Ontology highlight
ABSTRACT:
PROVIDER: PRJNA610837 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Pathways underlying miRNA biogenesis, degradation, and activity were established early in land plant evolution, but the 24-nt siRNA pathway that guides DNA methylation was incomplete in early land plants, especially lycophytes. We show that the functional diversification of key gene families such as DICER-LIKE and ARGONAUTE (AGO) as observed in angiosperms occurred early in land plants followed by parallel expansion of the AGO family in ferns and angiosperms. We uncovered an unexpected AGO family specific to lycophytes and ferns. Our phylogenetic analyses of miRNAs in lycophytes, bryophytes, ferns, and angiosperms refined the temporal origination of conserved miRNA families in land plants.
2017-07-20 | GSE98408 | GEO
Project description:We have systematically profiled DNA methylation at promoter CpG islands (CGIs) in ovarian cancer. Epithelial ovarian tumours, excluding mucinous and clear cell cancers, prospectively collected through a cohort study, were analyzed by differential methylation hybridization (DMH) (Nouzova M et al, 2004) in duplicates. The loci targeted by the custom-designed microarray are the promoter CpG islands (Gardiner-Garden and Frommer, 1987) of the genes involved in the Wnt, p53, AKT/mTOR, BRCA1/2 and Redox pathways, DNA repair (HR, NHEJ and MMR), FA family and IgLON family.
2011-06-01 | GSE23240 | GEO
Project description:We have systematically profiled DNA methylation at promoter CpG islands (CGIs) in ovarian cancer. Epithelial ovarian tumours, excluding mucinous and clear cell cancers, prospectively collected through a cohort study, were analyzed by differential methylation hybridization (DMH) (Nouzova M et al, 2004) in duplicates. The loci targeted by the custom-designed microarray are the promoter CpG islands (Gardiner-Garden and Frommer, 1987) of the genes involved in the Wnt, p53, AKT/mTOR, BRCA1/2 and Redox pathways, DNA repair (HR, NHEJ and MMR), FA family and IgLON family. 111 ovarian tumor samples were assayed by DMH in duplicates. McrBC digested (Cy5) and undigested (Cy3) samples were competitively hybridized on the Agilent custom-designed microarrays 8x15k.
2011-06-01 | E-GEOD-23240 | biostudies-arrayexpress
Project description:H2A.B is a unique histone H2A variant that shares only 40 ~ 50 % sequence identity with canonical H2A. It has only been identified in mammals and has quickly evolved with remarkable sequence diversity among different species. H2A.B is ubiquitously expressed in most cells and tissues. It is mainly deposited in gene body region. The localization of H2A.B is associated with methylated CpG islands in mouse ES cells. H2A.B facilitates transcription elongation to go through methylated CpG islands in the gene bodies. One typical example is that H2A.B regulates transcription elongation at imprinted loci. We found H2A.B enriched in some methylated loci. Using ChIP-seq and MeDIP-seq, we test the correlation of H2A.B and DNA methylation.
2013-12-24 | E-GEOD-48892 | biostudies-arrayexpress
Project description:Raw RNAseq data from ferns sampled in Singapore. Organ specific samples were selected for assembly via denovo assembly for comparative transcriptomics.
2024-03-01 | E-MTAB-13848 | biostudies-arrayexpress
Project description:Long noncoding RNAs (lncRNAs) cause Polycomb Repressive Complexes (PRCs) to spread over broad regions of the mammalian genome. We report that in mouse trophoblast stem cells, the Kcnq1ot1 and Airn lncRNAs induce PRC-dependent chromatin modifications over multi-megabase domains. Throughout the Airn-targeted domain, extent of PRC-dependent modification correlated with intra-nuclear distance to the Airn locus, pre-existing genome architecture, and the abundance of Airn itself. Specific CpG islands displayed characteristics indicating that they nucleate the spread of PRCs upon exposure to Airn. Chromatin environments surrounding Xist, Airn, and Kcnq1ot1 suggest common mechanisms of PRC engagement and spreading. Our data indicate that lncRNA potency can be tightly linked to lncRNA abundance, and that within lncRNA-targeted domains, PRCs are recruited to CpG islands via lncRNA-independent mechanisms. We propose that CpG islands that autonomously recruit PRCs interact with lncRNAs and their associated proteins through 3-dimensional space to nucleate the spread of PRCs in lncRNA-targeted domains.
2019-06-27 | GSE118399 | GEO
Project description:We report the generation and analysis of high-throughput DNA methylation profiles at nucleotide resolution in a subset of targeted gene trap mouse mutants. Using high-throughput sequencing of bisulfite treated DNA, we generated DNA methylation percentage for CpG islands, and LacZ (reporter) gene in mice with the apparent silencing of the targeted gene promoter reflected by reduced reporter mRNA level. These results were contrasted with findings for a set of mutants with no silencing or CpG methylation following targeted mutagenesis using the same gene trap vector. Our findings supports the hypothesis that presence of the exogenous DNA in the targeting vector may influence the expression of genes in close proximity or may lead to promoter silencing of the target where the promoter is marked by CpG methylation. Examination of CpG methylation profiles in Knock-out and wild type mice We evaluated targeted gene promoter silencing in a group of six mutants carrying the tm1a Knockout Mouse Project allele containing both a LacZ reporter gene driven by the native promoter and a neo selection cassette. Methylation of the promoter CpG islands and LacZ coding sequence were evaluated by sequencing of bisulfite-treated DNA. CpG Islands (samples labeled as CpG) and trans gene (samples labeled as LacZ) were amplified after Bisulfite treatment. Please note that the same gDNA was used to amplify CpG Island (Gene_CpG_KO ) and LacZ (Gene_LacZ_KO) reporter for the same gene. PCR product of amplification was gel separated, isolated and pooled. After libraries were prepared and sequenced, the alignment was performed. CpG island and LacZ alignments were done separately resulting in three different Processed Data files per gene investigated: Gene_CpG_KO, Gene_LacZ_KO and Gene_CpG_WT. LacZ reference is included in the submission, but is also available for download from KOMP Phenotype website (www.kompphenotype.org). Also please note that the libraries were prepared using Illumina TruSeq RNA Sample Prep Kit starting from adapter binding step as samples were double stranded Bisulfite treated DNA amplicons. So the library preparation was done as with RNASeq, but samples investigated were bisulfite treated.
2015-07-28 | E-GEOD-70317 | biostudies-arrayexpress
Project description:We report a method for specific capture of an arbitrary subset of genomic targets for single molecule bisulfite sequencing, and for digital quantitation of DNA methylation at a single nucleotide resolution. We used targeted bisulfite sequencing to characterize the changes of DNA methylation during the de-differentiation of human fibroblasts into hybrid stem cells, and into induced pluripotent stem cells. We compared the methylation level of approximately 66,000 CpG sites within 2020 CpG islands on chromosome 12, chromosome 20, and 34 selected regions. A total of 288 differentially methylated regions were identified between fibroblasts and pluripotent cells. Methylation cluster analysis revealed distinct methylation patterns between fibroblasts and pluripotent cells. Furthermore iPS cells are globally more methylated than human embryonic stem cells, which could be due to the reprogramming process. This targeted bisulfite sequencing method is particularly useful for efficient and large-scale analysis of DNA methylation in organisms with large genomes. Experiment Overall Design: Comparison of DNA methylation on 2020 CpG islands and 34 other selected regions among eleven human ES, iPS and fibroblast lines.
2009-08-28 | E-GEOD-15007 | biostudies-arrayexpress