gain/Loss syndromes. This dataset is intended to be used as a “Golden standard data set” for development of LC-WGS analysis method. It consists of patients (n=63) who have a mental delay and/or physical disability phenotype and normal (n=20) phenotype.

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CytoScan 750K array data for the ataxia patient's sample

Project description:CytoScan 750K array data for the ataxia patient's sample

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Next Generation Sequencing of human SMA and healthy control Motor Neurons

Project description:Spinal muscular atrophy (SMA) is a motor neuron (MN) disorder caused by mutations in SMN1. The reasons of MNs selective vulnerability linked to SMN reduction remain unclear. To address this question, we performed deep RNA sequencing on SMA human MNs to detect specific altered splicing/expressed genes and to identify the presence of a common sequence motif in these genes. Many deregulated genes, such as Neurexin and Synaptotagmin families, are implicated in critical MN-function like axonogenesis and synapses. Motif-enrichment analyses of differentially expressed/spliced genes, including Neurexin2 (NRXN2), revealed a common Motif, Motif-7, which is target of SYNCRIP protein. Interestingly, SYNCRIP interacts only with full-length SMN, binding and modulating several MN transcripts, including SMN itself. SYNCRIP overexpression rescued SMA-MNs, due to the consequent increase of SMN and their down-stream target NRXN2, through a positive loop mechanism. SMN/SYNCRIP complex through motif-7 might account for selective MN degeneration and represent a potential therapeutic target.

2018-10-12 | GSE108094 | GEO

Project description:SMN1 sequencing

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