Ontology highlight
ABSTRACT:
PROVIDER: PRJNA982548 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:MicroRNAs (miRNAs) are a class of endogenous small non-coding RNAs involved in the post-transcriptional gene regulation and play a critical role in plant growth, development and stress responses. Watermelon (Citrullus lanatus L.) is one of the important agricultural crops worldwide. Here we carried out computational and experimental analysis of miRNAs and phased small interfering RNAs (phasiRNAs) in watermelon by analyzing 14 small RNA profiles from roots, leaves, androecium, flowers, and fruits, and one published small RNA profile of mixed tissues. To identify the targets of miRNAs and phasiRNAs, we generated a degradome profile for watermelon leaf which is analyzed with the SeqTar algorithm. We identified 97 conserved pre-miRNAs, of which 58 have not been reported previously and 348 conserved mature miRNAs without precursors. We also found 9 novel pre-miRNAs encoding 18 mature miRNAs. One hundred and one 21 nucleotide (nt) PHAS loci, and two hundred and forty one 24 nt PHAS loci were also identified. We identified 120 conserved targets of the conserved miRNAs and TAS3-derived tasiRNAs by analyzing a degradome profile of watermelon leaf. The presented results provide a comprehensive view of small regulatory RNAs and their targets in watermelon.
2018-05-23 | GSE102028 | GEO
Project description:A microarray and quantitative Real-Time PCR-based study was conducted in watermelon [Citrullus lanatus (Thunb.) Matsum. & Nakai var. lanatus] in order to elucidate the flow of events associated with fruit development and ripening in this species. RNA from three different maturation stages of watermelon fruit, as well as leaf, were collected from field grown plants during three consecutive years, and hybridized to high-density, photolithography microarrays. Keywords: developmental time course, gene expression This experiment contained a single biological replicate, two tissue types (leaf, fruit flesh), and three time points (12 days post-pollination, 24 days post-pollination, and 36 days post-pollination. One hundred and twenty-seven genes were chosen from this experiments and used in conjunction with quantitative-PCR to examine two additional biological replications of the experiment.
2008-08-01 | E-GEOD-11246 | biostudies-arrayexpress
Project description:MicroRNAs (miRNAs) are a class of endogenous small non-coding RNAs involved in the post-transcriptional gene regulation and play a critical role in plant growth, development and stress responses. Watermelon (Citrullus lanatus L.) is one of the important agricultural crops worldwide. Here we carried out computational and experimental analysis of miRNAs and phased small interfering RNAs (phasiRNAs) in watermelon by analyzing 14 small RNA profiles from roots, leaves, androecium, flowers, and fruits, and one published small RNA profile of mixed tissues. To identify the targets of miRNAs and phasiRNAs, we generated a degradome profile for watermelon leaf which is analyzed with the SeqTar algorithm. We identified 97 conserved pre-miRNAs, of which 58 have not been reported previously and 348 conserved mature miRNAs without precursors. We also found 9 novel pre-miRNAs encoding 18 mature miRNAs. One hundred and one 21 nucleotide (nt) PHAS loci, and two hundred and forty one 24 nt PHAS loci were also identified. We identified 120 conserved targets of the conserved miRNAs and TAS3-derived tasiRNAs by analyzing a degradome profile of watermelon leaf. The presented results provide a comprehensive view of small regulatory RNAs and their targets in watermelon.
2018-05-23 | GSE102029 | GEO
Project description:Male sterility is important mechanism in watermelon for production of hybrid seed. While some fruit development related studies were widely performed in watermelon, there are no reports of profiling gene expression in floral organs of watermelon. RNA-seq analysis was performed in order to identify male sterility related genes from two different groups of watermelon (genetic male-sterile (GMS) DAH3615-MS line and male-fertile DAH3615 line, respectively) to identify the differentially expressed genes (DEGs). This study employed tophat and edgeR for transcriptome analysis of next-generation RNA-seq data, which included 2 tissues obtained from 2 different breeds of watermelon
2016-01-04 | E-GEOD-69073 | biostudies-arrayexpress
Project description:Total RNA was isolated from different tissues (leaf, stem and flesh, rind and placenta of the fruits) using TRIzol reagent and small RNA libraries were generated from four cucurbit species: bottle gourd (Lagenaria siceraria (accession Grif 1617 collection from India)), Cucurbita moschata (accession Grif 14244 Early Butternut) Cucurbita pepo (accession NSL98075 Table King), and watermelon (Citrullus lanatus var. lanatus) (PI 438676 Charleston Grey) by pooling equimolar amounts of total RNA from the aforesaid tissues. Construction of small RNA libraries from size fractionated RNA was carried out as described previously. In brief, small RNA fractions of 18–28 nt were isolated from 15% denaturing polyacrylamide gels and sequentially ligated to 5′ and 3′ RNA adapters. Small RNAs ligated with adapters were converted to DNA by RT-PCR following Solexa protocol. The final PCR product was gel purified and sequenced by Genome Analyser II (Illumina).
2012-08-03 | GSE38176 | GEO