Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

13 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

High-resolution custom array spanning Xq28 region to study patients carrying MECP2 copy number gain (part 1)

ABSTRACT: The goal of this experiment was to determine the size, genomic extent and gene content of each Xq28 rearrangement. We designed a tiling-path oligonucleotide microarray spanning 4.6 Mb surrounding the MECP2 region on Xq28. The custom 4x44k Agilent Technologies microarray was designed using the Agilent earray website. We selected 22,000 probes covering ChrX: 150,000,000-154,600,000 (NCBI build 36), including the MECP2 gene, which represents an average distribution of 1 probe per 209 bp. Each patient sample was run once using this array; hybridization was done using a gender-matched reference sample.

ORGANISM(S): Homo sapiens

SUBMITTER: James Lupski

PROVIDER: E-GEOD-49440 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

High-resolution custom array spanning Xq28 region to study patients carrying MECP2 copy number gain (part 2)

Project description:The goal of this experiment was to determine the size, genomic extent and gene content of each Xq28 rearrangement. We designed a tiling-path oligonucleotide microarray spanning 4.0 Mb surrounding the MECP2 region on Xq28. The custom 4x44k Agilent Technologies microarray was designed using the Agilent earray website. We selected 22,000 probes covering ChrX: 150,400,000-154,400,000 (NCBI build 35), including the MECP2 gene, which represents an average distribution of 1 probe per 500 bp. Each patient sample was run once using this array; hybridization was done using a gender-matched reference sample.

2013-08-02 | E-GEOD-49446 | biostudies-arrayexpress

Complex Genomic Rearrangements at the PLP1 Locus Include Triplication and Quadruplication

Project description:Inverted repeats (IRs) can facilitate structural variation as crucibles of genomic rearrangement. Complex DUP-TRP/INV-DUP rearrangements that contain breakpoint junctions within IRs have been recently associated with both MECP2 duplication syndrome (MIM#300260) and Pelizaeus-Merzbacher disease (PMD, MIM#312080). We investigated 17 unrelated PMD subjects with copy number gains at the PLP1 locus including triplication and quadruplication of specific genomic intervals M-bM-^@M-^S 16/17 were found to have a DUP-TRP/INV-DUP rearrangement product. An IR distal to PLP1 facilitates DUP-TRP/INV-DUP formation as well as an inversion structural variation found frequently amongst normal individuals. We show that a homologyM-bM-^@M-^Tor homeologyM-bM-^@M-^Tdriven replicative mechanism of DNA repair can apparently mediate template switches within stretches of microhomology. Moreover, we provide evidence that quadruplication, and potentially higher order amplification of a genomic interval, can occur in a manner consistent with rolling circle amplification as predicted by the microhomology mediated break induced replication (MMBIR) model. To determine size, genomic extent and gene content for each rearrangement, we used a customized tiling-path oligonucleotide microarray spanning the Xq22 chromosomal region to query the genomic DNA of 7 males with Pelizaeus-Merzbacher disease, and 5 unaffected or carrier/unaffected family members. A 4x44k Agilent Technologies (Santa Clara, CA) microarray was designed using the Agilent e-array website targeting the region of the genome encompassing the dosage-sensitive PLP1 gene.

2014-11-25 | E-GEOD-63594 | biostudies-arrayexpress

High-resolution custom array spanning Xq28 region to study patients carrying MECP2 copy number gain

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2013-08-02 | E-GEOD-49447 | biostudies-arrayexpress

Intragenic DNA methylation modulates alternative splicing by recruiting MeCP2 to promote exon recognition [RNA-Seq]

Project description:Although the function of DNA methylation in gene promoter regions is well established in transcriptional repression, the function of the evolutionarily conserved widespread distribution of DNA methylation in gene body regions remains incompletely understood. Here, we show that DNA methylation is enriched in included alternatively spliced exons (ASEs) and inhibiting DNA methylation results in aberrant splicing of ASEs. The methyl-CpG binding protein MeCP2 is enriched in included ASEs, particularly those that are also highly DNA methylated, and inhibition of DNA methylation disrupts specific targeting of MeCP2 to exons. Interestingly, ablation of MeCP2 results in increased nucleosome acetylation and aberrant skipping events of ASEs. We further show that inhibition of histone deacetylases leads to a highly significant overlap of exon skipping events caused by knocking-down MeCP2. Together, our data indicate that intragenic DNA methylation operates in exon definition to modulate alternative splicing and can enhance exon recognition via recruitment of the multifunctional protein MeCP2, which thereby maintains local histone hypoacetylation through its established interaction with HDACs. RNA-Seq in IMR90 and HCT116

2013-08-13 | E-GEOD-47488 | biostudies-arrayexpress

High-resolution custom array spanning Xq28 region to study patients carrying MECP2 copy number gain (part 2)

Project description:The goal of this experiment was to determine the size, genomic extent and gene content of each Xq28 rearrangement.

2013-08-02 | GSE49446 | GEO

High-resolution custom array spanning Xq28 region to study patients carrying MECP2 copy number gain (part 1)

Project description:The goal of this experiment was to determine the size, genomic extent and gene content of each Xq28 rearrangement.

2013-08-02 | GSE49440 | GEO

Over-expression of either MECP2_e1 or MECP2_e2 in mouse MECP2 knockout fibroblasts

Project description:Aim: to detect genes that are differentially transcribed in mouse MECP2 knockout fibroblasts over-expressing either of the two human MECP2 isoforms, MECP2_e1 or MECP2_e2. Methods: mouse Mecp2tm1.1Bird knockout fibroblast cell line was stably infected by lentiviral vectors over-expressing MECP2_e1, MECP2_e2, or eGFP. RNA extracted, and used for gene expression microarray analysis 3 biological replicates for MECP2_e1; 3 replicates for MECP2_e2; 3 replicates for eGFP as control; 3 replicates for MECP2_e1 with 9bp insertion mutation in N-terminal

2014-01-25 | E-GEOD-54261 | biostudies-arrayexpress

Reversal of MECP2 duplication syndrome using genetic rescue and antisense oligonucleotides [ASO time point 2]

Project description:MECP2 duplication syndrome, a childhood neurological disorder characterized by autism, intellectual disability, motor dysfunction, anxiety and epilepsy, is caused by a duplication on chromosome Xq28 spanning the MECP2 gene that results in doubling of MeCP2 levels. MECP2 overexpression in mice causes neurobehavioral and electroencephalographic defects similar to those of human patients, but the gross anatomy of the brain remains unaffected. We hypothesized that MECP2 duplication syndrome would be reversible and tested two methods to restore MeCP2 levels to normal: conditional genetic recombination and antisense oligonucleotide therapy. Both approaches rescued molecular, physiological and behavioral features of adult symptomatic mice. Antisense therapy also restored normal MeCP2 levels in lymphoblastoid cells from MECP2 duplication patients, in a dose-dependent manner. Our data indicate that antisense oligonucleotides could provide a viable therapeutic approach for human MECP2 duplication syndrome as well as other disorders involving copy number gains.

2015-11-27 | GSE71234 | GEO

Reversal of MECP2 duplication syndrome using genetic rescue and antisense oligonucleotides [ASO time point 1]

2015-11-27 | GSE71233 | GEO

Reversal of MECP2 duplication syndrome using genetic rescue and antisense oligonucleotides [Genetic Rescue Experiments]

2015-11-27 | GSE71229 | GEO