RNA-seq of human aneuploid cell lines with Trisomy 21
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA543056 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR9058970.fastq.gz | Fastqsanger.gz | |||
| SRR9058980.fastq.gz | Fastqsanger.gz | |||
| SRR9058971.fastq.gz | Fastqsanger.gz | |||
| SRR9058981.fastq.gz | Fastqsanger.gz | |||
| SRR9058972.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 15 |
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Project description:Trisomy 21, a form of aneuploidy, is one of the few viable forms of trisomy. The goal of this study was to assess the effect of an additional chromosome 21 on gene expression in two different human aneuploid model cell lines.
2019-05-16 | GSE131249 | GEO
Project description:Gene expression was measured in trisomy 21 and trisomy 13 human fetal samples. For TS21, regions assayed were cerebrum, cerebellum, heart, and cerebrum-derived astrocyte cell lines. Keywords = trisomy 21 Keywords = Down syndrome Keywords = aneuploidy Keywords = brain Keywords = heart Keywords = trisomy 13 Keywords: other
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Project description:Molecular consequences of trisomy in lymphoblastoid cell lines from patients with Down syndrome. This project analyses differentially expressed genes between humans with trisomy 21 and humans without trisomy 21.
2012-08-15 | GSE34458 | GEO
Project description:Molecular consequences of trisomy in lymphoblastoid cell lines from patients with Down syndrome. This project analyses differentially expressed genes between humans with trisomy 21 and humans without trisomy 21. Total RNA obtained from human lymphoblastoid cell lines without trisomy 21 compared to cell lines from human with trisomy 21.
2012-08-14 | E-GEOD-34458 | biostudies-arrayexpress
Project description:RNA-seq of lymphoblastoid cells from a family of individuals (one of which has Trisomy 21) was used to determine the molecular origin of dosage compensation in Trisomy 21.
2023-04-29 | GSE230995 | GEO
Project description:Down syndrome (DS) is caused by an extra copy of chromosome 21. We are characterizing protein changes in human skin fibroblasts. We propose to study corresponding changes at the DNA level (by SNP analysis) and the RNA level (using Affymetrix chips). These studies will detail transcriptional and translational regulation in trisomy. The Specific Aim is to obtain data on RNA transcript levels using Affymetrix expression arrays in a group of trisomy 21 and euploid fibroblast cell lines. In parallel, we will acquire SNP data to determine both genotype (call) and copy number changes for trisomic samples. The results will allow us to identify the patterns of change in a trisomic chromosome (relative to control). [1] We hypothesize that in genomic DNA samples derived from trisomy 21 (TS21) fibroblasts there will be an increased copy number on chr21 with additional microdeletions and microdeletions. [2] We hypothesize that the RNA transcripts derived from chr21 will be elevated relative to euploid controls. [3] We hypothesize that altered RNA transcript levels will be significantly correlated with altered protein levels from these same fibroblast cell lines. The experimental design is as follows. All samples are from deidentified individuals and were obtained from the Brain and Tissue Bank for Developmental Disorders at the University of Maryland, with Johns Hopkins IRB approval.[1] There are five trisomy 21 samples and five euploid samples (total n=10). Fibroblasts were grown in culture to comparable confluency and passage number. Cells were harvested. Total RNA was isolated with a Qiagen kit. The quantity and purity of the RNA was confirmed by spectrophotometry and by electrophoresing an aliquot on a 1% agarose gel. Approximately 10 micrograms of total RNA will be sent to TGen on dry ice for analysis on Affymetrix U133 PlusTwo arrays. Data analysis will be with Affymetrix and Partek software. Keywords: other
2007-12-04 | GSE9762 | GEO
Project description:GRO-seq of lymphoblastoid cells from a family of individuals (one of which has Trisomy 21) was used to determine the molecular origin of dosage compensation in Trisomy 21.
2023-04-29 | GSE230994 | GEO
Project description:Down syndrome, caused by trisomy 21, is a complex developmental disorder associated with intellectual disability and reduced growth of multiple organs. Structural pathologies are present at birth, reflecting embryonic origins. A fundamental unanswered question is how an extra copy of human chromosome 21 contributes to organ-specific pathologies that characterize individuals with Down syndrome. Relevant to the hallmark intellectual disability in Down syndrome, how does trisomy 21 affect neural development? We tested the hypothesis that trisomy 21 exerts effects on human neural development as early as neural induction. Bulk RNA sequencing was performed on isogenic trisomy 21 and euploid human induced pluripotent stem cells (iPSCs) at successive stages of neural induction: embryoid bodies at Day 6, early neuroectoderm at Day 10, and differentiated neuroectoderm at Day 17. Gene expression analysis revealed over 1,300 differentially expressed genes in trisomy 21 cells along the differentiation pathway compared to euploid controls. Less than 5% of the gene expression changes included upregulated chromosome 21 encoded genes at every timepoint. Genes involved in specific growth factor signaling pathways (Wnt and Notch), metabolism (including interferon response and oxidative stress), and extracellular matrix were altered in trisomy 21 cells. Further analysis revealed heterochronic expression of genes. This comprehensive analysis reveals that trisomy 21 impacts discrete developmental pathways at the earliest stages of neural development. Further, the results suggest that metabolic dysfunction arises early in embryogenesis in trisomy 21 and may thus affect development and function more broadly.
2024-01-31 | GSE247990 | GEO
Project description:Down syndrome (DS) is caused by an extra copy of chromosome 21. We are characterizing protein changes in human skin fibroblasts. We propose to study corresponding changes at the DNA level (by SNP analysis) and the RNA level (using Affymetrix chips). These studies will detail transcriptional and translational regulation in trisomy. The Specific Aim is to obtain data on RNA transcript levels using Affymetrix expression arrays in a group of trisomy 21 and euploid fibroblast cell lines. In parallel, we will acquire SNP data to determine both genotype (call) and copy number changes for trisomic samples. The results will allow us to identify the patterns of change in a trisomic chromosome (relative to control). [1] We hypothesize that in genomic DNA samples derived from trisomy 21 (TS21) fibroblasts there will be an increased copy number on chr21 with additional microdeletions and microdeletions. [2] We hypothesize that the RNA transcripts derived from chr21 will be elevated relative to euploid controls. [3] We hypothesize that altered RNA transcript levels will be significantly correlated with altered protein levels from these same fibroblast cell lines. The experimental design is as follows. All samples are from deidentified individuals and were obtained from the Brain and Tissue Bank for Developmental Disorders at the University of Maryland, with Johns Hopkins IRB approval.[1] There are five trisomy 21 samples and five euploid samples (total n=10). Fibroblasts were grown in culture to comparable confluency and passage number. Cells were harvested. Total RNA was isolated with a Qiagen kit. The quantity and purity of the RNA was confirmed by spectrophotometry and by electrophoresing an aliquot on a 1% agarose gel. Approximately 10 micrograms of total RNA will be sent to TGen on dry ice for analysis on Affymetrix U133 PlusTwo arrays. Data analysis will be with Affymetrix and Partek software.
2008-06-16 | E-GEOD-9762 | biostudies-arrayexpress
Project description:Down syndrome is a common disorder with enormous medical and social costs, caused by trisomy for Chr21. We tested the concept that gene imbalance across an extra chromosome can be de facto corrected in DS patient stem cells by manipulating a single gene, XIST. Using zinc finger nucleases, we targeted a large, inducible XIST transgene into the Chr21 DYRK1A locus, in DS pluripotent stem cells. XIST RNA coats Chr21 and triggers stable heterochromatin modifications, chromosome-wide transcriptional silencing and DNA methylation to form a “Chr21 Barr Body.” This provides a model to study human chromosome inactivation and creates a system to investigate genomic expression changes and cellular pathologies of trisomy 21, free from genetic and epigenetic noise. In this study, we used microarrays to understand the genome-wide impacts of inducible XIST expression on Chr21 in trisomy 21 human iPS cell lines, and to evaluate the extent of Chr21 silencing trisomic samples versus a disomic male iPS cell line.
2013-07-12 | GSE47014 | GEO