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Evaluation of the effects of 16p13.11 deletions on gene expression

ABSTRACT: We analyzed seven epilepsy patients with a heterozygous chr16p13.11 deletion and eight controls with no deletion at this locus to evaluate the impact of the deletion on gene expression.

ORGANISM(S): Homo sapiens

PROVIDER: GSE20977 | GEO | 2010/03/20

SECONDARY ACCESSION(S): PRJNA124479

REPOSITORIES: GEO

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Evaluation of the effects of 16p13.11 deletions on gene expression

Project description:We analyzed seven epilepsy patients with a heterozygous chr16p13.11 deletion and eight controls with no deletion at this locus to evaluate the impact of the deletion on gene expression. Seven subjects with a 16p13.11 deletion compared to eight controls with no deletion at this locus, no replicates were performed.

2010-03-20 | E-GEOD-20977 | biostudies-arrayexpress

Chromosomal deletions drove parallel domestication of plant architecture in Asian and African rice

Project description:Improving the yield by modifying plant architecture is key to progressive crop domestication. Here, we show that a 110-kb deletion on the short arm of chromosome 7 promotes the critical transition from semi-prostrate growth and low yield in wild rice (Oryza rufipogon), to erect growth and high yield in Asian cultivated rice (O. sativa). The microdeletion harbors a tandem repeat of seven putative Cys2-His2 zinc-finger genes. Three of these genes regulate the plant architecture in O. rufipogon and are closely linked to the previously identified PROSTRATE GROWTH 1 (PROG1) gene. Therefore, we refer to this locus as RICE PLANT ARCHITECTURE DOMESTICATION (RPAD). Furthermore, a similar but independent 113-kb deletion was detected at the RPAD locus in African cultivated rice. These results indicate that the deletions, coupled with the loss of a tandem repeat of zinc-finger genes, drove the parallel domestication of plant architecture in Asian and African rice.

2018-07-04 | GSE116423 | GEO

CLN3 patients with differing progression of the disease

Project description:Mutations in the CLN3 gene lead to juvenile neuronal ceroid lipofuscinosis, a pediatric neurodegenerative disorder characterized by visual loss, epilepsy and psychomotor deterioration. Although most CLN3 patients carry the same 1 kb deletion in the CLN3 gene, their disease phenotype can be variable. The aims of this study were (1) to identify genes that are dysregulated in CLN3 disease regardless of the clinical course that could be useful as biomarkers, and (2) to find modifier genes that affect the progression rate of the disease. Genome-wide expression profiling was performed in 8 CLN3 patients, homozygous for the 1 kb deletion, with different disease progression and compared to seven age and gender matched controls. Lymphocytes from eight patients diagnosed with CLN3 disease,all homozygous for the 1 kb deletion in the CLN3 gene and classified as having rapid (n = 2), average (n=4), and slow disease progression (n = 2), were used. These eight patients did not receive anticonvulsive medication. In addition, lymphocytes of seven age and gender matched controls were included in the study. Lymphocytes were prepared from fresh patient blood samples by Ficoll-gradient centrifugation (BiocollM-BM-., Biochrom AG, Berlin, Germany) according to the manufacturerM-bM-^@M-^Ys protocol and used for RNA isolation (RNeasyM-BM-. Micro Kit, Qiagen, Hilden, Germany).

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Molecular characterization of two unrelated patients ABCB4 deletions

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Transcription profiling by array of yeast heterozygous diploid deletions strains screened with 20 compounds to identify gene deletions that confer sensitivity to each compound

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Molecular characterization of two unrelated patients ABCB4 deletions

2011-10-05 | GSE28676 | GEO

Reversal of cell, circuit and seizure phenotypes in a mouse model of DNM1 epileptic encephalopathy

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2023-08-14 | PXD039667 | Pride

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Project description:SLC6A20A is a proline and glycine transporter known to regulate glycine homeostasis and NMDA receptor (NMDAR) function in the brain. A previous study on Slc6a20a-haploinsufficient mice reported increases in ambient glycine levels and NMDA receptor-mediated synaptic transmission in the brain, but whether Slc6a20a deficiency leads to disease-related behavioral deficits in mice remains unknown. Here, we report that Slc6a20a heterozygous and homozygous mutant mice display gene dosage-dependent behavioral phenotypes in locomotor, repetitive behavioral, and fear memory domains. In addition, Slc6a20a heterozygous and homozygous mutant brains showed transcriptomic changes in synapse, ribosome, and mitochondria-related genes as well as autism, epilepsy, and neuron-related genes. These results suggest that Slc6a20a deletion leads to gene dosage-dependent behavioral deficits in mice and transcriptomic changes in genes associated with synapse, ribosome, mitochondria, ASD, epilepsy, and neurons

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S.lividans TK24 protease deletions

Project description:Characterization of S.lividans TK24 secreted proteome changes upon deletion of certain proteases.

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