Ontology highlight
ABSTRACT:
PROVIDER: PRJNA663989 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Here we report genome-wide high resolution allele-specific maps of DNA methylation and histone H3 lysine 27 trimethylation (H3K27me3) in maize endosperm. To investigate the allele-specific DNA methylation pattern of maize endosperm on a genome-wide scale, we performed MethylC-seq for shoot, embryo, and endosperm tissue 12 d after pollination (DAP) of inbred B73, and the endosperm tissue 12 DAP of reciprocal crosses B73 Ã Mo17 (BM) and Mo17 Ã B73 (MB). We also performed additional RNA-seq for samples from 12-DAP and 10-DAP endosperm of both reciprocal crosses between inbreds B73 and Mo17
2013-10-17 | E-MTAB-4206 | biostudies-arrayexpress
Project description:We report the application of methylacytosine immunoprecipetation combined with Illumina sequencing (MeDIP-seq) for high-throughput profiling of DNA methylation in rice embryo 3, 6, 9 DAP and endosperm 2, 3, 6, 9 DAP. A total number of 12-14 million of 2×49 bp paired-end reads was generated for each sample, and BOWTIE2 was used for read mapping. We generated genome-wide DNA methylation profiles of rice embryo and endosperm. This study provides a framework to systemically characterize the effect of DNA methylation in developing seeds and will help to illustrate the epigenetic regulation of rice seed development. Rice embryo and endosperm were selected for DNA extraction and methylacytosine immunoprecipetation combined with Illumina sequencing. We sought to obtain the genome-wide DNA methylation profilings of embryo at 3,6,9 days after pollination(DAP) and endosperm at 2,3,6,9 DAP. To that end, we hand-selected embryo at 3,6,9 DAP and endosperm at 2,3,6,9 DAP according to morphological criteria.
2015-09-01 | E-GEOD-57706 | biostudies-arrayexpress
Project description:Daptomycin (DAP) is the last-resort treatment for heterogeneous Vancomycin-Intermediate-Staphylococcus aureus (hVISA) and Vancomycin-Intermediate-S.aureus (VISA), and DAP-resistance onset which is also linked to reduced vancomycin susceptibility, is an increasing public health problem. To have more insight into the mechanisms of daptomycin resistance, the comparative transcriptomes of two DAP-R (1C-3B) clinical isogenic isolates vs their DAP-S (1A-3A) counterparts were investigated by Illumina RNA-seq, the Rockhopper tool, computational filtering analyses and bioinformatic tools.
2020-08-07 | GSE121797 | GEO
Project description:To identify binding sites and nodule SAGs that are directly targeted by NAC094, we used DAP-seq, which allows the capture of the NAC094 regulatory targets at the whole-genome scale. A total of 2,819 binding peaks corresponding to 2,721 genes were identified from two repeats of the DAP-seq experiment.
2023-03-23 | GSE197359 | GEO
Project description:As 5-15% of higher eukaryotes genes are transcription factors (TFs), the lack of transcription factor binding site (TFBS) information for most factors in most organisms limits the study of gene regulation. Here we describe a next-generation sequencing method, DNA affinity purification (DAP-Seq), an in vitro gDNA/TF interaction assay that produces whole-genome TFBS annotation for any factor from any organism. Like ChIP-Seq, DAP-Seq resolves TFBS as discrete peaks at genomic locations which allows for accurate motif prediction direct assignment of functionally relevant target genes, and shows better overlap with ChIP-Seq peaks than indirect motif assignment approaches. We applied DAP-Seq to a set of 50 transcription factors in eight Arabidopsis thaliana and one Zea Mays families to gain novel biological insight into TFBS architectures, functions, evolution and methylation-sensitivity. Overall, DAP-Seq offers a low-cost high-throughput approach to identify TFBS in native sequence context for any organism complete with all DNA chemical modifications.
2016-05-25 | GSE60142 | GEO