Single-cell transcriptomics reveals diverse and complex gene expression alterations in human trisomy 18
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA591933 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10539910.fastq.gz | Fastqsanger.gz | |||
| SRR10539911.fastq.gz | Fastqsanger.gz | |||
| SRR10539912.fastq.gz | Fastqsanger.gz | |||
| SRR10539913.fastq.gz | Fastqsanger.gz | |||
| SRR10539914.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 13 |
Similar Datasets
Project description:we analyzed the transcriptomics of single cell of amniotic fluid both from normal and trisomy 18 individuals by using 10x Genomics.
2022-04-13 | GSE141074 | GEO
Project description:Trisomy 18 syndrome (Edwards Syndrome, ES) is a type of aneuploidy caused by the presence of an extra chromosome 18, and just the second most common autosomal trisomy syndrome after trisomy 21 (known as Down syndrome). Aneuploidy is the leading cause of early pregnancy loss, mental retardation, and multiple congenital anomalies. We used the commercial system Chromium platform (10x Genomics) to performed scATAC-seq to measure chromatin accessibility in 11,611 single umbilical cord blood cells, derived from 2 samples, respectively one Trisomy 18 Syndrome and one healthy donor. We obtain 13 distinct major clusters of cells, identified as 6 human umbilical cord blood mononuclear cell types marker-free and characterized the driving regulatory factors and differentially accessible loci that define each cluster. We set out to generate a single-cell atlas of chromatin accessibility among health and the 18 trisomy syndrome human umbilical cord blood. Finally, the cell-type-specific gene regulatory networks analysis at a single-cell resolution of this differential accessibility-related loci genes was carried out and disease-related transcription factors (TFs) and corresponding genes are predicted. These screened disease-related transcription factors (TFs) and corresponding genes provide a basis for further research and understanding of trisomy 18 syndrome. Finally, a cell-type-specific gene regulatory network analysis of these differentially accessible related locus genes was performed at single-cell resolution and predicted disease-related transcription factors (TFs) and corresponding genes. In detail, CCBN2 and MCM3 may be essential for the development of trisomy 18 and disease differential genes are enriched in the human T-cell leukemia virus 1 infection pathway.
2021-07-07 | GSE158178 | GEO
Project description:To understand the molecular mechanisms underlying the congenital anomalies observed in patients with Trisomy 18, we compared gene expression in uncultured amniotic fluid supernatant samples from second trimester fetuses with Trisomy 18 and from euploid controls. Analysis of differential expression using both individual-gene and gene-set or pathway methods indicated disrupted function in ion transport, MHCII/T-cell mediated immunity, DNA repair, G-protein mediated signaling, kinases, and glycosylation. Significant down-regulation of genes involved in adrenal development was also identified in the trisomic fetuses, possibly explaining both the abnormal maternal serum estriols and the pre- and postnatal growth restriction found in this condition.
2010-12-03 | GSE25634 | GEO
Project description:To understand the molecular mechanisms underlying the congenital anomalies observed in patients with Trisomy 18, we compared gene expression in uncultured amniotic fluid supernatant samples from second trimester fetuses with Trisomy 18 and from euploid controls. Analysis of differential expression using both individual-gene and gene-set or pathway methods indicated disrupted function in ion transport, MHCII/T-cell mediated immunity, DNA repair, G-protein mediated signaling, kinases, and glycosylation. Significant down-regulation of genes involved in adrenal development was also identified in the trisomic fetuses, possibly explaining both the abnormal maternal serum estriols and the pre- and postnatal growth restriction found in this condition. We compared expression in five female fetuses with confirmed metaphase karotypes 47, XX, +18 and six female controls (46, XX). The gestational ages of the samples ranged from 17 5/7 to 20 6/7 weeks.
2010-12-03 | E-GEOD-25634 | biostudies-arrayexpress
Project description:PCR based detection of trisomy 18 and trisomy 21 compared against results obtained by CGH microarrrays in Preimplantation Genetic Screening
2017-04-19 | GSE97903 | GEO
Project description:Background: Among full autosomal trisomies, only trisomies of chromosome 21 (Down syndrome, DS), 18 (Edward syndrome, ES) and 13 (Patau syndrome, PS) are compatible with postnatal survival. But the mechanisms, how a supernumerary chromosome disrupts the normal development and causes specific phenotypes, are still not fully explained. As an alternative to gene dosage effects due to the trisomic chromosome, a genome-wide transcriptional dysregulation has been postulated. The aim of this study was to define the transcriptional changes in trisomy 13, 18, and 21 during early fetal development in order to define whether (1) overexpression of genes of the trisomic chromosome contributes solely to the phenotype, if (2) all genes of the trisomic chromosome are upregulated similarly and whether the ratio of gene expression is in agreement with the gene dosis, (3) whether the different trisomies behave similarly in the characteristics of transcriptional dysregulation, and (4) whether transcriptional pattern can be potentially used in prenatal diagnosis. Methods: Using oligonucleotide microarrays (Affymetrix, U133 Plus 2.0), we analyzed whole genome expression profiles representing 54.000 probe sets in cultured amniocytes (AC) and chorion villus cells (CV) from pregnancies with a normal karyotype and with trisomies of human chromosomes 21, 18 and 13. Findings: We observed a low to moderate up-regulation for a subset of genes of the trisomic chromosomes. Transcriptional level of approximately 12-13 % of the supernumerary chromosome appeared similar to the respective chromosome pair in normal karyotypes. Expression values as well as the expression patterns of genes from the trisomic chromosome can distinguish the respective trisomic samples from euploid controls. A subset of chromosome 21-genes including the DSCR1-gene involved in fetal heart development was consistently up-regulated in different tissues (AC, CV) of trisomy 21 fetuses whereas only minor changes were found for genes of all other chromosomes. In contrast, in trisomy 13 and trisomy 18 vigorous downstream transcriptional changes were found. Interpretation: Global transcriptome analysis for autosomal trisomies 13, 18, and 21 supported a combination of the two major hypotheses. As several transcriptional pathways are altered, complex regulatory mechanisms are involved in the pathogenesis of autosomal trisomies. A genome-wide transcriptional dysregulation was predominantly observed in trisomies 13 and 18, whereas a more to chromosome 21 restricted expression alteration was found in trisomy 21. Experiment Overall Design: The study included the following samples: Three samples with normal chromosomes in Amniocytes (AC) and chorion villus cells (CV) each, three samples with trisomy 13 in AC, three samples with trisomy 18 in CV, and three samples with trisomy 21 in AC and CV each.
2008-06-14 | E-GEOD-6283 | biostudies-arrayexpress
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
2005-05-10 | GSE1397 | GEO
Project description:Down syndrome (DS, trisomy 21) is associated with developmental abnormalities and increased leukemia risk. To reconcile chromatin alterations with transcriptome changes in cells with trisomy 21, we performed paired exogenous spike-in normalized RNA and chromatin immunoprecipitation sequencing in DS models. Absolute per cell normalization unmasked global amplification of gene expression associated with trisomy 21. Overexpression of the nucleosome binding protein HMGN1 (encoded on chr21q22) recapitulated the transcriptional changes seen with triplication of a “Down syndrome critical region” on distal chromosome 21. Absolute exogenous normalized ChIP-seq (ChIP-Rx) also revealed a global increase in histone 3 lysine 27 acetylation caused by HMGN1. Genes most amplified downstream of HMGN1 were enriched for tumor- and developmental stage-specific programs of B-cell acute lymphoblastic leukemia dependent on the cellular context. These data offer a mechanistic explanation for DS transcriptional patterns, and suggest that further study of HMGN1 and RNA amplification in diverse DS phenotypes is warranted.
2018-11-13 | GSE121070 | GEO
Project description:Down syndrome (DS, trisomy 21) is associated with developmental abnormalities and increased leukemia risk. To reconcile chromatin alterations with transcriptome changes in cells with trisomy 21, we performed paired exogenous spike-in normalized RNA and chromatin immunoprecipitation sequencing in DS models. Absolute per cell normalization unmasked global amplification of gene expression associated with trisomy 21. Overexpression of the nucleosome binding protein HMGN1 (encoded on chr21q22) recapitulated the transcriptional changes seen with triplication of a “Down syndrome critical region” on distal chromosome 21. Absolute exogenous normalized ChIP-seq (ChIP-Rx) also revealed a global increase in histone 3 lysine 27 acetylation caused by HMGN1. Genes most amplified downstream of HMGN1 were enriched for tumor- and developmental stage-specific programs of B-cell acute lymphoblastic leukemia dependent on the cellular context. These data offer a mechanistic explanation for DS transcriptional patterns, and suggest that further study of HMGN1 and RNA amplification in diverse DS phenotypes is warranted.
2018-11-13 | GSE121062 | GEO
Project description:Single-Cell Chromatin Accessibility Landscape of Human Umbilical Cord Blood in Trisomy 18 Syndrome
| PRJNA664208 | ENA