Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1070437 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR27782655.fastq.gz | Fastqsanger.gz | |||
| SRR27782656.fastq.gz | Fastqsanger.gz |
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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
2008-08-01 | GSE11246 | 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: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
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.
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Project description:Watermelon (Citrullus lanatus) is one of the most important vegetable crops in the world and accounts for 20% of the world’s total area devoted to vegetable production. Fusarium wilt of watermelon is one of the most destructive diseases in watermelon worldwide. Transcriptome profiling of watermelon during its incompatible interactions with Fusarium oxysporum f.sp. niveum (FON) was generated using an Agilent custom microarray which contains 15,000 probes representing approximately 8,200 watermelon genes. A total of 24, 275, 596, 598, and 592 genes that are differentially expressed genes between FON- and mock-inoculated watermelon roots at 0.5, 1, 3, 5 and 8 days post inoculation (dpi), respectively, were identified. Bioinformatics analysis of these differentially expressed genes revealed that during the incompatible interaction between watermelon and FON, the expression of a number of pathogenesis-related (PR) genes, transcription factors, signaling/regulatory genes, and cell wall modification genes, was significantly induced. A number of genes for transporter proteins such as aquaporins were down-regulated, indicating that transporter proteins might contribute to the development of wilt symptoms after FON infection. In the incompatible interaction, most genes involved in biosynthesis of jasmonic acid (JA) showed expressed stronger and more sustained than those in compatible interaction in FON-infected tissues. Similarly, genes associated with shikimate-phenylpropanoid-lignin biosynthesis were also induced in incompatible interaction, but expression of these genes were not changed or repressed in the compatible interaction.
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Project description:Watermelon (Citrullus lanatus) is one of the most important vegetable crops in the world and accounts for 20% of the world’s total area devoted to vegetable production. Fusarium wilt of watermelon is one of the most destructive diseases in watermelon worldwide. Transcriptome profiling of watermelon during its incompatible interactions with Fusarium oxysporum f.sp. niveum (FON) was generated using an Agilent custom microarray which contains 15,000 probes representing approximately 8,200 watermelon genes. A total of 24, 275, 596, 598, and 592 genes that are differentially expressed genes between FON- and mock-inoculated watermelon roots at 0.5, 1, 3, 5 and 8 days post inoculation (dpi), respectively, were identified. Bioinformatics analysis of these differentially expressed genes revealed that during the incompatible interaction between watermelon and FON, the expression of a number of pathogenesis-related (PR) genes, transcription factors, signaling/regulatory genes, and cell wall modification genes, was significantly induced. A number of genes for transporter proteins such as aquaporins were down-regulated, indicating that transporter proteins might contribute to the development of wilt symptoms after FON infection. In the incompatible interaction, most genes involved in biosynthesis of jasmonic acid (JA) showed expressed stronger and more sustained than those in compatible interaction in FON-infected tissues. Similarly, genes associated with shikimate-phenylpropanoid-lignin biosynthesis were also induced in incompatible interaction, but expression of these genes were not changed or repressed in the compatible interaction. Fusarium oxysporum f.sp. niveum induced gene expression in watermelon root was measured at 0.5,1d, 3d, 5d and 8d after inoculation. Sample inoculated with water were used as the mock controls. Three independent experiments were performed.
2011-06-09 | E-GEOD-29804 | 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.
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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). Examination of small RNA transcriptomes in four plants species using Illumina/Solexa GA-II.
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