High-throughput sequencing of small RNAs in Vitis vinifera
Ontology highlight
ABSTRACT:
ORGANISM(S): Vitis vinifera
PROVIDER: GSE18405 | GEO | 2010/04/29
SECONDARY ACCESSION(S): PRJNA118253
REPOSITORIES: GEO
Similar Datasets
Project description:Vitis vinifera endogenous small RNAs Size fractionated small RNA from total RNA extracts of Vitis vinifera leaves, inflorescences, tendrils and small berries were ligated to adapters, purified again and reverse transcribed. After PCR amplification the sample was subjected to Solexa/Illumina high throughput pyrosequencing. Please see www.illumina.com for details of the sequencing technology.
2010-04-29 | E-GEOD-18405 | biostudies-arrayexpress
Project description:Small RNAs (21-24 nt) are pivotal regulators of gene expression that guide both transcriptional and post-transcriptional silencing mechanisms in diverse eukaryotes, including most if not all plants. MicroRNAs (miRNAs) and short interfering RNAs (siRNAs) are the two major types, both of which have a demonstrated and important role in plant development, stress responses and pathogen resistance. In this work, we used a deep sequencing approach (Sequencing-By-Synthesis, or SBS) to develop sequence resources of small RNAs from Vitis vinifera tissues (including leaves, flowers and berries). The high depth of the resulting datasets enabled us to examine in detail critical small RNA features as size distribution, tissue-specific regulation and sequence conservation between different organs in this species. We also developed database resources and a dedicated website (http://smallrna.udel.edu/) with computational tools for allowing other users to identify new miRNAs or siRNAs involved in specific regulatory pathways, verify the degree of conservation of these sequences in other plant species and map small RNAs on genes or larger regions of the genome under study. Small RNA libraries were derived from leaves flowers and berries of Vitis vinifera. Total RNA was isolated using the Plant RNA Purification Reagent (Invitrogen), and submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. The small RNA libraries were sequenced with the Sequencing-By-Synthesis (SBS) technology by Illumina. PERL scripts were designed to remove the adapter sequences and determine the abundance of each distinct small RNA. We thank Gabriele Di Gaspero for providing the plant material as well as Kan Nobuta and Gayathri Mahalingam for assistance with the computational methods.
2011-09-29 | E-GEOD-32479 | biostudies-arrayexpress
Project description:Small RNAs (21-24 nt) are pivotal regulators of gene expression that guide both transcriptional and post-transcriptional silencing mechanisms in diverse eukaryotes, including most if not all plants. MicroRNAs (miRNAs) and short interfering RNAs (siRNAs) are the two major types, both of which have a demonstrated and important role in plant development, stress responses and pathogen resistance. In this work, we used a deep sequencing approach (Sequencing-By-Synthesis, or SBS) to develop sequence resources of small RNAs from Vitis vinifera tissues (including leaves, flowers and berries). The high depth of the resulting datasets enabled us to examine in detail critical small RNA features as size distribution, tissue-specific regulation and sequence conservation between different organs in this species. We also developed database resources and a dedicated website (http://smallrna.udel.edu/) with computational tools for allowing other users to identify new miRNAs or siRNAs involved in specific regulatory pathways, verify the degree of conservation of these sequences in other plant species and map small RNAs on genes or larger regions of the genome under study.
2011-09-30 | GSE32479 | GEO
Project description:Vitis vinifera RNA degradome
2010-04-29 | GSE18406 | GEO
Project description:The objective of the study was to uncover the developmental dynamics in the artificially induced somatic embryogenesis of Vitis vinifera on the transcriptome level.
2024-07-23 | GSE234231 | GEO
Project description:In the present study we have generated a parallel analysis of the 5' RNA ends (PARE) referred to polyadenylated RNAs in somatic embryos from in vitro culture of immature anthers of Vitis vinifera. PARE analysis include also a shortRNA analysis of same material. We have submitted the sRNAseq to mirPROOF and miRCAT (srna_workbench software at http://srna-workbench.cmp.uea.ac.uk) in order to recognize known and putative novel miRNAs, respectively that could be present in somatic embryos. In addition, aRNAs and PARE libraries were integrated in order to identify those 5' RNA ends that could be explained by sRNAs (i.e. identify transcripts that could be cleaved by sRNAs). We have used publicly available annotations and we gained a deep insight into the gene families and the transcriptional regulation mediated by miRNAs in V. vinifera somatic embryos. Gene expression is finely regulated to specific paralogues in gene families such as the NADPH-dependent diflavin oxidoreductase, Phosphoserine aminotransferase, Ethylene-responsive transcription factors, glutathione S-transferase par C, just to name a few. We have indeed characterized at least 4,000 mRNA targets. Size fractionated small RNA from total RNA extracts of somatic Embryos cv. "Brachetto" were ligated to adapters, purified again and reverse transcribed. After PCR amplification the sample was subjected to Illumina high throughput pyrosequencing. The kit used is TrueSeq Small RNA kit, Illumina. Please see www.illumina.com for details of the sequencing technology. PARE libraries were generated starting from Poly(A) fraction. The protocol used have been previously described in German et al., 2009, Nature protocols. Please see www.illumina.com for details of the sequencing technology.
2024-04-22 | GSE150881 | GEO
Project description:High-throughput sequencing of small RNAs in Vitis vinifera
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Project description:High-throughput sequencing of small RNAs in Vitis vinifera
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Project description:Bud endodormancy induction response of two genotypes (Seyval, a hybrid white wine grape and Vitis riparia, PI588259, a native North American grape species) was compared under long (15 h) and short (13 h) photoperiods. Proteins were extracted from both genotypes for all time points and experimental conditions. The proteins were separaed by 2D-PAGE, trypsin digested, and the peptides identified with a MALDI-TOF-TOF mass spectrometer. A master gel was made and mapped with all proteins from both genotypes. The proteins were identified by matching the peptide sequences against the 8X Vitis vinifera grape genome in NCBI. This study was funded by NSF grant DBI064755 and is the result of a collaboration between Dr. Anne Fennell at South Dakota State University and Dr. Grant R. Cramer at the University of Nevada, Reno.
2010-08-09 | PRD000169 | Pride
Project description:Physiological changes in trunk wood of Vitis vinifera L. cv. Chardonnay in response to esca proper and apoplexy revealed by proteomic and transcriptomic analyses
2014-06-25 | PXD000015 | Pride