Similar Datasets
Project description:RNA-seq of hiPSCs derived mosaic Down syndrome (undi)
| PRJNA880683 | ENA
Project description:The Dp(10)2Yey mouse carries a ~2.3 Mb intra-chromosomal duplication of mouse chromosome 10 (Mmu10) that makes it an essential model for aspects of Down syndrome (DS, trisomy 21). Specifically, these animals carry extra copies of Mmu10 genes that are homologous to those on human chromosome 21 (Hsa21). Here, we report spatial memory impairment and anxiety-like behaviour in this model alongside altered neural activity in the medial prefrontal cortex (mPFC) and hippocampus (HPC). Specifically, Dp(10)2Yey DS mice showed impaired spatial alternation associated with increased ripple activity in mPFC during the period of memory consolidation, and reduced mobility in a novel environment accompanied by reduced theta-gamma phase-amplitude coupling in HPC. Finally, we found alterations in the number of interneuron subtypes in mPFC and HPC that may contribute to the observed phenotypes and highlight potential approaches to ameliorate the effects of human trisomy 21.
2023-02-22 | GSE214273 | GEO
Project description:Dysregulation of Sonic hedgehog (SHH) signaling may contribute to multiple Down syndrome-associated phenotypes, including cerebellar hypoplasia, congenital heart defects, craniofacial and skeletal dysmorphologies, and Hirschsprung disease. Granule cell precursors isolated from the developing cerebellum of Ts65Dn mice are less responsive to the mitogenic effects of SHH than euploid cells, and a single postnatal dose of the SHH pathway agonist SAG rescues cerebellar morphology and performance on learning and memory tasks in Ts65Dn mice. SAG treatment also normalizes expression levels of OLIG2 in neural progenitor cells derived from human trisomy 21 iPSCs. However, despite evidence that activating SHH signaling rescues Down syndrome-associated phenotypes, chromosome 21 does not encode any canonical components of the SHH pathway. Here, we screened 163 chromosome 21 cDNAs in a series of SHH-responsive cell lines to identify chromosome 21 genes that modulate SHH signaling and confirmed overexpression of trisomic candidate genes using RNA-seq in Ts65Dn and TcMAC21 cerebellum. Our study indicates that some chromosome 21 genes, including DYRK1A, activate SHH signaling while others, such as HMGN1 and MIS18A, inhibit SHH signaling. Moreover, overexpression of genes involved in chromatin structure and mitosis, but not genes previously implicated in ciliogenesis, regulate the SHH pathway. Our data suggest that cerebellar hypoplasia and other phenotypes related to aberrant SHH signaling arise from the net effect of trisomy for multiple chromosome 21 genes rather than the overexpression of a single trisomic gene. Identifying which chromosome 21 genes modulate SHH signaling may also suggest new therapeutic avenues for ameliorating Down syndrome phenotypes.
2022-05-16 | GSE202938 | GEO
Project description:Down syndrome is characterized by a wide spectrum of clinical signs, which include cognitive and endocrine disorders and haematological abnormalities. Although it is well established that the causative defect of Down syndrome is the trisomy of chromosome 21, the molecular bases of Down syndrome phenotype are still largely unknown. We used the Infinium HumanMethylation450 BeadChip to investigate DNA methylation patterns in whole blood from 29 subjects affected by Down syndrome (DS), using their healthy relatives as controls (mothers and unaffected siblings). This family-based model allowed us to monitor possible confounding effects on DNA methylation patterns deriving from genetic and environmental (lifestyle) factors. The identified epigenetic signature of Down syndrome includes differentially methylated regions that, although enriched on chromosome 21, interest most of the other chromosomes and can be functionally linked to the developmental and haematological defects characteristic of the disease.
2015-03-03 | GSE52588 | GEO
Project description:Background: Down syndrome is the most common genetic cause of mental retardation in humans, occurring in ~1 in 800 newborns. It is caused by chromosome 21 trisomy. Disruption of the phenotype is thought to be the result of gene dosage imbalance. The aim of the study was to classify chromosome 21 genes according to their level of expression in Down syndrome. Results: Variations in chromosome 21 gene expression were analyzed in lymphoblastoid cell lines derived from 10 Down syndrome patients and 11 control individuals. Of the 359 genes and predictions displayed on a specifically designed high content chromosome 21 oligoarray, 132 genes were expressed in lymphoblastoid cell lines. By using a powerful statistical analysis, 58 genes were found overexpressed and 42 unchanged in cell lines from Down syndrome patients. Microarray data were validated by quantitative PCR on 10 genes. Conclusions: The 132 chromosome 21 genes expressed by derived lymphoblastoid cell lines were classified into four categories: Class I: 24 genes controlled by the gene dosage effect with an increase in expression in Down syndrome between 1.4 and 1.6; Class II: 14 amplified genes with expression ratio above 1.6; Class III: 32 compensated genes with expression ratio between 0.82 to 1.4 and Class IV: 30 genes with high variability between individuals. Class I and II genes are likely to be involved in the Down syndrome phenotype, in contrast to the compensated Class III genes; Class IV genes could account for the variable phenotypes observed in patients. Keywords: HSA21 gene expression in Down syndrome
2007-05-01 | GSE6408 | GEO
Project description:To know gene expression patterns affected by 5-OXO-ETE and Calcitriol
2024-03-13 | GSE213410 | GEO
Project description:To investigate the physiological characteristics of endothelial cells (EC) harboring trisomy 21 (T21), we establised isogenic pairs of T21-iPSCs and corrected disomy 21 (cDi21)-iPSCs We then performed gene expression profiling analysis using data obtained from RNA-seq of 5 different iPSC-derived ECs.
2022-05-20 | GSE203257 | GEO
Project description:U1 small nuclear (sn)RNA, required for splicing of pre-mRNA, is encoded by genes on chromosome 1p36. Imperfect copies of these ‘true’ (t)U1 snRNA genes, located on chromosome 1q12-21, were thought to be pseudogenes. However, many of these ‘variant’ (v)U1 snRNA genes produce fully-processed transcripts that are packaged into potentially functional particles. Using antisense oligonucleotides, we have achieved functional knockdown of a specific vU1 snRNA in HeLa cells and identified over 400 transcriptome changes following interrogation of the Affymetrix Human Exon ST 1.0 array.
2012-10-01 | GSE37623 | GEO
Project description:Down syndrome (DS), caused by an extra copy of chromosome 21, affects 1 in 750 live births and is characterised by cognitive impairment and a constellation of congenital defects. Currently, little is known about the molecular pathogenesis and no direct genotype-phenotype relationship has yet been confirmed. Since DS amniocytes are expected to have a distinct biological behaviour compared to normal amniocytes, we hypothesise that relative quantification of proteins produced from trisomy and euploid (chromosomally normal) amniocytes will reveal dysregulated molecular pathways. Chromosomally normal- and Trisomy 21-amniocytes were quantitatively analyzed by using Stable Isotope Labeling of Amino acids in Cell culture and tandem mass spectrometry. The most extensive proteome of amniocytes and amniotic fluid has been generated and differentially expressed proteins from amniocytes with Trisomy 21 revealed molecular pathways that seem to be most significantly affected by the presence of an extra copy of chromosome 21. Mass spectra were analyzed using Mascot (version 2.2, Matrix Science), executing a spectral search against a concatenated International Protein Index (IPI) human protein database (version 3.54 containing 39,925 entries) and a decoy database. Parameters included: trypsin enzyme specificity, SILAC double measurements of Lys6 and Arg8, 1 missed cleavage, minimum peptide length of 7 amino acids, minimum of 1 unique peptide, top 6 MS/MS peaks per 100 Da, peptide mass tolerance of 20 ppm for precursor ion and MS/MS tolerance of 0.5 Da. Oxidation of methionine and N-terminal protein acetylation for variable modifications and cysteine caramidomethylation for fixed modification. All entries were filtered using a false positive rate of 1% both at the peptide and protein levels, and false positives were removed. Quantification via normalised H/L ratios was based on minimum of 3 peptide ratio counts. Protein group entries with a normalised ratio significance B score of =< 0.05 or significance A score of =< 0.05 were retained for further analysis.
2013-09-27 | PXD000385 | Pride
Project description:The Ts1Cje mouse strain (Sago, 1998) contains a segmental trisomy of mouse chromosome 16 orthologous to the region of human chromosome 21 commonly associated with Down Syndrome. In this study, fetuses were obtained from wildtype mothers bred with either wildtype or Ts1Cje males. Gene expression profiles in fetal liver and placenta of wildtype and Ts1Cje fetuses were compared, to identify potential markers for application in human prenatal DS screening.
2011-05-11 | GSE24272 | GEO