QqMetBour1
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB51391 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| CAKOFA01.dat.gz | Other | |||
| CAKOFA01.fasta.gz | Fasta.gz | |||
| CAKOFA01.master.dat | Other |
Items per page: 5 1 - 4 of 4 |
Similar Datasets
Project description:Meta bourneti genome assembly, qqMetBour1, alternate haplotype
| PRJEB51392 | ENA
Project description:The ATAC histone acetyl-transferase (HAT) and the Mediator coactivator complexes regulate independent and distinct steps during transcription initiation and elongation. Here we report the identification of a new stable molecular assembly formed between the ATAC and the Mediator complex in mouse embryonic stem cells. Moreover, we identify LUZP1 as a subunit of this meta coactivator complex (MECO). Finally, we demonstrate that MECO regulates a subset of RNA polymerase II transcribed non-coding RNA genes. Our findings establish that transcription coactivator complexes can form stable sub-complexes in order to facilitate their combined actions on specific target genes. For ChIP-seq analysis, 300µg of chromatin (DNA) was incubated with GST (mock), LUZP1 and GCN5 antibodies. Retrieved purified DNA was sequenced using Illumina Genome Analyzer II following manufacturer recommendations. Illumina raw files were aligned against reference (mouse mm9) genome using the eland program allowing one mismatch. Enrichment clusters were detected using MACS (Zhang et al., 2008). The retrieved peaks were filtered (max size 1000bp, min size 100bp) and repeat masked, to establish the final binding sites lists. Peaks were annotated using the GPAT web server (Krebs et al., 2008) using ENSEMBL gene 57 database.
2010-06-24 | E-GEOD-21717 | biostudies-arrayexpress
Project description:Accurate annotation of transcript isoforms is crucial to understand gene functions, but automated methods for reconstructing full-length transcripts from RNA sequencing (RNA-seq) data remain imprecise. We developed Bookend, a software package for transcript assembly that incorporates data from different RNA-seq techniques, with a focus on identifying and utilizing RNA 5′ and 3′ ends. Through end-guided assembly with Bookend we demonstrate that correct modeling of transcript start and end sites is essential for precise transcript assembly. Furthermore, we discovered that utilization of end-labeled reads present in full-length single-cell RNA-seq (scRNA-seq) datasets dramatically improves the precision of transcript assembly in single cells. Finally, we show that hybrid assembly across short-read, long-read, and end-capture RNA-seq datasets from Arabidopsis, as well as meta-assembly of RNA-seq from single mouse embryonic stem cells (mESCs) can produce end-to-end transcript annotations of comparable quality to reference annotations in these model organisms.
2022-01-08 | GSE189482 | GEO
Project description:The ATAC histone acetyl-transferase (HAT) and the Mediator coactivator complexes regulate independent and distinct steps during transcription initiation and elongation. Here we report the identification of a new stable molecular assembly formed between the ATAC and the Mediator complex in mouse embryonic stem cells. Moreover, we identify LUZP1 as a subunit of this meta coactivator complex (MECO). Finally, we demonstrate that MECO regulates a subset of RNA polymerase II transcribed non-coding RNA genes. Our findings establish that transcription coactivator complexes can form stable sub-complexes in order to facilitate their combined actions on specific target genes.
2010-06-25 | GSE21717 | GEO
Project description:We performed a meta analysis of publicly available TET1, 5mC, 5hmC and genome wide bisulfite profiling data mostly from mouse embryonic stem cells (ESC). Genome wide chromatin immunoprecipitation combined with deep sequencing (ChIP-seq) has revealed binding of the TET1 protein at CpG-island (CGI) promoters and at bivalent promoters. We show that TET1 also coincides with DNAseI hypersensitive sites (HS). Presence of TET1 at these THREE locations suggests that it may play a dual role: an active role at CpG-islands and DNAseI hypersensitive sites and a repressive role at bivalent loci. In line with the presence of TET1, significant enrichment of 5hmC but not 5mC is detected at bivalent promoters and DNaseI HS. Surprisingly, 5hmC is not detected or present at very low levels at CGI promoters notwithstanding the presence of TET1 at these loci. Our meta analysis suggest that asymmetric methylation is present at CA- and CT-repeats in the genome of some human ESC. Examination of the distribution of 5-methylcytosine and 5-hydroxymethylcytosine in the genome of mouse embryonic stem cells.
2011-11-24 | E-GEOD-31343 | biostudies-arrayexpress
Project description:We present evidence for a new level of genome folding, whereby distant domains megabases apart fuse to form meta-domains. Within meta-domains, certain gene promoters pair with structural intergenic elements in the distant TAD. These long-range associations occur in a large fraction of Drosophila neurons, but support transcription in only a subset of cells in the nervous system. Most of the associated genes encode neuronal determinants, including those engaged in axonal guidance and adhesion. We used single cell assay for transposase-accessible chromatin using sequencing (scATAC-seq) to identify regions of open chromatin at single cell resolution.
2023-08-01 | GSE214705 | GEO
Project description:The naked mole-rat (NMR; Heterocephalus glaber) has recently gained considerable attention in the scientific community for its unique potential to unveil novel insights in the fields of medicine, biochemistry, and evolution. NMRs exhibit unique adaptations that include protracted fertility, cancer resistance, eusociality, and anoxia. This suite of adaptations is not found in other rodent species, suggesting that interrogating conserved and accelerated regions in the NMR genome will find regions of the NMR genome fundamental to their unique adaptations. However, the current NMR genome assembly has limits that make studying structural variations, heterozygosity, and non-coding adaptations challenging. We present a complete diploid naked-mole rat genome assembly by integrating long-read and 10X-linked read genome sequencing of a male NMR and its parents, and Hi-C sequencing in the NMR hypothalamus (N=2). Reads were identified as maternal, paternal or ambiguous (TrioCanu). We then polished genomes with Flye, Racon and Medaka. Assemblies were then scaffolded using the following tools in order: Scaff10X, Salsa2, 3d-DNA, Minimap2-alignment between assemblies, and the Juicebox Assembly Tools. We then subjected the assemblies to another round of polishing, including short-read polishing with Freebayes. We assembled the NMR mitochondrial genome with mitoVGP. Y chromosome contigs were identified by aligning male and female 10X linked reads to the paternal genome and finding male-biased contigs not present in the maternal genome. Contigs were assembled with publicly available male NMR Fibroblast Hi-C-seq data (SRR820318). Both assemblies have their sex chromosome haplotypes merged so that both assemblies have a high-quality X and Y chromosome. Finally, assemblies were evaluated with Quast, BUSCO, and Merqury, which all reported the base-pair quality and contiguity of both assemblies as high-quality. The assembly will next be annotated by Ensembl using public RNA-seq data from multiple tissues (SRP061363). Together, this assembly will provide a high-quality resource to the NMR and comparative genomics communities.
2022-06-27 | E-MTAB-11830 | biostudies-arrayexpress