Ericales
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1200749 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:As the most widely used mammalian model organism, mice play a critical role in biomedical research for mechanistic study of human development and diseases. Today, functional sequences in the mouse genome are still poorly annotated a decade after its initial sequencing. We report here a map of nearly 300,000 cis-regulatory sequences in the mouse genome, representing active promoters, enhancers and CTCF binding sites in a diverse set of 19 tissues and cell types. This map provides functional annotation to nearly 11% of the genome, and over 70% of conserved, non-coding sequences. We define tissue-specific enhancers and identify potential transcription factors regulating gene expression in each tissue or cell type. Finally, we demonstrate that cis-regulatory sequences are organized into domains of coordinately regulated enhancers and promoters. Our results provide a valuable resource for the annotation of functional elements in the mammalian genome, and study of regulatory mechanisms for tissue-specific gene expression. 19 tissues and primary cell types were examined.
2012-07-01 | E-GEOD-29218 | biostudies-arrayexpress
Project description:We overexpress RUNX2 in ten human cell lines and identify genes that are affected by RUNX2 expression. These target genes provide a valuable resource into pathways regulated by RUNX2
2014-02-01 | E-MTAB-1875 | biostudies-arrayexpress
Project description:The study of paeoniaflorin biosynthesis in Paeonia lactiflora Pall.at a molecular level is scarce, and the regulatory network between small RNAs and mRNAs in paeoniaflorin biosynthesis has not been assessed. Here, we attempt to combine mRNA and miRNA expression data with degradome analysis to reveal the tissue-specific regulatory network of miRNAs and their targets in Paeonia, especially the complex network of paeoniaflorin biosynthesis.The results will advance our understanding of the miRNA-mediated molecular mechanisms of paeoniaflorin and monoterpenoids biosynthesis, and provide a valuable resource for further study on Paeonia.
2021-03-03 | GSE167994 | GEO
Project description:Transcriptome sequencing of non-model organisms is valuable resource of the genetic basis of ecological-meaningful traits. The Royal Irises, Iris section Oncocyclus (Iris: Iridaceae, order Asparagales), are a Middle-East group of species in the course of speciation. The species are characterized with extremely large flowers, a huge range of flower colors and a unique pollination system. The Royal Irises, which are a symbol of conservation in the Middle-east, serve as a model for evolutionary processes of speciation and plant ecology. However, there are not sufficient transcriptomic and genomic data for molecular characterization. Thus, it is necessary to generate massive transcript sequences for functional characterization and molecular marker development for the Royal Irises. The Iris transcriptome sequencing provides valuable resource for studying adaptation-associated traits in this non-model plant. Although intensive eco-evolutionary studies, this is the first reported transcriptome for the Royal Irises. The data available from this study will facilitate gene discovery, functional genomic studies and development of molecular markers in irises, and will provide genetic tools for their conservation.
2021-08-18 | GSE121786 | GEO
Project description:As the most widely used mammalian model organism, mice play a critical role in biomedical research for mechanistic study of human development and diseases. Today, functional sequences in the mouse genome are still poorly annotated a decade after its initial sequencing. We report here a map of nearly 300,000 cis-regulatory sequences in the mouse genome, representing active promoters, enhancers and CTCF binding sites in a diverse set of 19 tissues and cell types. This map provides functional annotation to nearly 11% of the genome, and over 70% of conserved, non-coding sequences. We define tissue-specific enhancers and identify potential transcription factors regulating gene expression in each tissue or cell type. Finally, we demonstrate that cis-regulatory sequences are organized into domains of coordinately regulated enhancers and promoters. Our results provide a valuable resource for the annotation of functional elements in the mammalian genome, and study of regulatory mechanisms for tissue-specific gene expression. 19 tissues and primary cell types were examined.
2012-06-30 | E-GEOD-29278 | biostudies-arrayexpress
Project description:As the most widely used mammalian model organism, mice play a critical role in biomedical research for mechanistic study of human development and diseases. Today, functional sequences in the mouse genome are still poorly annotated a decade after its initial sequencing. We report here a map of nearly 300,000 cis-regulatory sequences in the mouse genome, representing active promoters, enhancers and CTCF binding sites in a diverse set of 19 tissues and cell types. This map provides functional annotation to nearly 11% of the genome, and over 70% of conserved, non-coding sequences. We define tissue-specific enhancers and identify potential transcription factors regulating gene expression in each tissue or cell type. Finally, we demonstrate that cis-regulatory sequences are organized into domains of coordinately regulated enhancers and promoters. Our results provide a valuable resource for the annotation of functional elements in the mammalian genome, and study of regulatory mechanisms for tissue-specific gene expression. Cortex Hi-C experiment were conducted in biological replicates
2012-06-30 | E-GEOD-34587 | biostudies-arrayexpress
Project description:Epstein-Barr Virus (EBV), which is associated with multiple human tumors, persists as a minichromosome in the nucleus of B-lymphocytes and induces malignancies through incompletely understood mechanisms. Here, we present a large-scale functional genomic analysis of EBV. Our experimentally generated nucleosome positioning maps and viral protein binding data were integrated with over 700 publicly available high-throughput sequencing data sets for human lymphoblastoid cell lines mapped to the EBV genome. We found that viral lytic genes are coexpressed with cellular cancer-associated pathways, suggesting that the lytic cycle may play an unexpected role in virus-mediated oncogenesis. Host regulators of viral oncogene expression and chromosome structure were identified and validated, revealing a role for the B-cell-specific protein Pax5 in viral gene regulation and the cohesin complex in regulating higher order chromatin structure. Our findings provide a deeper understanding of latent viral persistence in oncogenesis and establish a valuable viral genomics resource for future exploration. Six sequencing experiments were performed. One EBNA1 ChIP-seq was controlled with IgG ChIP-seq. Two MNase-seq biological replicates were each conrolled by input seq using the same cells subjected to MNase digestion.
2012-08-28 | E-GEOD-39913 | biostudies-arrayexpress
Project description:A comparative profile of miRNAs in pre- and post-differentiated pigeon SMSCs (SMSC-1d and SMSC-5d) was performed by using high-throughput sequencing. We identified known porcine miRNAs, novel miRNAs, and miRNAs that are conserved in other birds and mammals. Our findings demonstrated that miRNAs are extensively involved in the differentiation of SMSCs in pigeons, and provide a valuable resource for the pigeon breeding.
2020-03-09 | GSE146603 | GEO