Johannesburg_20150706_autosomes
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00010002582 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:Genotype data and (in binary PLINK format) and imputed data (with merged 1000Gp3 and AGVP reference panel in GEMMA BIMBAM dosage format) for 750 individuals from Respiratory and Meningeal Pathogens Unit in Soweto, South Africa - X chromosome.
| EGAD00010002580 | EGA
Project description:Genotype data (in binary PLINK format) and imputed data (with merged 1000Gp3 and AGVP reference panel in GEMMA BIMBAM dosage format) for 355 individuals from the VAC050 trial performed in Banfora, Burkina Faso - autosomes.
| EGAD00010002581 | EGA
Project description:Genotype data (in binary PLINK format) and imputed data (with merged 1000Gp3 and AGVP reference panel in GEMMA BIMBAM dosage format) for 1391 individuals from EMaBS in Entebbe, Uganda.
| EGAD00010002578 | EGA
Project description:Genotype data (in binary PLINK format) and imputed data (with merged 1000Gp3 and AGVP reference panel in GEMMA BIMBAM dosage format) for 1391 individuals from EMaBS in Entebbe, Uganda - X chromosome.
| EGAD00010002583 | EGA
Project description:Genotype data (in binary PLINK format) and imputed data (with merged 1000Gp3 and AGVP reference panel in GEMMA BIMBAM dosage format) for 355 individuals from the VAC050 trial performed in Banfora, Burkina Faso - X chromosome.
| EGAD00010002579 | EGA
Project description:Gene dosage imbalance of heteromorphic sex chromosomes (XY or ZW) exists between the sexes, and with the autosomes. Mammalian X chromosome inactivation was long thought to imply a critical need for dosage compensation in vertebrates. However, mRNA abundance measurements that demonstrated sex chromosome transcripts are neither balanced between the sexes or with autosomes in monotreme mammals or birds brought sex chromosome dosage compensation into question. This study examines transcriptomic and proteomic levels of dosage compensation in platypus and chicken compared to mouse, a model eutherian species. We analyzed mRNA and protein levels in heart and liver tissues of chicken, mouse and platypus.
2024-07-30 | PXD040182 | Pride
Project description:Long noncoding RNAs known as roX (RNA on X) are crucial for male development in Drosophila, as their loss leads to male lethality from the late larval stages. While roX RNAs are recognized for their role in sex-chromosome dosage compensation, ensuring balanced expression of X-linked genes in both sexes, their potential influence on autosomal gene regulation remains unexplored. Our investigation reveals that roX RNAs not only govern the X chromosome but also target genes on autosomes that lack male-specific lethal (MSL) complex occupancy, together with Polycomb repressive complexes (PRCs). We observed that roX RNAs colocalize with MSL proteins on the X chromosome and PRC components on autosomes. Intriguingly, loss of roX function reduces H4K16ac levels on the X chromosome and H3K27me3 levels on autosomes. Correspondingly, X-linked genes display reduced expression, whereas many autosomal genes exhibit elevated expression upon roX gene deletion. Our findings propose a dual role for roX RNAs: activators of X-linked genes and repressors of autosomal genes, achieved through interactions with MSL and PRC complexes, respectively. This study uncovers the unconventional epigenetic repressive function of roX RNAs.
2024-11-14 | PXD047183 | Pride
Project description:Thymi from WT and Cd226 strain knockout mice were digested to obtain single-cell suspensions and then loaded onto microfluidic devices for scRNA-seq. The scRNA-seq libraries were constructed and sequencing outputs were demultiplexed using the bcl2fastq to convert Binary Base Call files into FASTQ format.
2022-01-27 | GSE194270 | GEO
Project description:Dosage compensation in mammals occurs at two levels. In addition to balancing X-chromosome dosage between males and females via X-inactivation, mammals also balance dosage of Xs and autosomes. It has been proposed that X-autosome equalization occurs by upregulation of Xa (active X). To investigate the mechanism, we perform allele-specific ChIP-seq for chromatin epitopes and analyze RNA-seq data (SRA010053). The hypertranscribed Xa demonstrates enrichment of active chromatin marks relative to autosomes. We derive predictive models for relationships among Pol II, active mark densities and gene expression, and we suggest that Xa upregulation involves increased transcription initiation and elongation. Enrichment of active marks on Xa does not scale proportionally with transcription output, a disparity explained by nonlinear quantitative dependencies among active histone marks, Pol II occupancy and transcription. Notably, the trend of nonlinear upregulation also occurs on autosomes. Thus, Xa upregulation involves combined increases of active histone marks and Pol II occupancy, without invoking X-specific dependencies between chromatin states and transcription.
2012-01-06 | GSE33823 | GEO
Project description:Dosage compensation in mammals occurs at two levels. In addition to balancing X-chromosome dosage between males and females via X-inactivation, mammals also balance dosage of Xs and autosomes. It has been proposed that X-autosome equalization occurs by upregulation of Xa (active X). To investigate the mechanism, we perform allele-specific ChIP-seq for chromatin epitopes and analyze RNA-seq data (SRA010053). The hypertranscribed Xa demonstrates enrichment of active chromatin marks relative to autosomes. We derive predictive models for relationships among Pol II, active mark densities and gene expression, and we suggest that Xa upregulation involves increased transcription initiation and elongation. Enrichment of active marks on Xa does not scale proportionally with transcription output, a disparity explained by nonlinear quantitative dependencies among active histone marks, Pol II occupancy and transcription. Notably, the trend of nonlinear upregulation also occurs on autosomes. Thus, Xa upregulation involves combined increases of active histone marks and Pol II occupancy, without invoking X-specific dependencies between chromatin states and transcription. Examination of 4 marks of active transcription (H3K4me3, H3K36me3, POL-II-S2P, POL-II-S5P) in a transformed female mouse embryonic fibroblast cell line (EY.T4).
2012-01-06 | E-GEOD-33823 | biostudies-arrayexpress