Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1018297 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Fragaria vesca, a diploid woodland strawberry with a small and sequenced genome, is an excellent model for studying fruit development. The strawberry fruit is unique in that the edible flesh is actually enlarged receptacle tissue. The true fruit are the numerous dry achenes dotting the receptacleM-^Rs surface. Auxin produced from the achene is essential for the receptacle fruit set, a paradigm for studying crosstalk between hormone signaling and development. To investigate the molecular mechanism underlying strawberry fruit set, next-generation sequencing was employed to profile early-stage fruit development with five fruit tissue types and five developmental stages from floral anthesis to enlarged fruits. This two-dimensional data set provides a systems-level view of molecular events with precise spatial and temporal resolution.
2013-10-01 | E-MTAB-1902 | biostudies-arrayexpress
Project description:Histone modifications mediate between genes and environment in plant growth and developmental events. To characterize the histone modification signatures in strawberry, we performed ChIP-seq experiments for seven histone marks in the immature and mature fruits, and leaves of the woodland strawberry F. vesca ('Ruegen'). The seven histone marks include H3K9/K14ac, H3K27ac, H3K4me1, H3K4me3, H3K36me3, H3K27me3 and H3K9me2. In addition, to reveal the effect of the histone deacetylase FvHDA6, H3K9/K14a was profiled in FvHDA6-OE fruits.
2024-09-25 | GSE208638 | GEO
Project description:With the development of high throughput sequencing technologies, plenty of non-coding RNAs (ncRNAs) have been discovered to play important roles in diverse plant biological processes. Although these ncRNAs extensively exist in plant, their biological functions are still remained to characterize. To obtain a comprehensive understanding of long non-coding RNA (lncRNA) function in strawberry fruit ripening progress, we performed transcriptomic analyses on the diploid strawberry Fragaria vesca in a time-course during fruit ripening. Here, we have identified 25,613 lncRNAs based on RNA-seq data from poly(A)-depleted libraries and rRNA-depleted libraries. Among them, most of lncRNAs exhibit stage-specific expression pattern. Functional analysis on F.vesca endogenous FRUIT RIPENING-RELATED LONG ANTISENSE INTERGENIC RNA (FRILAIR) in octaploid strawberry Falandi, we found that overexpression FRILAIR can compete miR397 to regulate its target laccase genes (LACs), and it may contribute to strawberry ripening. Our findings demonstrate that FRILAIR can act as a competing endogenous RNA (ceRNA) by disturbing miR397 to repress expression level of LACs, and would be valuable for strawberry ripening.
2020-01-21 | GSE129032 | GEO
Project description:diploid woodland strawberry Fragaria vesca Yellow wonder and Ruegen fruit raw sequence reads
| PRJNA297256 | ENA
Project description:Small RNA sequencing was performed in woodland strawberry fruits for study of chromatin structure.
2024-09-25 | GSE208609 | GEO
Project description:Transcriptome Response of Strawberry (Fragaria × ananassa) cultivar Camarosa to Colletotrichum acutatum Infection.
2017-02-09 | GSE56296 | GEO
Project description:In this RNA-seq study, we compared the transcriptome of three Fragaria vesca genotypes in response to Phytophthora cactorum. The goal of our study was to dissect the resistance mechanism of the diploid strawberry (F. vesca) that are resistant to P. cactorum. A susceptible genotype (NCGR1218) and two resistant (NCGR1603 and Bukammen) F. vesca genotypes were used for the comparative transcriptome analyses. Plants were inoculated with P. cactorum zoospores (2mL of 2 × 105 spores/mL) in the crown (rhizome) and sampled 48 hours later. The appropriate controls for each genotype were i) samples wounded and inoculated with water and sampled 48 hours after the treatment and ii) untreated samples. Four biological replicates, each consisting of four individual test plants from each genotype were used for the transcriptome study. All the samples were collected from the crown, flash-frozen in liquid nitrogen and stored at -80 °C until RNA isolation. Total RNA was isolated using the SpectrumTM Plant Total RNA Kit (Sigma-Aldrich, USA) according to the manufacturer’s instructions. For sequencing, the libraries were prepared using the TruSeqTM stranded total RNA library prep kit (Illumina, USA), indexed and pooled, and sequenced in four lanes using the Illumina HiSeq 3/4000 (2×150 bp) System by the Norwegian Sequencing Centre, Oslo, Norway. Raw reads were quality filtered, de novo assembled into transcripts and were analysed for differentially expressed genes between the inoculated and control samples.
2023-01-01 | E-MTAB-12152 | biostudies-arrayexpress
Project description:For exploring whether mRNA m6A modification participates in the regulation of strawberry fruit ripening, we performed m6A-seq in woodland strawberry fruit at three different development stages, including the S6 stage (almost 15 days post-anthsis (DPA)), the RS1 stage (21 DPA), and the RS3 stage (27 DPA), with three biological replicates. mRNA methylome analysis reveals that m6A methylation prevalently distributes in the strawberry transcriptome and highly enrichs in the coding sequence, stop codon and 3’ untranslated region.
2021-05-17 | GSE167183 | GEO
Project description:Fragaria vesca (wild strawberry), genomic and transcriptomic data
| PRJEB75182 | ENA