Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1059009 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR27381906_1.fastq.gz | Fastqsanger.gz | |||
| SRR27381906_2.fastq.gz | Fastqsanger.gz |
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Project description:Down syndrome (DS) is caused by triplication of Human chromosome 21 (Hsa21) and associated with an array of deleterious phenotypes, including mental retardation, heart defects and immunodeficiency. Genome-wide expression patterns of uncultured peripheral blood cells are useful to understanding of DS-associated immune dysfunction. We used a Human Exon microarray to characterize gene expression in uncultured peripheral blood cells derived from DS individuals and age-matched controls from two age groups: neonate (N) and child (C). A total of 174 transcript clusters (gene-level) with eight located on Hsa21 in N group and 383 transcript clusters including 56 on Hsa21 in C group were significantly dysregulated in DS individuals. Microarray data were validated by quantitative polymerase chain reaction. Functional analysis revealed that the dysregulated genes in DS were significantly enriched in two and six KEGG pathways in N and C group, respectively. These pathways included leukocyte trans-endothelial migration, B cell receptor signaling pathway and primary immunodeficiency, etc., which causally implicated dysfunctional immunity in DS. Our results provided a comprehensive picture of gene expression patterns in DS at the two developmental stages and pointed towards candidate genes and molecular pathways potentially associated with the immune dysfunction in DS.
2012-02-10 | GSE35665 | GEO
Project description:One in five people with Down syndrome (DS) are born with an atrioventricular septal defect (AVSD), an incidence 2,000 times higher than in the euploid population. The genetic loci that contribute to this risk are poorly understood. In this study, we tested two hypotheses: 1) individuals with DS carrying chromosome 21 copy number variants (CNVs) that interrupt exons may be protected from AVSD, because these CNVs return AVSD susceptibility loci back to disomy, and 2) individuals with DS carrying chromosome 21 genes spanned by microduplications are at greater risk for AVSD because these microduplications boost the dosage of AVSD susceptibility loci beyond a tolerable threshold. We tested 236 case individuals with DS+AVSD and 290 control individuals with DS and a normal heart using a custom microarray with dense probes tiled on chromosome 21 for array CGH. We found that neither an individual chromosome 21 CNV nor any individual gene intersected by a CNV was associated with AVSD in DS. Burden analyses revealed that African American controls had more bases covered by rare deletions than did African American cases. Inversely, we found that Caucasian cases had more genes intersected by rare duplications than did Caucasian controls. Pathway analyses indicated copy number perturbtations of genes involved in protein heterotrimerization and histone methylating proteins. Finally, we showed that previously DS+AVSD-associated common CNVs on chromosome 21 are likely false positives. This research adds to the swell of evidence indicating that DS-associated AVSD is similarly heterogeneous, as is AVSD in the euploid population.
2017-01-30 | GSE93004 | GEO
Project description:Down syndrome (DS) is caused by triplication of Human chromosome 21 (Hsa21) and associated with an array of deleterious phenotypes, including mental retardation, heart defects and immunodeficiency. Spatio-temporal patterns of genome-wide expression are critical to the understanding of DS. We used a Human Exon microarray to characterize gene expression in peripheral blood cells derived from DS and control individuals from two age groups: neonate (N) and child (C). A total of 174 transcript clusters (gene-level) with eight located on Hsa21 in N group and 383 transcript clusters including 57 on Hsa21 in C group were significantly dysregulated in DS individuals. Except for 22 commonly dysregulated genes in the two groups, the remaining dysregulated genes were different between N and C groups, reflecting temporally dynamic variation in gene expression in DS. Dramatically fewer dysregulated Hsa21 genes in N group than those in C group suggested that triplication of Hsa21 per se induces a moderate deregulation at early developmental stages. Further functional analysis revealed that the dysregulated genes in DS were significantly enriched in two KEGG pathways in N group and six pathways in C group. These pathways included leukocyte trans-endothelial migration, B cell receptor signaling pathway and primary immunodeficiency, etc., which causally implicated dysfunctional immunity in DS. Our results provided a comprehensive picture of expression patterns of DS at the two developmental stages and point towards candidate genes and molecular pathways potentially associated with the immune dysfunction in DS. All 37 samples, including 15 DS patients and 22 control individuals were analysized and divided into two age-matched groups: N group (5 DS versus 7 control individuals, age: 3 days to 38 days) and C group (10 DS versus 15 control individuals, age: 1 year to 13 years). N group includes DS (D11-D15) and Control (C16-C22), and C group includes DS (D1-D10) and Control (C1-C15).
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Project description:As part of a clinical trial of the MDM2 inhibitor DS-3032b, 41 primary tumor samples were obtained before treatment from 38 patients newly diagnosed with AML, or relapsed or refractory to standard induction chemotherapy Gene expression features of pretreatment samples, along with TP53 mutation status, were found to correlate with clinical response to DS-3032b (manuscript under review).
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Project description:The maize NAKED ENDOSPERM (NKD) genes Nkd1 and Nkd2 encode paralogous INDETERMINATE DOMAIN (IDD) transcription factors (TFs) that have previously been shown to play critical roles in regulating endosperm gene expression and development. However, the function of each individual NKD protein is unclear. To elucidate this, we performed a transcriptome analysis for nkd1-Ds and nkd2-Ds single mutant endosperm. We found that in nkd1-Ds single mutant, nkd2 gene expression is significantly lower than WT, and similar to the nkd2-Ds mutant.
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Project description:This is array CGH data of recurrent 17q21.31 deletions used to delineate breakpoints within segmental duplications in a study by Itsara et al. Somatic cell hybrids were generated from three parent-child trios probands with 17q21.31 deletions and three 17q21.31 probands for which no parental DNA was available that isolated individual chromosome 17 homologues. In parents, this isolated the H2 from the H1 haplotypes in distinct cell lines, and in probands, isolated the deletion-bearing chromosomes from the unaffected chromosome 17. In parent-child trios, the deletion-bearing chromosomes were hybridized against the progenitor parental chromosome. In probands with no parental DNA, the deletion-bearing chromosomes were hybridized against an H2 chromosome.
2012-06-02 | GSE34867 | GEO
Project description:Background: Trisomy 21 causes Down syndrome (DS), but the mechanisms by which the extra chromosome leads to deficient intellectual and immune function are not well understood. Results: Here, we profile CpG methylation in DS and control cerebral and cerebellar cortex of adults and cerebrum of fetuses. We purify neuronal and non-neuronal nuclei and T-lymphocytes and find biologically relevant genes with DS-specific methylation (DS-DM) in brain cells. Some genes show brain-specific DS-DM, while others show stronger DS-DM in T cells. Both 5-methyl-cytosine and 5-hydroxy-methyl-cytosine contribute to the DS-DM. Thirty percent of genes with DS-DM in adult brain cells also show DS-DM in fetal brains, indicating early onset of these epigenetic changes, and we find early maturation of methylation patterns in DS brain and lymphocytes. Some, but not all, of the DS-DM genes show differential expression. DS-DM preferentially affected CpGs in or near specific transcription factor binding sites, implicating a mechanism involving altered transcription factor binding. Methyl-seq of brain DNA from mouse models with sub-chromosomal duplications mimicking DS reveals partial but significant overlaps with human DS-DM and shows that multiple chromosome 21 genes contribute to the downstream epigenetic effects. Conclusions: These data point to novel biological mechanisms in DS and have general implications for trans effects of chromosomal duplications and aneuploidies on epigenetic patterning. Examination of methylation changes in two mouse models of Down syndrome with sub-chromosomal duplications, Dp(10)1Yey and Dp(16)1Yey, compared to one littermate wild type mouse using whole genome bisulfite sequencing.
2015-10-30 | E-GEOD-74505 | biostudies-arrayexpress
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